Journal: PLoS Computational Biology

Volume 13, Issue 9

0 -- 0Petter Holme, Nelly Litvak. Cost-efficient vaccination protocols for network epidemiology
0 -- 0Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjosne, Jan-Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne-Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael Hallett. Interactions between the tumor and the blood systemic response of breast cancer patients
0 -- 0Kirill Lykov, Yasaman Nematbakhsh, Menglin Shang, Chwee Teck Lim, Igor V. Pivkin. Probing eukaryotic cell mechanics via mesoscopic simulations
0 -- 0Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman. The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs
0 -- 0Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, Zaida Luthey-Schulten. Population FBA predicts metabolic phenotypes in yeast
0 -- 0Burcu Tepekule, Hildegard Uecker, Isabel Derungs, Antoine Frénoy, Sebastian Bonhoeffer. Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies
0 -- 0Harang Ju, Costa M. Colbert, William B. Levy. Limited synapse overproduction can speed development but sometimes with long-term energy and discrimination penalties
0 -- 0Kevin D. Murray, Christfried Webers, Cheng Soon Ong, Justin Borevitz, Norman Warthmann. kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
0 -- 0Julie J. Lee, Mehdi Keramati. Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans
0 -- 0Kristyn S. Masters, Pamela K. Kreeger. Ten simple rules for developing a mentor-mentee expectations document
0 -- 0Kyle P. Blum, Boris Lamotte d'Incamps, Daniel Zytnicki, Lena H. Ting. Force encoding in muscle spindles during stretch of passive muscle
0 -- 0André Voigt, Katja Nowick, Eivind Almaas. A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma
0 -- 0Michiel van Boven, Jan van de Kassteele, Marjolein J. Korndewal, Christiaan H. van Dorp, Mirjam Kretzschmar, Fiona van der Klis, Hester E. de Melker, Ann C. Vossen, Debbie van Baarle. Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence
0 -- 0Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas Close, Daqing Guo, Mario Negrello, Erik De Schutter. Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer
0 -- 0Jianfei Hu, Eli Boritz, William Wylie, Daniel C. Douek. Stochastic principles governing alternative splicing of RNA
0 -- 0Minseung Kim, Ameen Eetemadi, Ilias Tagkopoulos. DeepPep: Deep proteome inference from peptide profiles
0 -- 0Rafael Hernández-de-Diego, Etienne P. de Villiers, Tomas Klingström, Hadrien Gourlé, Ana Conesa, Erik Bongcam-Rudloff. The eBioKit, a stand-alone educational platform for bioinformatics
0 -- 0Yuewu Liu, Xiufen Zou. Mathematical modeling and quantitative analysis of HIV-1 Gag trafficking and polymerization
0 -- 0Pavel Sanda, Steven Skorheim, Maxim Bazhenov. Multi-layer network utilizing rewarded spike time dependent plasticity to learn a foraging task
0 -- 0Willem de Haan, Elisabeth C. W. van Straaten, Alida A. Gouw, Cornelis J. Stam. Altering neuronal excitability to preserve network connectivity in a computational model of Alzheimer's disease
0 -- 0Kaido Lepik, Tarmo Annilo, Viktorija Kukuskina, eQTLGen Consortium, Kai Kisand, Zoltán Kutalik, Pärt Peterson, Hedi Peterson. C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis
0 -- 0Ernesto Ruelas Inzunza, Gabriela I. Salazar-Rivera, Magdiel Láinez, María Guadalupe Ruiz-Gómez, Carlo A. Domínguez-Eusebio, Griselda Cristóbal-Sánchez, Issaac A. Teodosio Faustino, Edel Pérez-López, Meagan L. Campbell, Marcus Vinicius Merfa, Ivonne Tatiana Latorre Beltrán, Fernanda Armas, Claudio Mota-Vargas. Ten simple rules for successfully completing a graduate degree in Latin America
0 -- 0Siri Camee van Keulen, Ursula Rothlisberger. Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1
0 -- 0Marianne Bauer, Isabella R. Graf, Vudtiwat Ngampruetikorn, Greg J. Stephens, Erwin Frey. Exploiting ecology in drug pulse sequences in favour of population reduction
0 -- 0María E. Soler-Oliva, José A. Guerrero-Martínez, Valentina Bachetti, José C. Reyes. Analysis of the relationship between coexpression domains and chromatin 3D organization
0 -- 0Ruth Nussinov, Jason A. Papin. How can computation advance microbiome research?
0 -- 0Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans V. Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina. A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect
0 -- 0Alexey A. Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal. Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity
0 -- 0Paul Villoutreix, Joakim Andén, Bomyi Lim, Hang Lu, Ioannis G. Kevrekidis, Amit Singer, Stanislav Y. Shvartsman. Synthesizing developmental trajectories
0 -- 0Mark D. McDonnell, Bruce P. Graham. Phase changes in neuronal postsynaptic spiking due to short term plasticity
0 -- 0Mudassar Iqbal, Neil Doherty, Anna M. L. Page, Saara N. A. Qazi, Ishan Ajmera, Peter A. Lund, Theodore Kypraios, David J. Scott, Philip J. Hill, Dov J. Stekel. Reconstructing promoter activity from Lux bioluminescent reporters
0 -- 0Kiesha Prem, Alex R. Cook, Mark Jit. Projecting social contact matrices in 152 countries using contact surveys and demographic data
0 -- 0Volker Hofmann, Maurice J. Chacron. Differential receptive field organizations give rise to nearly identical neural correlations across three parallel sensory maps in weakly electric fish
0 -- 0Yanju Liu, Sheryl M. Gracewski, Jong-Hoon Nam. Two passive mechanical conditions modulate power generation by the outer hair cells
0 -- 0Richard B. Greaves, Sabine Dietmann, Austin Smith, Susan Stepney, Julianne D. Halley. A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells
0 -- 0Cai Wingfield, Li Su, Xunying Liu, Chao Zhang, Philip C. Woodland, Andrew Thwaites, Elisabeth Fonteneau, William D. Marslen-Wilson. Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem
0 -- 0Stefan M. Kallenberger, Anne L. Unger, Stefan Legewie, Konstantinos Lymperopoulos, Ursula Klingmüller, Roland Eils, Dirk-Peter Herten. Correlated receptor transport processes buffer single-cell heterogeneity
0 -- 0Abed Ghanbari, Aleksey Malyshev, Maxim Volgushev, Ian H. Stevenson. Estimating short-term synaptic plasticity from pre- and postsynaptic spiking
0 -- 0Pietro Balbi, Paolo Massobrio, Jeanette Hellgren Kotaleski. A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms
0 -- 0Sirin Yonucu, Defne Yiotalmaz, Colin Phipps, Mehmet Burcin Unlu, Mohammad Kohandel. Quantifying the effects of antiangiogenic and chemotherapy drug combinations on drug delivery and treatment efficacy
0 -- 0Brett Mensh, Konrad P. Körding. Ten simple rules for structuring papers
0 -- 0Evan M. Russek, Ida Momennejad, Matthew Botvinick, Samuel J. Gershman, Nathaniel D. Daw. Predictive representations can link model-based reinforcement learning to model-free mechanisms
0 -- 0Shintaroh Kubo, Wenfei Li, Shoji Takada. Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations
0 -- 0Xiaosheng Luo, Liufang Xu, Bo Han, Jin Wang. Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle
0 -- 0Jaideep Joshi, Iain D. Couzin, Simon A. Levin, Vishwesha Guttal. Mobility can promote the evolution of cooperation via emergent self-assortment dynamics
0 -- 0Jan Humplik, Gasper Tkacik. Probabilistic models for neural populations that naturally capture global coupling and criticality

Volume 13, Issue 8

0 -- 0Quan Wang, Constantin A. Rothkopf, Jochen Triesch. A model of human motor sequence learning explains facilitation and interference effects based on spike-timing dependent plasticity
0 -- 0Idan Alter, Loren Gragert, Stephanie Fingerson, Martin Maiers, Yoram Louzoun. HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes
0 -- 0Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler H. Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb
0 -- 0Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Céline Scornavacca. Rearrangement moves on rooted phylogenetic networks
0 -- 0Eduardo A. Aponte, Dario Schöbi, Klaas E. Stephan, Jakob Heinzle. The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades
0 -- 0Michal Bassani-Sternberg, Chloé Chong, Philippe Guillaume, Marthe Solleder, HuiSong Pak, Philippe O. Gannon, Lana E. Kandalaft, George Coukos, David Gfeller. Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity
0 -- 0Narimane Nekkab, Pascal Astagneau, Laura Temime, Pascal Crépey. Spread of hospital-acquired infections: A comparison of healthcare networks
0 -- 0Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A. Relman, Susan P. Holmes. Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment
0 -- 0Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio. Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
0 -- 0Peter J. Hellyer, Claudia Clopath, Angie A. Kehagia, Federico E. Turkheimer, Robert Leech. From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction
0 -- 0Lingfei Wang, Tom Michoel. Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
0 -- 0Tjibbe Donker, Timo Smieszek, Katherine L. Henderson, Alan P. Johnson, A. Sarah Walker, Julie V. Robotham. Measuring distance through dense weighted networks: The case of hospital-associated pathogens
0 -- 0Alexander V. Maltsev, Victor A. Maltsev, Michael D. Stern. Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels
0 -- 0Toby P. Aicher, Dániel L. Barabási, Benjamin D. Harris, Ajay Nadig, Kaitlin L. Williams. Ten simple rules for getting the most out of a summer laboratory internship
0 -- 0Michael A. Colman, Christian Pinali, Andrew W. Trafford, Henggui Zhang, Ashraf Kitmitto. A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions
0 -- 0Vickie Li, Santiago Herce Castañón, Joshua A. Solomon, Hildward Vandormael, Christopher Summerfield. Robust averaging protects decisions from noise in neural computations
0 -- 0Laura R. Emery, Sarah L. Morgan. The application of project-based learning in bioinformatics training
0 -- 0Matías A. Goldin, Gabriel B. Mindlin. Temperature manipulation of neuronal dynamics in a forebrain motor control nucleus
0 -- 0Johannes Friedrich, Weijian Yang, Daniel Soudry, Yu Mu, Misha Ahrens, Rafael Yuste, Darcy S. Peterka, Liam Paninski. Multi-scale approaches for high-speed imaging and analysis of large neural populations
0 -- 0Jinyuan Yan, Maxime Deforet, Kerry E. Boyle, Rayees Rahman, Raymond Liang, Chinweike Okegbe, Lars E. P. Dietrich, Weigang Qiu, João B. Xavier. Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network
0 -- 0Elsje Pienaar, Jansy Sarathy, Brendan Prideaux, Jillian Dietzold, Véronique Dartois, Denise E. Kirschner, Jennifer J. Linderman. Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach
0 -- 0Vikranth R. Bejjanki, Rava Azeredo da Silveira, Jonathan D. Cohen, Nicholas B. Turk-Browne. Noise correlations in the human brain and their impact on pattern classification
0 -- 0Jairo A. Navarrete, Pablo Dartnell. Towards a category theory approach to analogy: Analyzing re-representation and acquisition of numerical knowledge
0 -- 0Christopher B. Massa, Angela M. Groves, Smita U. Jaggernauth, Debra L. Laskin, Andrew J. Gow. Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation
0 -- 0Lore Thaler, Galen M. Reich, Xinyu Zhang, Dinghe Wang, Graeme E. Smith, Tao Zeng 0001, Raja Syamsul Azmir Raja Abdullah, Mikhail Cherniakov, Christopher J. Baker, Daniel Kish, Michail Antoniou. Mouth-clicks used by blind expert human echolocators - signal description and model based signal synthesis
0 -- 0Grégory Dumont, Alexandre Payeur, André Longtin. A stochastic-field description of finite-size spiking neural networks
0 -- 0Wesley M. Botello-Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jerome J. Lacroix, Jijun Hao, Yun Luo. Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
0 -- 0Xin Chen, Jeffrey M. Beck, John M. Pearson. Neuron's eye view: Inferring features of complex stimuli from neural responses
0 -- 0Honda Naoki. Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection
0 -- 0Jonas Liechti, Gabriel E. Leventhal, Sebastian Bonhoeffer. Host population structure impedes reversion to drug sensitivity after discontinuation of treatment
0 -- 0David Amar, Ron Shamir, Daniel Yekutieli. Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
0 -- 0Chiara Bruckmann, Endre Sebestyén. Ten simple rules to initiate and run a postdoctoral association
0 -- 0Marinho A. Lopes, Mark P. Richardson, Eugenio Abela, Christian Rummel, Kaspar Schindler, Marc Goodfellow, John R. Terry. An optimal strategy for epilepsy surgery: Disruption of the rich-club?
0 -- 0Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele. A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
0 -- 0Stefano Palminteri, Germain Lefebvre, Emma J. Kilford, Sarah-Jayne Blakemore. Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing
0 -- 0Daniel R. Amor, Raúl Montañez, Salva Duran-Nebreda, Ricard V. Solé. Spatial dynamics of synthetic microbial mutualists and their parasites
0 -- 0Mohamed A. Ghadie, Luke Lambourne, Marc Vidal, Yu Xia. Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing
0 -- 0Alexander J. Mastin, Frank van den Bosch, Timothy R. Gottwald, Vasthi Alonso Chávez, Stephen Parnell. A method of determining where to target surveillance efforts in heterogeneous epidemiological systems
0 -- 0Mark G. F. Sun, Philip M. Kim. Data driven flexible backbone protein design
0 -- 0Eilon Sharon, Hao Shi, Sandhya Kharbanda, Winston Koh, Lance R. Martin, Kiran K. Khush, Hannah A. Valantine, Jonathan K. Pritchard, Iwijn De Vlaminck. Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype

Volume 13, Issue 7

0 -- 0Peter Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
0 -- 0Warren D. Anderson, Danielle DeCicco, James S. Schwaber, Rajanikanth Vadigepalli. A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation
0 -- 0John H. C. Palmer, Adam Keane, Pulin Gong. Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits
0 -- 0Xinxian Shao, Andrew Mugler, Justin Kim, Ha Jun Jeong, Bruce R. Levin, Ilya Nemenman. Growth of bacteria in 3-d colonies
0 -- 0Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee. PCSF: An R-package for network-based interpretation of high-throughput data
0 -- 0Yang Li, Alexis A. Jourdain, Sarah E. Calvo, Jun S. Liu, Vamsi K. Mootha. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets
0 -- 0Roman A. Sandler, Dustin Fetterhoff, Robert E. Hampson, Sam A. Deadwyler, Vasilis Z. Marmarelis. Cannabinoids disrupt memory encoding by functionally isolating hippocampal CA1 from CA3
0 -- 0Gamze Gürsoy, Yun Xu, Jie Liang. Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model
0 -- 0András Szabó, Roeland M. H. Merks. Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach
0 -- 0Vehpi Yildirim, Suryakiran Vadrevu, Benjamin Thompson, Leslie S. Satin, Richard Bertram. Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets
0 -- 0Joni Vuorio, Ilpo Vattulainen, Hector Martinez-Seara. Atomistic fingerprint of hyaluronan-CD44 binding
0 -- 0Dariusz Matlak, Ewa Szczurek. Epistasis in genomic and survival data of cancer patients
0 -- 0Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus. Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks
0 -- 0Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors
0 -- 0Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara. Quantifying critical states of complex diseases using single-sample dynamic network biomarkers
0 -- 0Zixuan Cang, Guo-Wei Wei. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions
0 -- 0Pekka Marttinen, William P. Hanage. Speciation trajectories in recombining bacterial species
0 -- 0Meriç Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis. redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
0 -- 0Juliana C. Wortman, Marcos Nahmad, Pengcheng Zhang, Arthur D. Lander, Clare C. Yu. Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium
0 -- 0Jonathan Diamond, Daniel M. Wolpert, J. Randall Flanagan. Rapid target foraging with reach or gaze: The hand looks further ahead than the eye
0 -- 0Mathieu Bottier, Sylvain Blanchon, Gabriel Pelle, Emilie Bequignon, Daniel Isabey, André Coste, Estelle Escudier, James B. Grotberg, Jean-François Papon, Marcel Filoche, Bruno Louis. A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis
0 -- 0Connor Sharp, James E. Bray, Nicholas G. Housden, Martin C. J. Maiden, Colin Kleanthous. Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models
0 -- 0Marta Lukacisinová, Sebastian Novak, Tiago Paixão. Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes
0 -- 0Oliver J. Maclaren, Aimée Parker, Carmen Pin, Simon R. Carding, Alastair J. M. Watson, Alexander G. Fletcher, Helen M. Byrne, Philip K. Maini. A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium
0 -- 0Lukas Bartonek, Bojan Zagrovic. mRNA/protein sequence complementarity and its determinants: The impact of affinity scales
0 -- 0Hua-Qing Wu, Mei-Ling Cheng, Jin-mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F. Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang. Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a
0 -- 0Laurent Mackay, Hana Zemkova, Stanko S. Stojilkovic, Arthur Sherman, Anmar Khadra. Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models
0 -- 0Carla Aimé, Jean-Baptiste André, Michel Raymond. Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan
0 -- 0Sang-Woo Lee, Yoshihiro Morishita. Possible roles of mechanical cell elimination intrinsic to growing tissues from the perspective of tissue growth efficiency and homeostasis
0 -- 0Mathieu Bottier, Marta Peña Fernández, Gabriel Pelle, Daniel Isabey, Bruno Louis, James B. Grotberg, Marcel Filoche. A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling
0 -- 0Ethan Oblak, Jarrod A. Lewis-Peacock, James S. Sulzer. Self-regulation strategy, feedback timing and hemodynamic properties modulate learning in a simulated fMRI neurofeedback environment
0 -- 0Shuxiang Ruan, Gary D. Stormo. Inherent limitations of probabilistic models for protein-DNA binding specificity
0 -- 0Cesare V. Parise, Marc O. Ernst. Noise, multisensory integration, and previous response in perceptual disambiguation
0 -- 0Joanna Jedrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T. Blackwell. β-adrenergic signaling broadly contributes to LTP induction
0 -- 0Muhammet Uzuntarla, Ernest Barreto, Joaquín J. Torres. Inverse stochastic resonance in networks of spiking neurons
0 -- 0Aseel Shomar, Lukas Geyrhofer, Noam E. Ziv, Naama Brenner. Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics
0 -- 0Christopher Finn McQuaid, Frank van den Bosch, Anna Szyniszewska, Titus Alicai, Anthony Pariyo, Patrick Chiza Chikoti, Christopher A. Gilligan. Spatial dynamics and control of a crop pathogen with mixed-mode transmission
0 -- 0Koon-Kiu Yan, Shaoke Lou, Mark Gerstein. MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions
0 -- 0Joshua G. A. Cashaback, Heather R. McGregor, Ayman Mohatarem, Paul L. Gribble. Dissociating error-based and reinforcement-based loss functions during sensorimotor learning
0 -- 0Giorgos Minas, David A. Rand. Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference
0 -- 0Shihao Yang, Samuel C. Kou, Fred Lu, John S. Brownstein, Nicholas Brooke, Mauricio Santillana. Advances in using Internet searches to track dengue
0 -- 0Haruo Hosoya, Aapo Hyvärinen. A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing
0 -- 0Johan D. Carlin, Nikolaus Kriegeskorte. Adjudicating between face-coding models with individual-face fMRI responses
0 -- 0Kamran Kaveh, Yutaka Takahashi, Michael Farrar, Guy Storme, Marcucci Guido, Jamie Piepenburg, Jackson Penning, Jasmine Foo, Kevin Leder, Susanta K. Hui. Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance
0 -- 0William Gilpin, Marcus W. Feldman. A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape
0 -- 0Magdalena Zwierzyna, John P. Overington. Classification and analysis of a large collection of in vivo bioassay descriptions
0 -- 0François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J. Filion, Marc A. Martí-Renom. Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
0 -- 0Alexandra Vormberg, Felix Effenberger, Julia Muellerleile, Hermann Cuntz. Universal features of dendrites through centripetal branch ordering
0 -- 0James R. H. Cooke, Arjan C. ter Horst, Robert J. van Beers, W. Pieter Medendorp. Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective
0 -- 0Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn. A curated genome-scale metabolic model of Bordetella pertussis metabolism
0 -- 0Mikhail V. Pogorelyy, Yuval Elhanati, Quentin Marcou, Anastasiia L. Sycheva, Ekaterina Komech, Vadim I. Nazarov, Olga V. Britanova, Dmitry M. Chudakov, Ilgar Mamedov, Yury Lebedev, Thierry Mora, Aleksandra M. Walczak. Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires
0 -- 0Meriç Ataman, Vassily Hatzimanikatis. lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
0 -- 0Wilsaan M. Joiner, Gary C. Sing, Maurice A. Smith. Temporal specificity of the initial adaptive response in motor adaptation
0 -- 0Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo. Reconstructing the regulatory circuit of cell fate determination in yeast mating response
0 -- 0Franz Hamilton, Alun L. Lloyd, Kevin B. Flores. Hybrid modeling and prediction of dynamical systems

Volume 13, Issue 6

0 -- 0C. Victor Jongeneel, Ovokeraye Achinike-Oduaran, Ezekiel F. Adebiyi, Marion O. Adebiyi, Seun Adeyemi, Bola Akanle, Shaun Aron, Efejiro Ashano, Hocine Bendou, Gerrit Botha, Emile R. Chimusa, Ananyo Choudhury, Ravikiran Donthu, Jenny Drnevich, Oluwadamila Falola, Christopher J. Fields, Scott Hazelhurst, Liesl Hendry, Itunuoluwa Isewon, Radhika S. Khetani, Judit Kumuthini, Magambo Phillip Kimuda, Lerato Magosi, Liudmila S. Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Danny Mugutso, Phelelani T. Mpangase, Richard Munthali, Victoria Nembaware, Andrew Ndhlovu, Trust Odia, Adaobi Okafor, Olaleye Oladipo, Sumir Panji, Venesa Pillay, Gloria Rendon, Dhriti Sengupta, Nicola J. Mulder. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network
0 -- 0Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein. Landscape and variation of novel retroduplications in 26 human populations
0 -- 0En-Yu Lai, Yi-Hau Chen, Kun-Pin Wu. A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data
0 -- 0Darshan Bryner, Stephen Criscione, Andrew Leith, Quyen Huynh, Fred W. Huffer, Nicola Neretti. GINOM: A statistical framework for assessing interval overlap of multiple genomic features
0 -- 0Patricia Wollstadt, Kristin K. Sellers, Lucas Rudelt, Viola Priesemann, Axel Hutt, Flavio Fröhlich, Michael Wibral. Breakdown of local information processing may underlie isoflurane anesthesia effects
0 -- 0Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou. A comprehensive overview and evaluation of circular RNA detection tools
0 -- 0Jae Kyoung Kim, Eduardo D. Sontag. Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation
0 -- 0David M. Fox, Hua-an Tseng, Tomasz G. Smolinski, Horacio G. Rotstein, Farzan Nadim. Mechanisms of generation of membrane potential resonance in a neuron with multiple resonant ionic currents
0 -- 0Dominic G. Whittaker, Haibo Ni, Aziza El Harchi, Jules C. Hancox, Henggui Zhang. Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria
0 -- 0Jhuma Das, Andrei A. Aleksandrov, Liying Cui, Lihua He, John R. Riordan, Nikolay V. Dokholyan. Transmembrane helical interactions in the CFTR channel pore
0 -- 0Caroline Baroukh, Violette Turon, Olivier Bernard. Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes
0 -- 0Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. 2017 Outstanding Contributions to ISCB Award: Fran Lewitter
0 -- 0Peyman Khorsand, Alireza Soltani. Optimal structure of metaplasticity for adaptive learning
0 -- 0Diego A. Gutnisky, Jianing Yu, Samuel Andrew Hires, Minh-Son To, Michael Ross Bale, Karel Svoboda, David Golomb. Mechanisms underlying a thalamocortical transformation during active tactile sensation
0 -- 0Marine Le Morvan, Andrei Zinovyev, Jean-Philippe Vert. NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis
0 -- 0Meng Ke, Yafei Yuan, Xin Jiang, Nieng Yan, Haipeng Gong. Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE
0 -- 0Sonia Cortassa, Steven J. Sollott, Miguel Antonio Aon. Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study
0 -- 0Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. 2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner
0 -- 0Stefano Castellana, Caterina Fusilli, Gianluigi Mazzoccoli, Tommaso Biagini, Daniele Capocefalo, Massimo Carella, Angelo L. Vescovi, Tommaso Mazza. High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE
0 -- 0Yuriy Sverchkov, Mark Craven. A review of active learning approaches to experimental design for uncovering biological networks
0 -- 0Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. 2017 ISCB Overton Prize awarded to Christoph Bock
0 -- 0Mathieu Ouellet, Gérald Guillebaud, Valerie Gervais, David Lupien St-Pierre, Marc Germain. A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images
0 -- 0Michael A. Colman, Haibo Ni, Bo Liang, Nicole Schmitt, Henggui Zhang. In silico assessment of genetic variation in KCNA5 reveals multiple mechanisms of human atrial arrhythmogenesis
0 -- 0Gen Kurosawa, Atsuko Fujioka, Satoshi Koinuma, Atsushi Mochizuki, Yasufumi Shigeyoshi. Temperature-amplitude coupling for stable biological rhythms at different temperatures
0 -- 0Peter Marx, Peter Antal, Bence Bolgár, Gyorgy Bagdy, Bill Deakin, Gabriella Juhász. Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression
0 -- 0Gabriel Koch Ocker, Kresimir Josic, Eric Shea-Brown, Michael A. Buice. Linking structure and activity in nonlinear spiking networks
0 -- 0Tobias Kühn, Moritz Helias. Locking of correlated neural activity to ongoing oscillations
0 -- 0Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R. Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E. M. Nordling, Elin Nyman, Sylvie Schulze, Colm E. Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson. LASSIM - A network inference toolbox for genome-wide mechanistic modeling
0 -- 0David L. Gibbs, Ilya Shmulevich. Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle
0 -- 0Daniel L. Barton, Silke Henkes, Cornelis J. Weijer, Rastko Sknepnek. Active Vertex Model for cell-resolution description of epithelial tissue mechanics
0 -- 0Matthew Chalk, Paul Masset, Sophie Denève, Boris S. Gutkin. Sensory noise predicts divisive reshaping of receptive fields
0 -- 0Raony G. C. C. L. Cardenas, Natália Duarte Linhares, Raquel L. Ferreira, Sérgio D. Junho Pena. Mendel, MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders
0 -- 0Shaohuan Wu, Ke Li, Yingshu Li, Tong Zhao, Ting Li, Yu-Fei Yang, Wenfeng Qian. Independent regulation of gene expression level and noise by histone modifications
0 -- 0Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
0 -- 0Samira Abbasi, Amber E. Hudson, Selva K. Maran, Ying Cao, Ataollah Abbasi, Detlef H. Heck, Dieter Jaeger. Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice
0 -- 0Yiming Hu, Qiongshi Lu, Ryan Powles, Xinwei Yao, Can Yang, Fang Fang, Xinran Xu, Hongyu Zhao. Leveraging functional annotations in genetic risk prediction for human complex diseases
0 -- 0Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R. Grant, Elizabeth A. Heller. Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain
0 -- 0Rocío Espada, R. Gonzalo Parra, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro. Inferring repeat-protein energetics from evolutionary information
0 -- 0Jim R. Potvin, Andrew J. Fuglevand. A motor unit-based model of muscle fatigue
0 -- 0Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, Tracy K. Teal. Good enough practices in scientific computing
0 -- 0Noga Mosheiff, Haggai Agmon, Avraham Moriel, Yoram Burak. An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules
0 -- 0Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer. Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation
0 -- 0Daniel Durstewitz. A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements
0 -- 0Sebastián A. Romano, Verónica Pérez-Schuster, Adrien Jouary, Jonathan Boulanger-Weill, Alessia Candeo, Thomas Pietri, Germán Sumbre. An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics
0 -- 0David W. Rogers, Marvin A. Böttcher, Arne Traulsen, Duncan Greig. Ribosome reinitiation can explain length-dependent translation of messenger RNA
0 -- 0Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. 2017 ISCB Innovator Award: Aviv Regev
0 -- 0Mattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad. Fast and general tests of genetic interaction for genome-wide association studies
0 -- 0Jens Christian Claussen, Jurgita Skieceviciene, Jun Wang, Philipp Rausch, Tom H. Karlsen, Wolfgang Lieb, John F. Baines, Andre Franke, Marc-Thorsten Hütt. Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome
0 -- 0Andreas Kühne, Urs Mayr, Daniel C. Sévin, Manfred Claassen, Nicola Zamboni. Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data
0 -- 0Maxwell B. Wang, Julia P. Owen, Pratik Mukherjee, Ashish Raj. Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease
0 -- 0Hadi Maboudi, Hideaki Shimazaki, Martin Giurfa, Lars Chittka. Olfactory learning without the mushroom bodies: Spiking neural network models of the honeybee lateral antennal lobe tract reveal its capacities in odour memory tasks of varied complexities
0 -- 0Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose. MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures
0 -- 0Patrick Löffler, Samuel Schmitz, Enrico Hupfeld, Reinhard Sterner, Rainer Merkl. Rosetta: MSF: a modular framework for multi-state computational protein design
0 -- 0Miquel Duran-Frigola, Lydia Siragusa, Eytan Ruppin, Xavier Barril, Gabriele Cruciani, Patrick Aloy. Detecting similar binding pockets to enable systems polypharmacology
0 -- 0Aliza B. Rubenstein, Manasi A. Pethe, Sagar D. Khare. MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory
0 -- 0Nargesalsadat Dorratoltaj, Achla Marathe, Bryan L. Lewis, Samarth Swarup, Stephen G. Eubank, Kaja M. Abbas. Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions
0 -- 0Sheng Wang, Jian Peng 0001. Network-assisted target identification for haploinsufficiency and homozygous profiling screens

Volume 13, Issue 5

0 -- 0Thomas O. Richardson, Jonas Liechti, Nathalie Stroeymeyt, Sebastian Bonhoeffer, Laurent Keller. Short-term activity cycles impede information transmission in ant colonies
0 -- 0Nicolás Tomasini, Paula Gabriela Ragone, Sébastien Gourbière, Juan Pablo Aparicio, Patricio Diosque. Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans
0 -- 0Gerald Hahn, Adrián Ponce-Alvarez, Cyril Monier, Giacomo Benvenuti, Arvind Kumar, Frédéric Chavane, Gustavo Deco, Yves Frégnac. Spontaneous cortical activity is transiently poised close to criticality
0 -- 0Alexander Franks, Edoardo M. Airoldi, Nikolai Slavov. Post-transcriptional regulation across human tissues
0 -- 0Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers
0 -- 0Jeffrey P. Nguyen, Ashley N. Linder, George S. Plummer, Joshua W. Shaevitz, Andrew M. Leifer. Automatically tracking neurons in a moving and deforming brain
0 -- 0Jin Hyun Ju, Sushila A. Shenoy, Ronald G. Crystal, Jason G. Mezey. An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci
0 -- 0Yujiang Wang, Andrew J. Trevelyan, Antonio Valentín, Gonzalo Alarcón, Peter Neal Taylor, Marcus Kaiser. Mechanisms underlying different onset patterns of focal seizures
0 -- 0Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo. ROTS: An R package for reproducibility-optimized statistical testing
0 -- 0Raphaël Mourad, Lang Li 0001, Olivier Cuvier. Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach
0 -- 0Benjamin Risse, Dimitri Berh, Nils Otto, Christian Klämbt, Xiaoyi Jiang 0001. FIMTrack: An open source tracking and locomotion analysis software for small animals
0 -- 0Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp, Pavel A. Pevzner. Single-molecule protein identification by sub-nanopore sensors
0 -- 0Yogi A. Patel, Ansel George, Alan D. Dorval II, John A. White, David J. Christini, Robert J. Butera. Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI)
0 -- 0Gabriel F. Dorlhiac, Clyde Fare, Jasper J. van Thor. PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data
0 -- 0Thomas H. B. FitzGerald, Dorothea Hämmerer, Karl J. Friston, Shu-Chen Li, Raymond J. Dolan. Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions
0 -- 0Wesley P. Clawson, Nathaniel C. Wright, Ralf Wessel, Woodrow L. Shew. Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection
0 -- 0Megan Yu, Yu-Min Kuo. Ten simple rules to make the most out of your undergraduate research career
0 -- 0Rodrigo D. Requião, Luiza Fernandes, Henrique José Araujo de Souza, Silvana Rossetto, Tatiana Domitrovic, Fernando L. Palhano. Protein charge distribution in proteomes and its impact on translation
0 -- 0Poppy Miller, Jonathan Marshall, Nigel French, Chris Jewell. sourceR: Classification and source attribution of infectious agents among heterogeneous populations
0 -- 0Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee. Transcriptomics technologies
0 -- 0Christopher M. Jakobson, Danielle Tullman-Ercek, Marilyn F. Slininger, Niall M. Mangan. A systems-level model reveals that 1, 2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration
0 -- 0Eghbal A. Hosseini, Katrina P. Nguyen, Wilsaan M. Joiner. The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning
0 -- 0Robert C. Jackson, Giovanni Y. Di Veroli, Siang-Boon Koh, Ian Goldlust, Frances M. Richards, Duncan I. Jodrell. Modelling of the cancer cell cycle as a tool for rational drug development: A systems pharmacology approach to cyclotherapy
0 -- 0Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark S. Alber. Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia
0 -- 0Luca Ambrogioni, Marcel A. J. van Gerven, Eric Maris. Dynamic decomposition of spatiotemporal neural signals
0 -- 0Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J. Gavaghan, Charlotte M. Deane, Bernhard Knapp. Ten simple rules for surviving an interdisciplinary PhD
0 -- 0Tad Dallas, Andrew W. Park, John M. Drake. Predicting cryptic links in host-parasite networks
0 -- 0Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li. Co-occurring protein phosphorylation are functionally associated
0 -- 0Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey A. Lukyanov, Dmitry M. Chudakov. MAGERI: Computational pipeline for molecular-barcoded targeted resequencing
0 -- 0Pierre Bonnin, Norbert Kern, Neil T. Young, Ian Stansfield, M. Carmen Romano. Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile
0 -- 0Rita Bhui, Heather N. Hayenga. An agent-based model of leukocyte transendothelial migration during atherogenesis
0 -- 0Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta. BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
0 -- 0Philip E. Bourne, Jessica K. Polka, Ronald D. Vale, Robert Kiley. Ten simple rules to consider regarding preprint submission
0 -- 0Thaddeus Cybulski, Edward S. Boyden, George M. Church, Keith E. J. Tyo, Konrad P. Körding. Nucleotide-time alignment for molecular recorders
0 -- 0Semidán Robaina-Estévez, Zoran Nikoloski. On the effects of alternative optima in context-specific metabolic model predictions
0 -- 0Zachary R. Sailer, Michael J. Harms. High-order epistasis shapes evolutionary trajectories
0 -- 0Nimrod Shaham, Yoram Burak. Slow diffusive dynamics in a chaotic balanced neural network
0 -- 0Andreas Tuerk, Gregor Wiktorin, Serhat Güler. Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates
0 -- 0Silvan Quax, Ole Jensen, Paul H. E. Tiesinga. Top-down control of cortical gamma-band communication via pulvinar induced phase shifts in the alpha rhythm
0 -- 0Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott J. Emrich, Patricia L. Clark. Widespread position-specific conservation of synonymous rare codons within coding sequences
0 -- 0Yusuke Matsui, Atsushi Niida, Ryutaro Uchi, Koshi Mimori, Satoru Miyano, Teppei Shimamura. phyC: Clustering cancer evolutionary trees
0 -- 0William R. Holmes, Jinseok Park, Andre Levchenko, Leah Edelstein-Keshet. A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns
0 -- 0Don Klinkenberg, Jantien A. Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga. Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks
0 -- 0Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas. SteadyCom: Predicting microbial abundances while ensuring community stability
0 -- 0Florian Berger, A. J. Hudspeth. Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms
0 -- 0Veith Andreas Weilnhammer, Heiner Stuke, Guido Hesselmann, Philipp Sterzer, Katharina Schmack. A predictive coding account of bistable perception - a model-based fMRI study

Volume 13, Issue 4

0 -- 0David J. Albers, Matthew E. Levine, Bruce J. Gluckman, Henry N. Ginsberg, George Hripcsak, Lena Mamykina. Personalized glucose forecasting for type 2 diabetes using data assimilation
0 -- 0Andrea K. Barreiro, Cheng Ly. When do correlations increase with firing rates in recurrent networks?
0 -- 0Charles K. Fisher, Thierry Mora, Aleksandra M. Walczak. Variable habitat conditions drive species covariation in the human microbiota
0 -- 0Joel Zylberberg, Alexandre Pouget, Peter E. Latham, Eric Shea-Brown. Robust information propagation through noisy neural circuits
0 -- 0Kostas Kouvaris, Jeff Clune, Loizos Kounios, Markus Brede, Richard A. Watson. How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation
0 -- 0Eduardo D. Sontag. Dynamic compensation, parameter identifiability, and equivariances
0 -- 0Anne-Claire M. F. Martines, Karen van Eunen, Dirk-Jan Reijngoud, Barbara M. Bakker. The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation
0 -- 0Irene Otero-Muras, Pencho Yordanov, Jörg Stelling. Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling
0 -- 0Mónica L. García-Gómez, Eugenio Azpeitia, Elena R. Álvarez-Buylla. A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana
0 -- 0Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara. Modeling disordered protein interactions from biophysical principles
0 -- 0Xiaoliang Yang, Zihua Wang, Zhichu Xiang, Dan Li, Zhiyuan Hu, Wei Cui, Lingling Geng, Qiaojun Fang. Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging
0 -- 0Dipjyoti Das, Supravat Dey, Robert C. Brewster, Sandeep Choubey. Effect of transcription factor resource sharing on gene expression noise
0 -- 0Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf. Semantic prioritization of novel causative genomic variants
0 -- 0Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller 0009. From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints
0 -- 0Wan Yang, Liang Wen, Shen-Long Li, Kai Chen, Wen-yi Zhang, Jeffrey Shaman. Geospatial characteristics of measles transmission in China during 2005-2014
0 -- 0Vijay Singh, Ilya Nemenman. Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor
0 -- 0Jonas Ranft, Leandro G. Almeida, Pamela C. Rodriguez, Antoine Triller, Vincent Hakim. An aggregation-removal model for the formation and size determination of post-synaptic scaffold domains
0 -- 0Iman Habibi, Raymond Cheong, Tomasz Lipniacki, Andre Levchenko, Effat S. Emamian, Ali Abdi. Computation and measurement of cell decision making errors using single cell data
0 -- 0Nicolas Gauvrit, Hector Zenil, Fernando Soler-Toscano, Jean-Paul Delahaye, Peter Brugger. Human behavioral complexity peaks at age 25
0 -- 0Xiuli Chen, Kieran Mohr, Joseph M. Galea. Predicting explorative motor learning using decision-making and motor noise
0 -- 0Thomas A. Peterson, Iris Ivy M. Gauran, Junyong Park, DoHwan Park, Maricel G. Kann. Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples
0 -- 0Tobias U. Hauser, Michael Moutoussis, Reto Iannaccone, Silvia Brem, Susanne Walitza, Renate Drechsler, Peter Dayan, Raymond J. Dolan. Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD)
0 -- 0Viveca Lindahl, Alessandra Villa, Berk Hess. Sequence dependency of canonical base pair opening in the DNA double helix
0 -- 0Mireya Plass, Simon H. Rasmussen, Anders Krogh. Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors
0 -- 0Abdellali Kelil, Benjamin Dubreuil, Emmanuel D. Levy, Stephen W. Michnick. Exhaustive search of linear information encoding protein-peptide recognition
0 -- 0Tom Sumner, Richard J. Orton, Darren M. Green, Rowland R. Kao, Simon Gubbins. Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock
0 -- 0Francesca Mastrogiuseppe, Srdjan Ostojic. Intrinsically-generated fluctuating activity in excitatory-inhibitory networks
0 -- 0Hildur Knutsdottir, Cole Zmurchok, Dhananjay Bhaskar, Eirikur Palsson, Damian Dalle Nogare, Ajay B. Chitnis, Leah Edelstein-Keshet. Polarization and migration in the zebrafish posterior lateral line system
0 -- 0Tilo Schwalger, Moritz Deger, Wulfram Gerstner. Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size
0 -- 0Wen-Ting Chu, Jane Clarke, Sarah L. Shammas, Jin Wang. Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1
0 -- 0Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz. Inferring modulators of genetic interactions with epistatic nested effects models
0 -- 0Jörn Diedrichsen, Nikolaus Kriegeskorte. Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis
0 -- 0Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas M. Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis, George Kollias. Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL)
0 -- 0Andrew F. Brouwer, Mark H. Weir, Marisa C. Eisenberg, Rafael Meza, Joseph N. S. Eisenberg. Dose-response relationships for environmentally mediated infectious disease transmission models
0 -- 0Anish K. Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T. Vogelstein, Kristina D. Micheva, Richard J. Weinberg, Stephen J. Smith, Guillermo Sapiro. Probabilistic fluorescence-based synapse detection
0 -- 0Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun. ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time
0 -- 0Ofir Shukron, David Holcman. Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data
0 -- 0Morgan Taschuk, Greg Wilson. Ten simple rules for making research software more robust
0 -- 0Serena Bradde, Marija Vucelja, Tiberiu Tesileanu, Vijay Balasubramanian. Dynamics of adaptive immunity against phage in bacterial populations
0 -- 0Yonatan Savir, Alexander Martynov, Michael Springer. Achieving global perfect homeostasis through transporter regulation
0 -- 0Yann Zerlaut, Alain Destexhe. Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons
0 -- 0Claus Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J. Lercher. Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
0 -- 0Mindaugas Snipas, Lina Rimkute, Tadas Kraujalis, Kestutis Maciunas, Feliksas F. Bukauskas. Functional asymmetry and plasticity of electrical synapses interconnecting neurons through a 36-state model of gap junction channel gating
0 -- 0Fayyaz ul Amir Afsar Minhas, Eric D. Ross, Asa Ben-Hur. Amino acid composition predicts prion activity

Volume 13, Issue 3

0 -- 0Matthew B. Biggs, Jason A. Papin. Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA
0 -- 0Johannes Friedrich, Pengcheng Zhou, Liam Paninski. Fast online deconvolution of calcium imaging data
0 -- 0Cibele Vieira Falkenberg, Evren U. Azeloglu, Mark Stothers, Thomas J. Deerinck, Yibang Chen, John C. He, Mark H. Ellisman, James C. Hone, Ravi Iyengar, Leslie M. Loew. Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability
0 -- 0Andrew F. Brouwer, Rafael Meza, Marisa C. Eisenberg. Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis
0 -- 0David C. Farrow, Logan C. Brooks, Sangwon Hyun, Ryan J. Tibshirani, Donald S. Burke, Roni Rosenfeld. A human judgment approach to epidemiological forecasting
0 -- 0Rashmi Priya, Guillermo A. Gomez, Srikanth Budnar, Bipul R. Acharya, Andras Czirok, Alpha S. Yap, Zoltan Neufeld. Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions
0 -- 0Alexander Byers Brummer, Van M. Savage, Brian J. Enquist. A general model for metabolic scaling in self-similar asymmetric networks
0 -- 0Polydefkis Diamantis, Oliver T. Unke, Markus Meuwly. Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
0 -- 0Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capota, M. Mallar Chakravarty, Nathan William Churchill, Alexander L. Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher J. Steele, Pierre-Olivier Quirion, Robert E. Smith 0002, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack. BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
0 -- 0Christopher J. Lortie. Ten simple rules for short and swift presentations
0 -- 0Xuejin Li, E. Du, Ming Dao, Subra Suresh, George E. Karniadakis. Patient-specific modeling of individual sickle cell behavior under transient hypoxia
0 -- 0Joris Paijmans, David K. Lubensky, Pieter Rein ten Wolde. A thermodynamically consistent model of the post-translational Kai circadian clock
0 -- 0Paul M. Bays, Ben A. Dowding. Fidelity of the representation of value in decision-making
0 -- 0Matthew Zook, Solon Barocas, Danah Boyd, Kate Crawford 0002, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara König 0002, Jacob Metcalf, Arvind Narayanan, Alondra Nelson, Frank Pasquale. Ten simple rules for responsible big data research
0 -- 0Julien Vibert, Veronique Thomas-Vaslin. Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background
0 -- 0Daniele Caligiore, Francesco Mannella, Michael A. Arbib, Gianluca Baldassarre. Dysfunctions of the basal ganglia-cerebellar-thalamo-cortical system produce motor tics in Tourette syndrome
0 -- 0Etay Hay, Petra Ritter, Nancy J. Lobaugh, Anthony R. McIntosh. Multiregional integration in the brain during resting-state fMRI activity
0 -- 0Lindsay E. Clegg, Feilim Mac Gabhann. A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands
0 -- 0Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia V. Ponomarenko, Roderic Guigó, Rory Johnson. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion
0 -- 0David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler. Phylodynamics on local sexual contact networks
0 -- 0Junjiajia Long, Steven W. Zucker, Thierry Emonet. Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation
0 -- 0Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi. Network perturbation by recurrent regulatory variants in cancer
0 -- 0Mauricio González-Forero, Timm Faulwasser, Laurent Lehmann. A model for brain life history evolution
0 -- 0Amir Bitran, Wei-Yin Chiang, Erel Levine, Mara Prentiss. Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA
0 -- 0Tohar S. Yarden, Israel Nelken. Stimulus-specific adaptation in a recurrent network model of primary auditory cortex
0 -- 0James T. Yurkovich, Laurence Yang, Bernhard O. Palsson. Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
0 -- 0Erick A. Perez Alday, Michael A. Colman, Philip Langley, Henggui Zhang. Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study
0 -- 0Mahamar Dicko, Pierre Saramito, Guy B. Blanchard, Claire M. Lye, Bénédicte Sanson, Jocelyn Étienne. Geometry can provide long-range mechanical guidance for embryogenesis
0 -- 0Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks
0 -- 0Marie Devaine, Jean Daunizeau. Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment
0 -- 0Binwu Zhao, Martien A. Cohen Stuart, Carol K. Hall. Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide
0 -- 0Zhu-Hong You, Zhi-an Huang, Zexuan Zhu, Guiying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen. PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction
0 -- 0Sang Woo Park, Benjamin M. Bolker. Effects of contact structure on the transient evolution of HIV virulence
0 -- 0Bruno A. Gaëta, Javier De Las Rivas, Paul Horton, Pieter Meysman, Nicola J. Mulder, Paolo Romano 0001, Lonnie R. Welch. Ten simple rules for forming a scientific professional society
0 -- 0Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon. Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification
0 -- 0Michiel J. M. Niesen, Connie Y. Wang, Reid C. Van Lehn, Thomas Miller III. Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration
0 -- 0Sergey G. Aleksin, Kaiyu Zheng, Dmitri A. Rusakov, Leonid Savtchenko. ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing
0 -- 0. PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You
0 -- 0Matthew J. Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P. Roth, Anne-Claude Gavin, Peer Bork, Robert B. Russell. Systematic identification of phosphorylation-mediated protein interaction switches
0 -- 0Susmita Roy, Heiko Lammert, Ryan L. Hayes, Bin Chen, Regan LeBlanc, T. Kwaku Dayie, José N. Onuchic, Karissa Y. Sanbonmatsu. A magnesium-induced triplex pre-organizes the SAM-II riboswitch
0 -- 0Jeffrey Chen, Thomas MacCarthy. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes
0 -- 0Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce Randall Donald. A critical analysis of computational protein design with sparse residue interaction graphs
0 -- 0Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson. High GC content causes orphan proteins to be intrinsically disordered
0 -- 0Emma Saulnier, Olivier Gascuel, Samuel Alizon. Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study
0 -- 0Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, José N. Onuchic. Interrogating the topological robustness of gene regulatory circuits by randomization
0 -- 0Jonathan T. Young, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko. Dynamics robustness of cascading systems
0 -- 0Aurélien Naldi, Romain M. Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu. Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells
0 -- 0Daniel Howsmon, Uwe Kruger, Stepan Melnyk, S. Jill James, Juergen Hahn. Classification and adaptive behavior prediction of children with autism spectrum disorder based upon multivariate data analysis of markers of oxidative stress and DNA methylation

Volume 13, Issue 2

0 -- 0Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins
0 -- 0Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
0 -- 0David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga. Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
0 -- 0Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark Coles, Marika C. Kullberg, Jon Timmis. ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
0 -- 0Didac Santesmasses, Marco Mariotti, Roderic Guigó. Computational identification of the selenocysteine tRNA (tRNASec) in genomes
0 -- 0Guillaume Lajoie, Nedialko I. Krouchev, John F. Kalaska, Adrienne L. Fairhall, Eberhard E. Fetz. Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface
0 -- 0Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti. Unifying view of mechanical and functional hotspots across class A GPCRs
0 -- 0Jannis Schuecker, Maximilian Schmidt, Sacha J. van Albada, Markus Diesmann, Moritz Helias. Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome
0 -- 0Miguel Won, Manuel Marques-Pita, Carlota Louro, Joana Gonçalves-Sá. Early and Real-Time Detection of Seasonal Influenza Onset
0 -- 0Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S. Yen, Chen-Hsiang Yeang. A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons
0 -- 0Yihao Zhang, Krithika Abiraman, He Li, David M. Pierce, Anastasios V. Tzingounis, George Lykotrafitis. Modeling of the axon membrane skeleton structure and implications for its mechanical properties
0 -- 0Pierre Millard, Kieran Smallbone, Pedro Mendes. Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli
0 -- 0Jarred R. Mondoñedo, Béla Suki. Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema
0 -- 0Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta. Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism
0 -- 0Olga K. Kamneva. Genome composition and phylogeny of microbes predict their co-occurrence in the environment
0 -- 0Vinal V. Lakhani, Timothy C. Elston. Testing the limits of gradient sensing
0 -- 0Naomi V. Bradbury, William J. M. Probert, Katriona Shea, Michael C. Runge, Christopher Fonnesbeck, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley. Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns
0 -- 0John F. Magnotti, Michael S. Beauchamp. A Causal Inference Model Explains Perception of the McGurk Effect and Other Incongruent Audiovisual Speech
0 -- 0Julia V. Ponomarenko, Romina Garrido, Roderic Guigó. Ten Simple Rules on How to Organize a Scientific Retreat
0 -- 0Vivek Charu, Scott Zeger, Julia R. Gog, Ottar N. Bjørnstad, Stephen Kissler, Lone Simonsen, Bryan T. Grenfell, Cécile Viboud. Human mobility and the spatial transmission of influenza in the United States
0 -- 0Arno Klein, Satrajit S. Ghosh, Forrest Sheng Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter 0001, Elias Chaibub Neto, Anisha Keshavan. Mindboggling morphometry of human brains
0 -- 0Tracey M. Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor. Representing high throughput expression profiles via perturbation barcodes reveals compound targets
0 -- 0Qian Qin, Jianxing Feng. Imputation for transcription factor binding predictions based on deep learning
0 -- 0Johannes Burge, Priyank Jaini. Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise
0 -- 0James M. Osborne, Alexander G. Fletcher, Joe Pitt-Francis, Philip K. Maini, David J. Gavaghan. Comparing individual-based approaches to modelling the self-organization of multicellular tissues
0 -- 0Sean M. Gibbons, Sean M. Kearney, Chris S. Smillie, Eric J. Alm. Two dynamic regimes in the human gut microbiome
0 -- 0Miguel A. Fortuna, Luis Zaman, Charles Ofria, Andreas Wagner. The genotype-phenotype map of an evolving digital organism
0 -- 0Jung-Min Han, Akihiko Tanimura, Vivien Kirk, James Sneyd. A mathematical model of calcium dynamics in HSY cells
0 -- 0Dong Ping Yang, Hai-Jun Zhou, Changsong Zhou. Co-emergence of multi-scale cortical activities of irregular firing, oscillations and avalanches achieves cost-efficient information capacity
0 -- 0Hojjat Bazzazi, Aleksander S. Popel. Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells
0 -- 0William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard. Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression
0 -- 0Mark P. Little, Jolyon H. Hendry. Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer
0 -- 0Alexander Miguel Monzon, Diego J. Zea, María Silvina Fornasari, Tadeo E. Saldaño, Sebastian Fernandez Alberti, Silvio C. E. Tosatto, Gustavo D. Parisi. Conformational diversity analysis reveals three functional mechanisms in proteins
0 -- 0Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert Podolsky, Gregory Dyson, Robert P. Hausinger, Gerardo Andrés Cisneros. ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding
0 -- 0Mark Roper, Chrisantha Fernando, Lars Chittka. Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees
0 -- 0Daniel Magee, Marc A. Suchard, Matthew Scotch. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction
0 -- 0Berta Verd, Anton Crombach, Johannes Jaeger. Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
0 -- 0Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina. Elucidation of molecular kinetic schemes from macroscopic traces using system identification
0 -- 0Christoph Thiel, Henrik Cordes, Lorenzo Fabbri, Hélène Eloise Aschmann, Vanessa Baier, Ines Smit, Francis Atkinson, Lars Mathias Blank, Lars Kuepfer. A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations
0 -- 0Dyoni M. de Oliveira, Marcos S. Buckeridge, Wanderley Dantas dos Santos. Ten Simple Rules for Developing a Successful Research Proposal in Brazil
0 -- 0Julia Chifman, Seda Arat, Zhiyong Deng, Erica Lemler, James C. Pino, Leonard A. Harris, Michael A. Kochen, Carlos F. Lopez, Steven A. Akman, Frank M. Torti, Suzy V. Torti, Reinhard C. Laubenbacher. Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective
0 -- 0Franziska Oschmann, Konstantin Mergenthaler, Evelyn Jungnickel, Klaus Obermayer. Spatial separation of two different pathways accounting for the generation of calcium signals in astrocytes
0 -- 0Franca Schmid, Philbert S. Tsai, David Kleinfeld, Patrick Jenny, Bruno Weber. Depth-dependent flow and pressure characteristics in cortical microvascular networks
0 -- 0Sophie K. Kay, Heather A. Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M. Osborne, David J. Gavaghan, Helen M. Byrne. The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt
0 -- 0Jerome M. Karp, Samuel Sparks, David Cowburn. Effects of FGFR2 kinase activation loop dynamics on catalytic activity
0 -- 0Felipe Gerhard, Moritz Deger, Wilson Truccolo. On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs
0 -- 0Dongjun Chung, Hang J. Kim, Hongyu Zhao. graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
0 -- 0István Bartha, Paul J. Mclaren, Chanson J. Brumme, P. Richard Harrigan, Amalio Telenti, Jacques Fellay. Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

Volume 13, Issue 12

0 -- 0. Correction: Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression
0 -- 0Andrea Tacchetti, Leyla Isik, Tomaso A. Poggio. Invariant recognition drives neural representations of action sequences
0 -- 0Patrick Meyer, Pallab Maity, Andre Burkovski, Julian Schwab, Christoph Müssel, Karmveer Singh, Filipa F. Ferreira, Linda Krug, Harald J. Maier, Meinhard Wlaschek, Thomas Wirth, Hans A. Kestler, Karin Scharffetter-Kochanek. A model of the onset of the senescence associated secretory phenotype after DNA damage induced senescence
0 -- 0Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A. Porter, Dima Kozakov, Ora Schueler-Furman. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
0 -- 0Xinxin Wang, Anders E. Carlsson. A master equation approach to actin polymerization applied to endocytosis in yeast
0 -- 0Dylan R. Muir, Patricia Molina-Luna, Morgane M. Roth, Fritjof Helmchen, Björn Kampa. Specific excitatory connectivity for feature integration in mouse primary visual cortex
0 -- 0Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P. Nolan, Wing Hung Wong. Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
0 -- 0Rico Rueedi, Roger Mallol, Johannes Raffler, David Lamparter, Nele Friedrich, Peter Vollenweider, Gérard Waeber, Gabi Kastenmüller, Zoltán Kutalik, Sven Bergmann. Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy
0 -- 0Austin E. Soplata, Michelle M. McCarthy, Jason Sherfey, Shane Lee, Patrick L. Purdon, Emery N. Brown, Nancy Kopell. Thalamocortical control of propofol phase-amplitude coupling
0 -- 0William M. McFadden, Patrick M. McCall, Margaret L. Gardel, Edwin M. Munro. Filament turnover tunes both force generation and dissipation to control long-range flows in a model actomyosin cortex
0 -- 0Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini. pSSAlib: The partial-propensity stochastic chemical network simulator
0 -- 0Bryan T. Weinstein, Maxim O. Lavrentovich, Wolfram Möbius, Andrew W. Murray, David R. Nelson. Genetic drift and selection in many-allele range expansions
0 -- 0Rebecca F. Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L. Dolan, Jeffrey J. Gray. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design
0 -- 0Nadav Ben-Shushan, Misha Tsodyks. Stabilizing patterns in time: Neural network approach
0 -- 0Zhengnan Huang, Hongjiu Zhang, Jonathan Boss, Stephen A. Goutman, Bhramar Mukherjee, Ivo D. Dinov, Yuanfang Guan. Complete hazard ranking to analyze right-censored data: An ALS survival study
0 -- 0Gábor Erdös, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi. Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway
0 -- 0James N. Ingram, Mohsen Sadeghi, J. Randall Flanagan, Daniel M. Wolpert. An error-tuned model for sensorimotor learning
0 -- 0Jinglin Li, Jens Peter Lindemann, Martin Egelhaaf. Local motion adaptation enhances the representation of spatial structure at EMD arrays
0 -- 0. Correction: Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions
0 -- 0Maria C. Quintero, Robert W. Putnam, Juan M. Cordovez. Theoretical perspectives on central chemosensitivity: CO2/H+-sensitive neurons in the locus coeruleus
0 -- 0Tom Dupré la Tour, Lucille Tallot, Laetitia Grabot, Valérie Doyère, Virginie van Wassenhove, Yves Grenier, Alexandre Gramfort. Non-linear auto-regressive models for cross-frequency coupling in neural time series
0 -- 0Amit Yashar, Rachel N. Denison. Feature reliability determines specificity and transfer of perceptual learning in orientation search
0 -- 0Crystal M. Botham, Joshua A. Arribere, Sky W. Brubaker, Kevin T. Beier. Ten simple rules for writing a career development award proposal
0 -- 0. Correction: Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species
0 -- 0Sanjay Sonney, Jeremy Leipzig, Marie T. Lott, Shiping Zhang, Vincent Procaccio, Douglas C. Wallace, Neal Sondheimer. Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP
0 -- 0Thomas D. Gaddy, Qianhui Wu, Alyssa D. Arnheim, Stacey D. Finley. Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment
0 -- 0Kaitlin E. Frasier, Marie A. Roch, Melissa S. Soldevilla, Sean M. Wiggins, Lance P. Garrison, John A. Hildebrand. Automated classification of dolphin echolocation click types from the Gulf of Mexico
0 -- 0Vincent Jacob, Christelle Monsempès, Jean-Pierre Rospars, Jean-Baptiste Masson, Philippe Lucas. Olfactory coding in the turbulent realm
0 -- 0Xing Chen, Li Huang. LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
0 -- 0Takaho Tsuchiya, Masashi Fujii, Naoki Matsuda, Katsuyuki Kunida, Shinsuke Uda, Hiroyuki Kubota, Katsumi Konishi, Shinya Kuroda. System identification of signaling dependent gene expression with different time-scale data
0 -- 0Chieh Lo, Radu Marculescu. MPLasso: Inferring microbial association networks using prior microbial knowledge
0 -- 0Loan Huynh, Chris Neale, Régis Pomès, Hue Sun Chan. Molecular recognition and packing frustration in a helical protein
0 -- 0Siwei Wang, Alexander Borst, Noga Zaslavsky, Naftali Tishby, Idan Segev. Efficient encoding of motion is mediated by gap junctions in the fly visual system
0 -- 0. Correction: Signatures of criticality arise from random subsampling in simple population models
0 -- 0Go Ashida, Daniel J. Tollin, Jutta Kretzberg. Physiological models of the lateral superior olive
0 -- 0Diego A. Forero, Sandra Lopez-Leon, George P. Patrinos. Ten simple rules for international short-term research stays
0 -- 0Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada. Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
0 -- 0Alexander Martynov, Konstantin Severinov, Iaroslav Ispolatov. Optimal number of spacers in CRISPR arrays
0 -- 0Christoph Baldow, Sebastian Salentin, Michael Schroeder 0001, Ingo Roeder, Ingmar Glauche. MAGPIE: Simplifying access and execution of computational models in the life sciences
0 -- 0. Correction: Identifying influential neighbors in animal flocking
0 -- 0Tsvetomira Radeva, Anna R. Dornhaus, Nancy A. Lynch, Radhika Nagpal, Hsin-Hao Su. Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems
0 -- 0Shyr-Shea Chang, Shenyinying Tu, Kyung In Baek, Andrew Pietersen, Yu-Hsiu Liu, Van M. Savage, Sheng-Ping L. Hwang, Tzung K. Hsiai, Marcus Roper. Optimal occlusion uniformly partitions red blood cells fluxes within a microvascular network

Volume 13, Issue 11

0 -- 0Suzan Farhang-Sardroodi, Amir Hossein Darooneh, Moladad Nikbakht, Natalia L. Komarova, Mohammad Kohandel. The effect of spatial randomness on the average fixation time of mutants
0 -- 0Tetsuhiro S. Hatakeyama, Chikara Furusawa. Metabolic dynamics restricted by conserved carriers: Jamming and feedback
0 -- 0Daniel R. Romano, Matthew C. Pharris, Neal M. Patel, Tamara Kinzer-Ursem. Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins
0 -- 0Yanli Wang, Wing-Cheong Lo, Ching-Shan Chou. A modeling study of budding yeast colony formation and its relationship to budding pattern and aging
0 -- 0Emyr Bakker, Kun Tian, Luciano Mutti, Constantinos Demonacos, Jean-Marc Schwartz, Marija Krstic-Demonacos. Insight into glucocorticoid receptor signalling through interactome model analysis
0 -- 0Stefano Anzellotti, Alfonso Caramazza, Rebecca Saxe. Multivariate pattern dependence
0 -- 0Daniel Monsivais, Asim Ghosh, Kunal Bhattacharya, Robin I. M. Dunbar, Kimmo Kaski. Tracking urban human activity from mobile phone calling patterns
0 -- 0Stefan Albert, Katharina Schmack, Philipp Sterzer, Gaby Schneider. A hierarchical stochastic model for bistable perception
0 -- 0Mark A. Walker, Viatcheslav Gurev, John Jeremy Rice, Joseph L. Greenstein, Raimond L. Winslow. Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue
0 -- 0Sushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli. A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer
0 -- 0Yun-Ching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski. Significant associations between driver gene mutations and DNA methylation alterations across many cancer types
0 -- 0John A. P. Sekar, José Juan Tapia, James R. Faeder. Automated visualization of rule-based models
0 -- 0Alexis T. Baria, Brian Maniscalco, Biyu J. He. Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception
0 -- 0Anthony Szedlak, Spencer Sims, Nicholas Smith, Giovanni Paternostro, Carlo Piermarocchi. Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
0 -- 0Thomas Coudrat, John Simms, Arthur Christopoulos, Denise Wootten, Patrick M. Sexton. Improving virtual screening of G protein-coupled receptors via ligand-directed modeling
0 -- 0Gonzalo E. Mena, Lauren E. Grosberg, Sasidhar Madugula, Pawel Hottowy, Alan M. Litke, John P. Cunningham, E. J. Chichilnisky, Liam Paninski. Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays
0 -- 0Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet. Characterizing steady states of genome-scale metabolic networks in continuous cell cultures
0 -- 0Philip M. Tan, Kyle S. Buchholz, Jeffrey H. Omens, Andrew D. McCulloch, Jeffrey J. Saucerman. Predictive model identifies key network regulators of cardiomyocyte mechano-signaling
0 -- 0Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao. mixOmics: An R package for 'omics feature selection and multiple data integration
0 -- 0Li Jiang, Luca Giuggioli, Andrea Perna, Ramón Escobedo, Valentin Lecheval, Clément Sire, Zhangang Han, Guy Theraulaz. Identifying influential neighbors in animal flocking
0 -- 0Edwin van Leeuwen, Petra Klepac, Dominic Thorrington, Richard Pebody, Marc Baguelin. fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks
0 -- 0Michael F. Sloma, David H. Mathews. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs
0 -- 0Masoud Nickaeen, Igor L. Novak, Stephanie Pulford, Aaron Rumack, Jamie Brandon, Boris M. Slepchenko, Alex Mogilner. A free-boundary model of a motile cell explains turning behavior
0 -- 0Marie Devaine, Aurore San-Galli, Cinzia Trapanese, Giulia Bardino, Christelle Hano, Michel Saint Jalme, Sébastien Bouret, Shelly Masi, Jean Daunizeau. Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species
0 -- 0Richard D. Smith, Jing Lu, Heather A. Carlson. Are there physicochemical differences between allosteric and competitive ligands?
0 -- 0Alizée Lopez-Persem, Lionel Rigoux, Sacha Bourgeois-Gironde, Jean Daunizeau, Mathias Pessiglione. Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks
0 -- 0David J. Price, Alexandre Breuzé, Richard Dybowski, Piero Mastroeni, Olivier Restif. An efficient moments-based inference method for within-host bacterial infection dynamics
0 -- 0Rosemary M. McCloskey, Art F. Y. Poon. A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation
0 -- 0Shaima Hashem, Matteo Tiberti, Arianna Fornili. Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil
0 -- 0Alejandro Fernández Villaverde, Julio R. Banga. Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation
0 -- 0Ronny Straube, Meera Shah, Dietrich Flockerzi, Dieter A. Wolf. Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire
0 -- 0Emma Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower. A Bayesian method for detecting pairwise associations in compositional data
0 -- 0Teresa K. Yamana, Sasikiran Kandula, Jeffrey Shaman. Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States
0 -- 0Guo-Shi Li, Thomas A. Cleland. A coupled-oscillator model of olfactory bulb gamma oscillations
0 -- 0Yuriy Pichugin, Jorge Peña 0001, Paul B. Rainey, Arne Traulsen. Fragmentation modes and the evolution of life cycles
0 -- 0Jeffrey Shaman, Sasikiran Kandula, Wan Yang, Alicia Karspeck. The use of ambient humidity conditions to improve influenza forecast
0 -- 0Franciszek Rakowski, Jan Karbowski. Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost
0 -- 0André Luzardo, Eduardo Alonso, Esther Mondragón. A Rescorla-Wagner drift-diffusion model of conditioning and timing
0 -- 0Ruolin Liu, Julie A. Dickerson. Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq
0 -- 0Zoltan Neufeld, William von Witt, Dora Lakatos, Jiaming Wang, Balazs Hegedus, Andras Czirok. The role of Allee effect in modelling post resection recurrence of glioblastoma

Volume 13, Issue 10

0 -- 0Kensuke Arai, Robert E. Kass. Inferring oscillatory modulation in neural spike trains
0 -- 0Tiziano D'albis, Richard Kempter. A single-cell spiking model for the origin of grid-cell patterns
0 -- 0Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg. Vicus: Exploiting local structures to improve network-based analysis of biological data
0 -- 0Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones. Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster
0 -- 0Jiawen Chen, Steven C. Almo, Yinghao Wu. General principles of binding between cell surface receptors and multi-specific ligands: A computational study
0 -- 0Phuong Dao, Yoo Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka. BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions
0 -- 0Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold. Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization
0 -- 0Carsten Conradi, Elisenda Feliu, Maya Mincheva, Carsten Wiuf. Identifying parameter regions for multistationarity
0 -- 0Gudrun Gygli, Maria Fátima Lucas, Victor Guallar, Willem J. H. van Berkel. The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
0 -- 0Shiran Abadi, Winston X. Yan, David Amar, Itay Mayrose. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
0 -- 0Guoshi Li, Craig S. Henriquez, Flavio Fröhlich. Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation
0 -- 0Lindsay Barone, Jason Williams, David Micklos. Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators
0 -- 0Kim T. Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu, Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola J. Mulder, H3ABioNet Consortium. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience
0 -- 0Emine Guven-Maiorov, Chung-Jung Tsai, Ruth Nussinov. Structural host-microbiota interaction networks
0 -- 0Ekaterina Kotelnikova, Narsis A. Kiani, Elena Abad, Elena H. Martinez-Lapiscina, Magí Andorrà, Irati Zubizarreta, Irene Pulido-Valdeolivas, Inna Pertsovskaya, Leonidas G. Alexopoulos, Tomas Olsson, Roland Martin, Friedemann Paul, Jesper Tegnér, Jordi García-Ojalvo, Pablo Villoslada. Dynamics and heterogeneity of brain damage in multiple sclerosis
0 -- 0Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony. Deconvolving sequence features that discriminate between overlapping regulatory annotations
0 -- 0Thomas Heidlauf, Thomas Klotz, Christian Rode, Tobias Siebert, Oliver Röhrle. A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation
0 -- 0Spencer J. Fox, Joel C. Miller, Lauren Ancel Meyers. Seasonality in risk of pandemic influenza emergence
0 -- 0Vijay Vedula, Juhyun Lee, Hao Xu, C. C. Jay Kuo, Tzung K. Hsiai, Alison L. Marsden. A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling
0 -- 0Trey Ideker, Ruth Nussinov. Network approaches and applications in biology
0 -- 0Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker. Network propagation in the cytoscape cyberinfrastructure
0 -- 0Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan. A unifying Bayesian account of contextual effects in value-based choice
0 -- 0Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford. Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
0 -- 0Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano. Systematic, network-based characterization of therapeutic target inhibitors
0 -- 0Kris Parag, Glenn Vinnicombe. Point process analysis of noise in early invertebrate vision
0 -- 0Evelina Gabasova, John E. Reid, Lorenz Wernisch. Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
0 -- 0Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly. A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system
0 -- 0James Rankin, Frédéric Chavane. Neural field model to reconcile structure with function in primary visual cortex
0 -- 0John Joseph Valletta, Mario Recker. Identification of immune signatures predictive of clinical protection from malaria
0 -- 0Thomas G. Fai, Alejandra Leo-Macias, David L. Stokes, Charles S. Peskin. Image-based model of the spectrin cytoskeleton for red blood cell simulation
0 -- 0Niklas Hübel, Mahshid S. Hosseini-Zare, Jokubas Ziburkus, Ghanim Ullah. The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization
0 -- 0Marcel Nonnenmacher, Christian Behrens, Philipp Berens, Matthias Bethge, Jakob H. Macke. Signatures of criticality arise from random subsampling in simple population models
0 -- 0Cynthia Sandor, Nicola L. Beer, Caleb Webber. Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network
0 -- 0Andrew J. K. Phillips, Elizabeth B. Klerman, James P. Butler. Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery
0 -- 0Mark L. Ioffe, Michael J. Berry II. The structured 'low temperature' phase of the retinal population code
0 -- 0Mengjia Xu, Dimitrios P. Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George E. Karniadakis. A deep convolutional neural network for classification of red blood cells in sickle cell anemia
0 -- 0Louis Verny, Nadir Sella, Séverine Affeldt, Param Priya Singh, Hervé Isambert. Learning causal networks with latent variables from multivariate information in genomic data
0 -- 0Nicolas E. Martin, Siddharth Malik, Nicolas Calimet, Jean-Pierre Changeux, Marco Cecchini. Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
0 -- 0Amir Houshang Bahrami, Mary G. Lin, Xuefeng Ren, James H. Hurley, Gerhard Hummer. Scaffolding the cup-shaped double membrane in autophagy
0 -- 0William Stafford Noble. Ten simple rules for writing a response to reviewers
0 -- 0Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis. Transcriptomic correlates of neuron electrophysiological diversity
0 -- 0Emre Akbas, Miguel P. Eckstein. Object detection through search with a foveated visual system
0 -- 0Alex Finnegan, Jun S. Song. Maximum entropy methods for extracting the learned features of deep neural networks
0 -- 0Kevin S. Bonham, Melanie I. Stefan. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology
0 -- 0Andreas Handel. Learning infectious disease epidemiology in a modern framework
0 -- 0Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda. Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling
0 -- 0Giray Enkavi, Heikki Mikkolainen, Burçin Güngör, Elina Ikonen, Ilpo Vattulainen. Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin
0 -- 0Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte. Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets
0 -- 0Jaron T. Colas, Wolfgang M. Pauli, Tobias Larsen, J. Michael Tyszka, John P. O'Doherty. Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI
0 -- 0Kalinga Pavan T. Silva, Prithiviraj Chellamuthu, James Q. Boedicker. Quantifying the strength of quorum sensing crosstalk within microbial communities
0 -- 0Alex D. M. Dewar, Antoine Wystrach, Andrew Philippides, Paul Graham. Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours?
0 -- 0Max S. Y. Lau, Gavin J. Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, C. Jessica E. Metcalf, Benjamin D. Dalziel, Bryan T. Grenfell. A mechanistic spatio-temporal framework for modelling individual-to-individual transmission - With an application to the 2014-2015 West Africa Ebola outbreak
0 -- 0Vahid Rostami, PierGianLuca Porta Mana, Sonja Grün, Moritz Helias. Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models
0 -- 0Philip E. Bourne. Ten simple rules in considering a career in academia versus government
0 -- 0Aziz M. Mezlini, Anna Goldenberg. Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases
0 -- 0Marina E. Wosniack, Marcos C. Santos, Ernesto P. Raposo, Gandhi M. Viswanathan, Marcos G. E. da Luz. The evolutionary origins of Lévy walk foraging
0 -- 0Theodore Roman, Lu Xie, Russell Schwartz. Automated deconvolution of structured mixtures from heterogeneous tumor genomic data
0 -- 0Roman Shevchuk, Jochen S. Hub. Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
0 -- 0Anna Hake, Nico Pfeifer. Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time
0 -- 0Agne Tilunaite, Wayne Croft, Noah Russell, Tomas C. Bellamy, Rüdiger Thul. A Bayesian approach to modelling heterogeneous calcium responses in cell populations
0 -- 0Vadim Puller, Richard Neher, Jan Albert. Estimating time of HIV-1 infection from next-generation sequence diversity
0 -- 0Timothy N. Rubin, Oluwasanmi Koyejo, Krzysztof J. Gorgolewski, Michael N. Jones, Russell A. Poldrack, Tal Yarkoni. Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition
0 -- 0Peter Ashcroft, Markus G. Manz, Sebastian Bonhoeffer. Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments
0 -- 0Ryan Thomas Philips, Mriganka Sur, V. Srinivasa Chakravarthy. The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective
0 -- 0Nan Lin, Yun Zhu, Ruzong Fan, Momiao Xiong. A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

Volume 13, Issue 1

0 -- 0James M. Kunert, Pedro D. Maia, J. Nathan Kutz. Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage
0 -- 0Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M. Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann. Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes
0 -- 0Ignacio A. Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz. Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses
0 -- 0Aysima Hacisuleyman, Burak Erman. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin
0 -- 0Iris Reuveni, Sourav Ghosh, Edi Barkai. Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons
0 -- 0Oded Barzelay, Miriam Furst, Omri Barak. A New Approach to Model Pitch Perception Using Sparse Coding
0 -- 0David Lamparter, Daniel Marbach, Rico Rueedi, Sven Bergmann, Zoltan Kutalik. Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility
0 -- 0Mina A. Khoei, Guillaume S. Masson, Laurent U. Perrinet. The Flash-Lag Effect as a Motion-Based Predictive Shift
0 -- 0Gianluigi Rossi, Giulio A. De Leo, Stefano Pongolini, Silvano Natalini, Luca Zarenghi, Matteo Ricchi, Luca Bolzoni. The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks
0 -- 0Heiner Stuke, Hannes Stuke, Veith Andreas Weilnhammer, Katharina Schmack. Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning
0 -- 0Federica Giardina, Ethan O. Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner. Inference of Transmission Network Structure from HIV Phylogenetic Trees
0 -- 0Abby Tabor, Michael A. Thacker, G. Lorimer Moseley, Konrad P. Körding. Pain: A Statistical Account
0 -- 0Bethany Levick, Andy South, Ian M. Hastings. A Two-Locus Model of the Evolution of Insecticide Resistance to Inform and Optimise Public Health Insecticide Deployment Strategies
0 -- 0Christian Donner, Klaus Obermayer, Hideaki Shimazaki. Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations
0 -- 0Hualou Liang, Hongbin Wang. Structure-Function Network Mapping and Its Assessment via Persistent Homology
0 -- 0Cox Lwaka Tamba, Yuan-Li Ni, Yuan-Ming Zhang. Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies
0 -- 0Antonella Paladino, Monica Civera, Laura Belvisi, Giorgio Colombo. High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design
0 -- 0Luca Cardelli, Rosa D. Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikász-Nagy. Efficient Switches in Biology and Computer Science
0 -- 0Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti. Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing
0 -- 0Gabrielle Stetz, Gennady M. Verkhivker. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication
0 -- 0Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms
0 -- 0Richard John Wheeler. Use of chiral cell shape to ensure highly directional swimming in trypanosomes
0 -- 0Hoyon Hwang, Jiou Wang. Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans
0 -- 0Veronika Koren, Sophie Denève. Computational Account of Spontaneous Activity as a Signature of Predictive Coding
0 -- 0Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
0 -- 0Oliver Pohl, Marius Hintsche, Zahra Alirezaeizanjani, Maximilian Seyrich, Carsten Beta, Holger Stark. Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients
0 -- 0Christopher M. Siwy, Christopher Lockhart, Dmitri K. Klimov. Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent?
0 -- 0Markus List, Peter Ebert, Felipe Albrecht. Ten Simple Rules for Developing Usable Software in Computational Biology
0 -- 0Andrea Insabato, Mario Pannunzi, Gustavo Deco. Multiple Choice Neurodynamical Model of the Uncertain Option Task
0 -- 0Tamara Carla Bidone, Wonyeong Jung, Daniel Maruri, Carlos Borau, Roger D. Kamm, Taeyoon Kim. Morphological Transformation and Force Generation of Active Cytoskeletal Networks
0 -- 0Christoph Zimmer, Reza Yaesoubi, Ted Cohen. A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models
0 -- 0Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng, Chao Cheng. Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome
0 -- 0Nicholas A. Rossi, Mary J. Dunlop. Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA
0 -- 0Stewart Heitmann, Michael Rule, Wilson Truccolo, Bard Ermentrout. Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation
0 -- 0Nikolay Chenkov, Henning Sprekeler, Richard Kempter. Memory replay in balanced recurrent networks
0 -- 0Ruth Nussinov, Jason A. Papin, Ilya A. Vakser. Computing the Dynamic Supramolecular Structural Proteome
0 -- 0Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem. An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts
0 -- 0Marie Amalric, Liping Wang, Pierre Pica, Santiago Figueira, Mariano Sigman, Stanislas Dehaene. The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers
0 -- 0William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie. Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst
0 -- 0Kaitlyn M. Gayvert, Omar Aly, James Platt, Marcus W. Bosenberg, David F. Stern, Olivier Elemento. A Computational Approach for Identifying Synergistic Drug Combinations
0 -- 0Eric Jonas, Konrad Paul Körding. Could a Neuroscientist Understand a Microprocessor?
0 -- 0Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas Schilling, Qing Nie. Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains
0 -- 0Chen Zhao, Jeffrey S. Isenberg, Aleksander S. Popel. Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model
0 -- 0Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast
0 -- 0Edward S. Lee, Paul G. Thomas, Jeff E. Mold, Andrew J. Yates. Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing
0 -- 0Martina Michalikova, Michiel W. H. Remme, Richard Kempter. Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma
0 -- 0Shenshen Wang. Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction
0 -- 0Hilje M. Doekes, Christophe Fraser, Katrina A. Lythgoe. Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels
0 -- 0Hsiao-Han Chang, Colin J. Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R. Kamya, Sarah G. Staedke, Grant Dorsey, Maxwell Murphy, Daniel E. Neafsey, Anna E. Jeffreys, Christina Hubbart, Kirk A. Rockett, Roberto Amato, Dominic Kwiatkowski, Caroline O. Buckee, Bryan Greenhouse. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites
0 -- 0Austin W. T. Chiang, Walt Y. L. Wu, Ting Wang, Ming-Jing Hwang. Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs
0 -- 0Sheng Wang 0001, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
0 -- 0Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel. Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
0 -- 0Alireza Yazdani, He Li, Jay D. Humphrey, George E. Karniadakis. A General Shear-Dependent Model for Thrombus Formation
0 -- 0Weikang Wang, Kuan Tao, Jing Wang, Gen Yang, Qi Ouyang, Yugang Wang, Lei Zhang, Feng Liu. Exploring the inhibitory effect of membrane tension on cell polarization
0 -- 0Stuart P. Wilson. Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling
0 -- 0Pia Abel zur Wiesch, Fabrizio Clarelli, Ted Cohen. Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies
0 -- 0Max Hinne, Annet Meijers, Rembrandt Bakker, Paul H. E. Tiesinga, Morten Mørup, Marcel A. J. van Gerven. The missing link: Predicting connectomes from noisy and partially observed tract tracing data
0 -- 0Te Wu, Long Wang 0001, Feng Fu. Coevolutionary dynamics of phenotypic diversity and contingent cooperation
0 -- 0Luc E. Coffeng, Cornelus Hermsen, Robert W. Sauerwein, Sake J. de Vlas. The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection
0 -- 0James M. Kunert, Joshua L. Proctor, Steven L. Brunton, J. Nathan Kutz. Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion
0 -- 0Yaroslav Pollak, Sarah Goldberg, Roee Amit. A Looping-Based Model for Quenching Repression
0 -- 0Tanmay A. Gokhale, Jong M. Kim, Robert D. Kirkton, Nenad Bursac, Craig S. Henriquez. Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies
0 -- 0Gaurav Bajpai, Ishutesh Jain, Mandar M. Inamdar, Dibyendu Das 0004, Ranjith Padinhateeri. Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure
0 -- 0Mihaela Enculescu, Christoph Metzendorf, Richard Sparla, Maximilian Hahnel, Johannes G. Bode, Martina U. Muckenthaler, Stefan Legewie. Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms
0 -- 0Elyse H. Norton, Stephen M. Fleming, Nathaniel D. Daw, Michael S. Landy. Suboptimal Criterion Learning in Static and Dynamic Environments