Journal: PLoS Computational Biology

Volume 10, Issue 9

0 -- 0David R. Blair, Kanix Wang, Svetlozar Nestorov, James A. Evans, Andrey Rzhetsky. Quantifying the Impact and Extent of Undocumented Biomedical Synonymy
0 -- 0Thu Thuy Nguyen, Jeremie Guedj, Elisabeth Chachaty, Jean de Gunzburg, Antoine Andremont, France Mentré. Mathematical Modeling of Bacterial Kinetics to Predict the Impact of Antibiotic Colonic Exposure and Treatment Duration on the Amount of Resistant Enterobacteria Excreted
0 -- 0Vassiliki Lila Koumandou, Sophia Kossida. 1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes
0 -- 0Diana Chang, Alon Keinan. Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
0 -- 0Rachel A. Mak-McCully, Stephen R. Deiss, Burke Q. Rosen, Ki-Young Jung, Terrence J. Sejnowski, Hélène Bastuji, Marc Rey, Sydney S. Cash, Maxim Bazhenov, Eric Halgren. Synchronization of Isolated Downstates (K-Complexes) May Be Caused by Cortically-Induced Disruption of Thalamic Spindling
0 -- 0James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane. Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design
0 -- 0Erin M. Stuckey, Thomas Smith, Nakul Chitnis. Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations
0 -- 0Peter R. Murphy, Joachim Vandekerckhove, Sander Nieuwenhuis. Pupil-Linked Arousal Determines Variability in Perceptual Decision Making
0 -- 0Hong Yang, Elias W. Krumholz, Evan D. Brutinel, Nagendra P. Palani, Michael J. Sadowsky, Andrew M. Odlyzko, Jeffrey A. Gralnick, Igor G. L. Libourel. Shewanella oneidensis Using Transposon Insertion Frequency Analysis
0 -- 0David A. Sivak, Matt Thomson. Environmental Statistics and Optimal Regulation
0 -- 0Xiakun Chu, Fei Liu, Brian A. Maxwell, Yong Wang, Zucai Suo, Haijun Wang, Wei Han, Jin Wang. Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA
0 -- 0Michal Brylinski. eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models
0 -- 0Sharlee Climer, Alan R. Templeton, Weixiong Zhang. Allele-Specific Network Reveals Combinatorial Interaction That Transcends Small Effects in Psoriasis GWAS
0 -- 0Jean-Baptiste Pettit, Raju Tomer, Kaia Achim, Sylvia Richardson, Lamiae Azizi, John C. Marioni. Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets
0 -- 0Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling. Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products
0 -- 0Qing Xie, Qi Liu, Fengbiao Mao, Wanshi Cai, Honghu Wu, Mingcong You, Zhen Wang, Bingyu Chen, Zhongsheng Sun, Jinyu Wu. A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data
0 -- 0. Correction: Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility
0 -- 0Melissa M. Norström, Nazle M. Veras, Wei Huang, Mattia C. F. Prosperi, Jennifer Cook, Wendy Hartogensis, Frederick M. Hecht, Annika C. Karlsoon, Marco Salemi. + T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression
0 -- 0N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond. IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
0 -- 0Thomas H. Hraha, Matthew J. Westacott, Marina Pozzoli, Aleena M. Notary, P. Mason McClatchey, Richard K. P. Benninger. Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability
0 -- 0Stefan Nowak, Johannes Neidhart, Ivan G. Szendro, Joachim Krug. Multidimensional Epistasis and the Transitory Advantage of Sex
0 -- 0Marti Bernardo-Faura, Stefan Massen, Christine S. Falk, Nathan R. Brady, Roland Eils. Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma
0 -- 0Masato Yasui, Satomi Matsuoka, Masahiro Ueda. PTEN Hopping on the Cell Membrane Is Regulated via a Positively-Charged C2 Domain
0 -- 0Andreea Oliviana Diaconescu, Christoph Mathys, Lilian A. E. Weber, Jean Daunizeau, Lars Kasper, Ekaterina I. Lomakina, Ernst Fehr, Klaas E. Stephan. Inferring on the Intentions of Others by Hierarchical Bayesian Learning
0 -- 0Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne. Ten Simple Rules for Better Figures
0 -- 0Amit Ghosh, Jerome P. Nilmeier, Daniel Weaver, Paul D. Adams, Jay D. Keasling, Aindrila Mukhopadhyay, Christopher J. Petzold, Héctor García Martín. 13C Metabolic Flux Analysis in Microbial Communities
0 -- 0Stefano Luccioli, Eshel Ben-Jacob, Ari Barzilai, Paolo Bonifazi, Alessandro Torcini. Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks
0 -- 0Tamás Székely Jr., Kevin Burrage, Marc Mangel, Michael B. Bonsall. Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages
0 -- 0Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean D. Mooney, Rachel Karchin. A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing
0 -- 0Penelope A. Hancock, Yasmin Rehman, Ian M. Hall, Obaghe Edeghere, Leon Danon, Thomas A. House, Matthew J. Keeling. Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set
0 -- 0Jinyu Li, Giulia Rossetti, Jens Dreyer, Simone Raugei, Emiliano Ippoliti, Bernhard Lüscher, Paolo Carloni. Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer
0 -- 0Sara Teller, Clara Granell, Manlio De Domenico, Jordi Soriano, Sergio Gómez, Alex Arenas. Emergence of Assortative Mixing between Clusters of Cultured Neurons
0 -- 0Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi, Satoshi Tabata. NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles
0 -- 0Sam Meyer, Guillaume Beslon. Torsion-Mediated Interaction between Adjacent Genes
0 -- 0Eric Libby, William Ratcliff, Michael Travisano, Ben Kerr. Geometry Shapes Evolution of Early Multicellularity
0 -- 0Alex J. Cornish, Florian Markowetz. SANTA: Quantifying the Functional Content of Molecular Networks
0 -- 0Apichat Suratanee, Martin H. Schaefer, Matthew J. Betts, Zita Soons, Heiko A. Mannsperger, Nathalie Harder, Marcus Oswald, Markus Gipp, Ellen Ramminger, Guillermo Marcus Martinez, Reinhard Männer, Karl Rohr, Erich E. Wanker, Robert B. Russell, Miguel A. Andrade-Navarro, Roland Eils, Rainer König. Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen
0 -- 0Simone Vincenzi, Marc Mangel, Alain J. Crivelli, Stephan Munch, Hans J. Skaug. Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method
0 -- 0Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang. The Structural Basis of ATP as an Allosteric Modulator
0 -- 0Angela Simeone, Giovanni Marsico, Claudio Collinet, Thierry Galvez, Yannis Kalaidzidis, Marino Zerial, Andreas Beyer. Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data
0 -- 0Thea Hogan, Ulrich D. Kadolsky, Sim Tung, Benedict Seddon, Andrew J. Yates. In Vivo
0 -- 0Krishnendu Chatterjee, Andreas Pavlogiannis, Ben Adlam, Martin A. Nowak. The Time Scale of Evolutionary Innovation
0 -- 0Melanie I. Stefan, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy. Multi-state Modeling of Biomolecules
0 -- 0Gaetano Invernizzi, Matteo Tiberti, Matteo Lambrughi, Kresten Lindorff-Larsen, Elena Papaleo. Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
0 -- 0Sijia Huang, Cameron Yee, Travers Ching, Herbert Yu, Lana X. Garmire. A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer
0 -- 0Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard O. Palsson. A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

Volume 10, Issue 8

0 -- 0Shuo Gu, Daniel-Adriano Silva, Luming Meng, Alexander Yue, Xuhui Huang. Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis
0 -- 0Johannes Textor, Sarah E. Henrickson, Judith N. Mandl, Ulrich H. von Andrian, Jürgen Westermann, Rob J. De Boer, Joost B. Beltman. Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment
0 -- 0Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor Lemischka, Avi Ma'ayan. Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells
0 -- 0Eric L. Haseltine, Sandra De Meyer, Inge Dierynck, Doug J. Bartels, Anne Ghys, Andrew Davis, Eileen Z. Zhang, Ann M. Tigges, Joan Spanks, Gaston Picchio, Tara L. Kieffer, James C. Sullivan. Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment
0 -- 0. Correction: Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks
0 -- 0Cyril F. Reboul, James C. Whisstock, Michelle A. Dunstone. A New Model for Pore Formation by Cholesterol-Dependent Cytolysins
0 -- 0Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo. OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis
0 -- 0Samat Moldakarimov, Maxim Bazhenov, Terrence J. Sejnowski. Top-Down Inputs Enhance Orientation Selectivity in Neurons of the Primary Visual Cortex during Perceptual Learning
0 -- 0Dov A. Pechenick, Joshua L. Payne, Jason H. Moore. Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks
0 -- 0Jonathan Laudanski, Benjamin Torben-Nielsen, Idan Segev, Shihab Shamma. Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input
0 -- 0Eizaburo Doi, Michael S. Lewicki. A Simple Model of Optimal Population Coding for Sensory Systems
0 -- 0Gerald Hahn, Alejandro F. Bujan, Yves Frégnac, Ad Aertsen, Arvind Kumar. Communication through Resonance in Spiking Neuronal Networks
0 -- 0Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J. Sanderson, James Sneyd. A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells
0 -- 0Xiakun Chu, Jin Wang. Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography
0 -- 0Miri Adler, Avi E. Mayo, Uri Alon. Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection
0 -- 0Victor J. Barranca, Gregor Kovacic, Douglas Zhou, David Cai. Sparsity and Compressed Coding in Sensory Systems
0 -- 0Sean Ekins, Ethan O. Perlstein. Ten Simple Rules of Live Tweeting at Scientific Conferences
0 -- 0Frantisek Honti, Stephen Meader, Caleb Webber. Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
0 -- 0Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung'u. In Vitro Testing
0 -- 0Andries J. van Tonder, Shilan Mistry, James E. Bray, Dorothea M. C. Hill, Alison J. Cody, Chris L. Farmer, Keith P. Klugman, Anne von Gottberg, Stephen D. Bentley, Julian Parkhill, Keith A. Jolley, Martin C. J. Maiden, Angela B. Brueggemann. Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model
0 -- 0Priscilla Ambrosi, Juan Sebastian Chahda, Hannah R. Koslen, Hillel J. Chiel, Claudia Mieko Mizutani. Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution
0 -- 0Peter T. McHale, Arthur D. Lander. The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage
0 -- 0. Correction: A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction
0 -- 0Gang Zhao, Gitanjali Dharmadhikari, Kathrin Maedler, Michael Meyer-Hermann. Possible Role of Interleukin-1β in Type 2 Diabetes Onset and Implications for Anti-inflammatory Therapy Strategies
0 -- 0Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You. Phenotypic Signatures Arising from Unbalanced Bacterial Growth
0 -- 0Geir Villy Isaksen, Johan Åqvist, Bjørn Olav Brandsdal. Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin
0 -- 0Delphine Pessoa, Caetano Souto-Maior, Erida Gjini, Joao S. Lopes, Bruno Ceña, Cláudia T. Codeço, M. Gabriela M. Gomes. Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens
0 -- 0Christopher A. Miller, Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William Schierding, John F. DiPersio, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding. SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution
0 -- 0Erwan Hingant, Pascaline Fontes, Maria Teresa Alvarez-Martinez, Jacques-Damien Arnaud, Jean-Pierre Liautard, Laurent Pujo-Menjouet. A Micellar On-Pathway Intermediate Step Explains the Kinetics of Prion Amyloid Formation
0 -- 0Jessica M. Conway, Alan S. Perelson. A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis
0 -- 0Seungyeul Yoo, Tao Huang, Joshua D. Campbell, Eunjee Lee, Zhidong Tu, Mark W. Geraci, Charles A. Powell, Eric E. Schadt, Avrum Spira, Jun Zhu. MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis
0 -- 0Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier. Dynamic Mechanisms of Neocortical Focal Seizure Onset
0 -- 0Kanghoon Jung, Hyeran Jang, Jerald D. Kralik, Jaeseung Jeong. Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions
0 -- 0Qiang Cui, Ruth Nussinov. Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era
0 -- 0Piero Dalle Pezze, Glyn Nelson, Elsje G. Otten, Viktor I. Korolchuk, Thomas B. L. Kirkwood, Thomas von Zglinicki, Daryl P. Shanley. Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions
0 -- 0. Correction: Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
0 -- 0Tetsuhiro S. Hatakeyama, Kunihiko Kaneko. Kinetic Memory Based on the Enzyme-Limited Competition
0 -- 0Nik J. Cunniffe, Francisco F. Laranjeira, Franco M. Neri, R. Erik DeSimone, Christopher A. Gilligan. Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus
0 -- 0René F. M. van Oers, Elisabeth G. Rens, Danielle J. LaValley, Cynthia A. Reinhart-King, Roeland M. H. Merks. Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro
0 -- 0Sébastien Benzekry, Clare Lamont, Afshin Beheshti, Amanda Tracz, John M. L. Ebos, Lynn Hlatky, Philip Hahnfeldt. Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth
0 -- 0Alexis M. Dubreuil, Yali Amit, Nicolas Brunel. Memory Capacity of Networks with Stochastic Binary Synapses
0 -- 0. In Vitro, with Negative Feedback through PPM1A Upregulation
0 -- 0Anne-Florence Bitbol, David J. Schwab. Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes
0 -- 0Umut Güçlü, Marcel A. J. van Gerven. Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images
0 -- 0Albert B. Kao, Noam Miller, Colin J. Torney, Andrew Hartnett, Iain D. Couzin. Collective Learning and Optimal Consensus Decisions in Social Animal Groups
0 -- 0Alex H. Lang, Hu Li, James J. Collins, Pankaj Mehta. Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes
0 -- 0Brian Y. Chen. VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
0 -- 0Alec Solway, Carlos Diuk, Natalia Córdova, Debbie Yee, Andrew G. Barto, Yael Niv, Matthew Botvinick. Optimal Behavioral Hierarchy
0 -- 0Yuan Zhang, Yanni Sun, James R. Cole. A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
0 -- 0Bernhard Knapp, James Dunbar, Charlotte M. Deane. Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study
0 -- 0Tarun Mishra, R. Gonzalo Parra, Thomas Abeel. The Upside of Failure: How Regional Student Groups Learn from Their Mistakes
0 -- 0Ken Daigoro Yokoyama, Yang Zhang, Jian Ma. Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework
0 -- 0Fang-Chieh Chou, Jan Lipfert, Rhiju Das. Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque
0 -- 0Rui Xia, Selina Vattathil, Paul Scheet. Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

Volume 10, Issue 7

0 -- 0Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie Nickerson, ChaoZhong Song, Daniela Witten, C. Anthony Blau, William Stafford Noble. Inferring Clonal Composition from Multiple Sections of a Breast Cancer
0 -- 0Alka A. Potdar, Joydeep Sarkar, Nupur K. Das, Paroma Ghosh, Miklos Gratzl, Paul L. Fox, Gerald M. Saidel. Computational Modeling and Analysis of Iron Release from Macrophages
0 -- 0Robert Ton, Gustavo Deco, Andreas Daffertshofer. Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks
0 -- 0Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, Stein Aerts. iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
0 -- 0Hugo Gravato Marques, Arjun Bharadwaj, Fumiya Iida. From Spontaneous Motor Activity to Coordinated Behaviour: A Developmental Model
0 -- 0Kathryn A. Loving, Andy Lin, Alan C. Cheng. Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility
0 -- 0Richard Lonsdale, Sarah L. Rouse, Mark S. P. Sansom, Adrian J. Mulholland. A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
0 -- 0Mahmoud Ghandi, Dongwon Lee, Morteza Mohammad Noori, Michael A. Beer. k-mer Features
0 -- 0Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis. ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
0 -- 0Song Ke, Eugen N. Timin, Anna Stary-Weinzinger. VMs Suggested by Molecular Dynamics Simulations
0 -- 0Urs Köster, Jascha Sohl-Dickstein, Charles M. Gray, Bruno A. Olshausen. Modeling Higher-Order Correlations within Cortical Microcolumns
0 -- 0Sergey Hosid, Ilya Ioshikhes. H. sapiens Lose Nucleosomes in GC-Rich Promoters
0 -- 0Ankur P. Parikh, Ross E. Curtis, Irene Kuhn, Sabine Becker-Weimann, Mina J. Bissell, Eric P. Xing, Wei Wu. Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm
0 -- 0Andrew E. Teschendorff, Xiaoping Liu, Helena Caren, Steve M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen. The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis
0 -- 0Christophe Restif, Carolina Ibáñez-Ventoso, Mehul M. Vora, Suzhen Guo, Dimitris N. Metaxas, Monica Driscoll. C. elegans Swim Behavior Reveals Novel Features of Locomotion
0 -- 0Stanca M. Ciupe, Ruy M. Ribeiro, Alan S. Perelson. Antibody Responses during Hepatitis B Viral Infection
0 -- 0Gabriel Gonzalez, Brett Hannigan, William F. DeGrado. A Real-Time All-Atom Structural Search Engine for Proteins
0 -- 0Rocio Rebollido-Rios, Shyam Bandari, Christoph Wilms, Stanislav Jakuschev, Andrea Vortkamp, Kay Grobe, Daniel Hoffmann. Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase
0 -- 0Alessandro Attanasi, Andrea Cavagna, Lorenzo Del Castello, Irene Giardina, Stefania Melillo, Leonardo Parisi, Oliver Pohl, Bruno Rossaro, Edward Shen, Edmondo Silvestri, Massimiliano Viale. Collective Behaviour without Collective Order in Wild Swarms of Midges
0 -- 0Bradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye. Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins
0 -- 0Athanasia Papoutsi, Kyriaki Sidiropoulou, Panayiota Poirazi. Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model
0 -- 0Daria A. Beshnova, Andrey G. Cherstvy, Yevhen Vainshtein, Vladimir B. Teif. In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions
0 -- 0Lewis J. Martin, Ben Corry. Locating the Route of Entry and Binding Sites of Benzocaine and Phenytoin in a Bacterial Voltage Gated Sodium Channel
0 -- 0Fabrizio Pucci, Marianne Rooman. Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials
0 -- 0Aniket Magarkar, Nawel Mele, Noha Abdel-Rahman, Sarah A. Butcher, Mika Torkkeli, Ritva Serimaa, Arja Paananen, Markus Linder, Alex Bunker. Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation
0 -- 0James H. Kaufman, Justin Lessler, April Harry, Stefan Edlund, Kun Hu, Judith V. Douglas, Christian Thoens, Bernd Appel, Annemarie Käsbohrer, Matthias Filter. A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
0 -- 0Marc Griesemer, Carissa Young, Anne S. Robinson, Linda Petzold. BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum
0 -- 0Tom Serge Weber, Irene Jaehnert, Christian Schichor, Michal Or-Guil, Jorge Carneiro. Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling
0 -- 0Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz. Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics
0 -- 0Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks. Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding
0 -- 0Junil Kim, Drieke Vandamme, Jeong-Rae Kim, Amaya Garcia Munoz, Walter Kolch, Kwang-Hyun Cho. Robustness and Evolvability of the Human Signaling Network
0 -- 0Benjamin T. Miller, Rishi P. Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S. Miller, Stefan Boresch, Toshiko Ichiye, Bernard R. Brooks, H. Lee Woodcock III. Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
0 -- 0Raphy Zarecki, Matthew A. Oberhardt, Leah Reshef, Uri Gophna, Eytan Ruppin. A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness
0 -- 0Antonio Rausell, Pejman Mohammadi, Paul J. Mclaren, Istvan Bartha, Ioannis Xenarios, Jacques Fellay, Amalio Telenti. Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes
0 -- 0Benedict Anchang, Mary T. Do, Xi Zhao, Sylvia K. Plevritis. CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells
0 -- 0Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen. Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
0 -- 0Michele Tizzoni, Paolo Bajardi, Adeline Decuyper, Guillaume Kon Kam King, Christian M. Schneider, Vincent D. Blondel, Zbigniew Smoreda, Marta C. González, Vittoria Colizza. On the Use of Human Mobility Proxies for Modeling Epidemics
0 -- 0Huiyong Sun, Youyong Li, sheng Tian, Junmei Wang, Tingjun Hou. P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
0 -- 0Allan Haldane, Michael Manhart, Alexandre V. Morozov. Biophysical Fitness Landscapes for Transcription Factor Binding Sites
0 -- 0Assaf Zaritsky, Doron Kaplan, Inbal Hecht, Sari Natan, Lior Wolf, Nir S. Gov, Eshel Ben-Jacob, Ilan Tsarfaty. Propagating Waves of Directionality and Coordination Orchestrate Collective Cell Migration
0 -- 0Alex H. Lang, Hu Li, James J. Collins, Pankaj Mehta. Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes
0 -- 0Hsuan-Chao Chiu, Roie Levy, Elhanan Borenstein. Emergent Biosynthetic Capacity in Simple Microbial Communities
0 -- 0Adam M. Gifford, Yale E. Cohen, Alan A. Stocker. Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior
0 -- 0Jacob D. Durrant, Rommie E. Amaro. LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
0 -- 0Karl Fogelmark, Carl Troein. Arabidopsis Circadian Clock
0 -- 0Isaure Chauvot de Beauchêne, Ariane Allain, Nicolas Panel, Elodie Laine, Alain Trouvé, Patrice Dubreuil, Luba Tchertanov. Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity
0 -- 0Param Priya Singh, Séverine Affeldt, Giulia Malaguti, Hervé Isambert. Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication
0 -- 0Jeroen de Ridder, Pieter Meysman, Olugbenga O. Oluwagbemi, Thomas Abeel. Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities
0 -- 0James B. Smadbeck, Kiat Hwa Chan, George A. Khoury, Bo Xue, Robert C. Robinson, Charlotte A. E. Hauser, Christodoulos A. Floudas. De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides
0 -- 0Christopher J. R. Illingworth, Andrej Fischer, Ville Mustonen. Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data
0 -- 0Alessandro Barardi, Belén Sancristóbal, Jordi García-Ojalvo. Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations
0 -- 0Eder Zavala, Tatiana T. Marquez-Lago. The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis
0 -- 0Santiago Esteban-Martín, Robert Bryn Fenwick, Jörgen Ådén, Benjamin P. Cossins, Carlos W. Bertoncini, Victor Guallar, Magnus Wolf-Watz, Xavier Salvatella. Correlated Inter-Domain Motions in Adenylate Kinase
0 -- 0Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo. Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells
0 -- 0Rubén Moreno-Bote. Poisson-Like Spiking in Circuits with Probabilistic Synapses
0 -- 0Suchin S. Gururangan, Alexander J. Sadovsky, Jason N. MacLean. Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex
0 -- 0Yong Wang, Chun Tang, Erkang Wang, Jin Wang. PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape
0 -- 0Federico Pedraja, Pedro Aguilera, Angel A. Caputi, Ruben Budelli. Electric Imaging through Evolution, a Modeling Study of Commonalities and Differences
0 -- 0Alejandro Barrera, Ana Alastruey-Izquierdo, María J. Martín, Isabel Cuesta, Juan Antonio Vizcaíno. Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets
0 -- 0Jean-Luc Schwartz, Christophe Savariaux. No, There Is No 150 ms Lead of Visual Speech on Auditory Speech, but a Range of Audiovisual Asynchronies Varying from Small Audio Lead to Large Audio Lag
0 -- 0Peter Cassey, Andrew Heathcote, Scott D. Brown. Brain and Behavior in Decision-Making
0 -- 0Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork. Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
0 -- 0Bradley Kossmann, Ivaylo Ivanov. Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases
0 -- 0Bernhard Knapp, James Dunbar, Charlotte M. Deane. Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study
0 -- 0Anton Arkhipov, Yibing Shan, Eric T. Kim, David E. Shaw. Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor

Volume 10, Issue 6

0 -- 0Johanni Brea, Robert Urbanczik, Walter Senn. A Normative Theory of Forgetting: Lessons from the Fruit Fly
0 -- 0Michael J. McGeachie, Hsun-Hsien Chang, Scott T. Weiss. CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data
0 -- 0Xin Tang, Alireza Tofangchi, Sandeep V. Anand, Taher A. Saif. A Novel Cell Traction Force Microscopy to Study Multi-Cellular System
0 -- 0Narjes Javaheri, Roland Dries, Jaap A. Kaandorp. Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization
0 -- 0Rubén Moreno-Bote. Poisson-Like Spiking in Circuits with Probabilistic Synapses
0 -- 0Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng. Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
0 -- 0Doron Shem-Tov, Eran Halperin. Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
0 -- 0Christian Diener, Gabriele Schreiber, Wolfgang Giese, Gabriel del Rio, Andreas Schröder, Edda Klipp. Yeast Mating and Image-Based Quantification of Spatial Pattern Formation
0 -- 0Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch. Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference
0 -- 0Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings. Pierced Lasso Bundles Are a New Class of Knot-like Motifs
0 -- 0Ruth Barshir, Omer Shwartz, Ilan Y. Smoly, Esti Yeger Lotem. Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases
0 -- 0Steven W. Sowa, Michael Baldea, Lydia M. Contreras. Optimizing Metabolite Production Using Periodic Oscillations
0 -- 0Shannon R. Moore, Gerald M. Saidel, Ulf Knothe, Melissa L. Knothe Tate. Mechanistic, Mathematical Model to Predict the Dynamics of Tissue Genesis in Bone Defects via Mechanical Feedback and Mediation of Biochemical Factors
0 -- 0Patricia Garcia-Canadilla, Paula A. Rudenick, Fátima Crispi, Monica Cruz-Lemini, Georgina Palau-Caballero, Oscar Camara, Eduard Gratacos, Bart H. Bijnens. A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction
0 -- 0David B. Searls. A New Online Computational Biology Curriculum
0 -- 0Anca Doloc-Mihu, Ronald L. Calabrese. Identifying Crucial Parameter Correlations Maintaining Bursting Activity
0 -- 0Junjie Wang, Lisa Tucker-Kellogg, Inn Chuan Ng, Ruirui Jia, P. S. Thiagarajan, Jacob K. White, Hanry Yu. In Vitro, with Negative Feedback through PPM1A Upregulation
0 -- 0Jerry S. Chen, Abygail M. Gumbayan, Robert W. Zeller, Joseph M. Mahaffy. An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation
0 -- 0Carlos Castro-Gonzalez, Miguel A. Luengo-Oroz, Louise Duloquin, Thierry Savy, Barbara Rizzi, Sophie Desnoulez, René Doursat, Yannick L. Kergosien, María J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, Andrés Santos. A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis
0 -- 0Borislav Savkovic, James Nichols, Donald Birkett, Tanya Applegate, Scott Ledger, Geoff Symonds, John M. Murray. A Quantitative Comparison of Anti-HIV Gene Therapy Delivered to Hematopoietic Stem Cells versus CD4+ T Cells
0 -- 0Noah C. Benson, Jeremy R. Manning, David H. Brainard. Unsupervised Learning of Cone Spectral Classes from Natural Images
0 -- 0Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis Shasha. Negative Example Selection for Protein Function Prediction: The NoGO Database
0 -- 0Qingrun Zhang, Quan Long, Jürg Ott. AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects
0 -- 0Martin H. Schaefer, Jae-Seong Yang, Luis Serrano, Christina Kiel. Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways
0 -- 0Bruce Bobier, Terrence C. Stewart, Chris Eliasmith. A Unifying Mechanistic Model of Selective Attention in Spiking Neurons
0 -- 0Nadine Töpfer, Federico Scossa, Alisdair R. Fernie, Zoran Nikoloski. Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses
0 -- 0Lorena Sigaut, John E. Pearson, Alejandro Colman-Lerner, Silvina Ponce Dawson. Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient
0 -- 0Mamiko Arai, Vicky Brandt, Yuri Dabaghian. The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map
0 -- 0. Correction: Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria
0 -- 0Bo Hu, Yuhai Tu. Behaviors and Strategies of Bacterial Navigation in Chemical and Nonchemical Gradients
0 -- 0Jake M. Ferguson, Jessica B. Langebrake, Vincent L. Cannataro, Andres J. Garcia, Elizabeth A. Hamman, Maia Martcheva, Craig W. Osenberg. Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics
0 -- 0Trygve Solstad, Hosam N. Yousif, Terrence J. Sejnowski. Place Cell Rate Remapping by CA3 Recurrent Collaterals
0 -- 0. Correction: Collective Cell Motion in an Epithelial Sheet Can be Quantitatively Described by a Stochastic Interacting Particle Model
0 -- 0Philip E. Bourne. Ten Simple Rules for Approaching a New Job
0 -- 0. Correction: Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study
0 -- 0Joshua T. Herbeck, John E. Mittler, Geoffrey S. Gottlieb, James I. Mullins. An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load
0 -- 0Jaime Iranzo, Manuel J. Gómez, Francisco J. López de Saro, Susanna C. Manrubia. Large-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes
0 -- 0Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra. Integrating Diverse Datasets Improves Developmental Enhancer Prediction
0 -- 0Sergei V. Krivov, Hayley Fenton, Paul J. Goldsmith, Rajendra K. Prasad, Julie Fisher, Emanuele Paci. Optimal Reaction Coordinate as a Biomarker for the Dynamics of Recovery from Kidney Transplant
0 -- 0Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh. An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
0 -- 0Daniel J. Laydon, Anat Melamed, Aaron Sim, Nicolas A. Gillet, Kathleen Sim, Sam Darko, J. Simon Kroll, Daniel C. Douek, David A. Price, Charles R. M. Bangham, Becca Asquith. Quantification of HTLV-1 Clonality and TCR Diversity
0 -- 0Joe DeBartolo, Mikko Taipale, Amy E. Keating. Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins
0 -- 0Daniel Silk, Paul D. W. Kirk, Chris P. Barnes, Tina Toni, Michael P. H. Stumpf. Model Selection in Systems Biology Depends on Experimental Design
0 -- 0Christiana N. Fogg, Diane E. Kovats. International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014
0 -- 0Ondrej Podlaha, Subhajyoti De, Mithat Gonen, Franziska Michor. Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells
0 -- 0Julia R. Gog, Sébastien Ballesteros, Cécile Viboud, Lone Simonsen, Ottar N. Bjornstad, Jeffrey Shaman, Dennis L. Chao, Farid Khan, Bryan T. Grenfell. Spatial Transmission of 2009 Pandemic Influenza in the US
0 -- 0Sebastian Pechmann, Judith Frydman. Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks
0 -- 0Yann S. Dufour, Xiongfei Fu, Luis Hernandez-Nunez, Thierry Emonet. Limits of Feedback Control in Bacterial Chemotaxis
0 -- 0Michael Kuhn 0004, Anthony A. Hyman, Andreas Beyer. Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome
0 -- 0Luigi Acerbi, Sethu Vijayakumar, Daniel M. Wolpert. On the Origins of Suboptimality in Human Probabilistic Inference
0 -- 0Ankit Gupta, Corentin Briat, Mustafa Khammash. A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks
0 -- 0Kristin Blacklock, Gennady M. Verkhivker. Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

Volume 10, Issue 5

0 -- 0Rajesh Balagam, Douglas B. Litwin, Fabian Czerwinski, Mingzhai Sun, Heidi B. Kaplan, Joshua W. Shaevitz, Oleg A. Igoshin. Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility
0 -- 0Drazen Petrov, Bojan Zagrovic. Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
0 -- 0Fabiano Baroni, Anthony N. Burkitt, David B. Grayden. Interplay of Intrinsic and Synaptic Conductances in the Generation of High-Frequency Oscillations in Interneuronal Networks with Irregular Spiking
0 -- 0Virginie Bernard, Sebastian J. Schultheiss, Magali Michaut. Learn from the Best
0 -- 0Olugbenga O. Oluwagbemi, Marion O. Adebiyi, Segun A. Fatumo, Geoff Macintyre. Paving the Way Towards a Successful and Fulfilling Career in Computational Biology
0 -- 0Christiana N. Fogg, Diane E. Kovats. 2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers
0 -- 0Jisoo Park, Heather C. Wick, Daniel E. Kee, Keith Noto, Jill L. Maron, Donna K. Slonim. Finding Novel Molecular Connections between Developmental Processes and Disease
0 -- 0. Correction: Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress
0 -- 0Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo, Diego di Bernardo. In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks
0 -- 0Devin Greene, Kristina Crona. The Changing Geometry of a Fitness Landscape Along an Adaptive Walk
0 -- 0César Rennó-Costa, John E. Lisman, Paul F. M. J. Verschure. A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus
0 -- 0Ali Neishabouri, A. Aldo Faisal. Axonal Noise as a Source of Synaptic Variability
0 -- 0Umeshkanta S. Thounaojam, Jianxia Cui, Sharon E. Norman, Robert J. Butera, Carmen C. Canavier. Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks
0 -- 0Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne. Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine
0 -- 0Wendy J. Adams, James H. Elder. Effects of Specular Highlights on Perceived Surface Convexity
0 -- 0Aistis Stankevicius, Quentin J. M. Huys, Aditi Kalra, Peggy Seriès. Optimism as a Prior Belief about the Probability of Future Reward
0 -- 0Fianne L. P. Sips, Christian A. Tiemann, Maaike H. Oosterveer, Albert K. Groen, Peter A. J. Hilbers, Natal A. W. van Riel. A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism
0 -- 0Marko Jusup, Tadasu Matsuo, Yoh Iwasa. Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse
0 -- 0Jussi T. Koivumäki, Gunnar Seemann, Mary M. Maleckar, Pasi Tavi. In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation
0 -- 0Charles J. Wilson, David Barraza, Todd Troyer, Michael A. Farries. Predicting the Responses of Repetitively Firing Neurons to Current Noise
0 -- 0Marc S. Sherman, Barak A. Cohen. A Computational Framework for Analyzing Stochasticity in Gene Expression
0 -- 0Niklas Hübel, Eckehard Schöll, Markus A. Dahlem. Bistable Dynamics Underlying Excitability of Ion Homeostasis in Neuron Models
0 -- 0Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth. High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues
0 -- 0Marcus J. Tindall, Angela Clerk. Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation
0 -- 0Neetika Nath, John B. O. Mitchell, Gustavo Caetano-Anollés. The Natural History of Biocatalytic Mechanisms
0 -- 0Tal Neiman, Yonatan Loewenstein. Spatial Generalization in Operant Learning: Lessons from Professional Basketball
0 -- 0. Correction: Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
0 -- 0Matthew S. Graus, Carolyn Pehlke, Michael J. Wester, Lisa B. Davidson, Stanly L. Steinberg, Aaron K. Neumann. A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction
0 -- 0Oriol Güell, Francesc Sagués, M. Ángeles Serrano. Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis
0 -- 0Ronny Straube. Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase
0 -- 0Klas H. Pettersen, Scott M. Bugenhagen, Javaid Nauman, Daniel A. Beard, Stig W. Omholt. Arterial Stiffening Provides Sufficient Explanation for Primary Hypertension
0 -- 0Ciira Wa Maina, Antti Honkela, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrence, Magnus Rattray. Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data
0 -- 0Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist, Mark Craven. Inferring Host Gene Subnetworks Involved in Viral Replication
0 -- 0Nan Zhao, Jing Ginger Han, Chi-Ren Shyu, Dmitry Korkin. Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
0 -- 0Ann M. Hermundstad, Kevin S. Brown, Danielle S. Bassett, Elissa M. Aminoff, Amy Frithsen, Arianne Johnson, Christine M. Tipper, Michael B. Miller, Scott T. Grafton, Jean M. Carlson. Structurally-Constrained Relationships between Cognitive States in the Human Brain
0 -- 0Eric A. Yen, Aaron Tsay, Jérôme Waldispühl, Jackie Vogel. Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks
0 -- 0Rodolphe Thiébaut, Julia Drylewicz, Mélanie Prague, Christine Lacabaratz, Stéphanie Beq, Ana Jarne, Thérèse Croughs, Rafick-Pierre Sekaly, Michael M. Lederman, Irini Sereti, Daniel Commenges, Yves Lévy. +T Cells in HIV-1 Infection
0 -- 0Julien Papaïx, Jeremy J. Burdon, Christian Lannou, Peter H. Thrall. Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal
0 -- 0Julian Tejada, Norberto Garcia-Cairasco, Antônio C. Roque-da-Silva. Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus
0 -- 0Dan Yamin, Arieh Gavious, Eyal Solnik, Nadav Davidovitch, Ran D. Balicer, Alison P. Galvani, Joseph S. Pliskin. An Innovative Influenza Vaccination Policy: Targeting Last Season's Patients
0 -- 0Nicolas Altemose, Karen H. Miga, Mauro Maggioni, Huntington F. Willard. Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly
0 -- 0Sílvia G. Estácio, Heinrich Krobath, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F. N. Faísca. 2-Microglobulin Amyloidogenic Behavior
0 -- 0Ignacio J. General, Ying Liu, Mandy E. Blackburn, Wenzhi Mao, Lila M. Gierasch, Ivet Bahar. ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones
0 -- 0. Correction: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
0 -- 0Mauricio Macossay-Castillo, Simone Kosol, Peter Tompa, Rita Pancsa. Synonymous Constraint Elements Show a Tendency to Encode Intrinsically Disordered Protein Segments
0 -- 0Daphna Rothschild, Erez Dekel, Jean Hausser, Anat Bren, Guy Aidelberg, Pablo Szekely, Uri Alon. Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions
0 -- 0Sven Dähne, Niko Wilbert, Laurenz Wiskott. Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells
0 -- 0Bin Chen. Ten Simple Rules for Internship in a Pharmaceutical Company
0 -- 0Masafumi Oizumi, Larissa Albantakis, Giulio Tononi. From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0
0 -- 0Michael V. LeVine, Harel Weinstein. NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
0 -- 0Vitaly V. Ganusov, Jeremy Auerbach. Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism

Volume 10, Issue 4

0 -- 0Adam M. Feist, Harish Nagarajan, Amelia-Elena Rotaru, Pier-Luc Tremblay, Tian Zhang, Kelly P. Nevin, Derek R. Lovley, Karsten Zengler. Geobacter metallireducens
0 -- 0Grace W. Tang, Russ B. Altman. Knowledge-based Fragment Binding Prediction
0 -- 0Bharath Ananthasubramaniam, Erik D. Herzog, Hanspeter Herzel. Timing of Neuropeptide Coupling Determines Synchrony and Entrainment in the Mammalian Circadian Clock
0 -- 0Kinya Hotta, Soumya Ranganathan, Ruchuan Liu, Fei Wu, Hiroaki Machiyama, Rong Gao, Hiroaki Hirata, Neelesh Soni, Takashi Ohe, Christopher W. V. Hogue, M. S. Madhusudhan, Yasuhiro Sawada. Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain - Implication in Mechanosensing
0 -- 0Jeffrey P. Perley, Judith Mikolajczak, Marietta L. Harrison, Gregery T. Buzzard, Ann E. Rundell. Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics
0 -- 0Christiana N. Fogg, Diane E. Kovats. ISMB 2014 - The Premier Conference for the World's Computational Biologists
0 -- 0Leonardo L. Gollo, Claudio R. Mirasso, Olaf Sporns, Michael Breakspear. Mechanisms of Zero-Lag Synchronization in Cortical Motifs
0 -- 0Dominik Wodarz, Ron Sorace, Natalia L. Komarova. Dynamics of Cellular Responses to Radiation
0 -- 0Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux. Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model
0 -- 0. Correction: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
0 -- 0Segun A. Fatumo, Moses P. Adoga, Opeolu O. Ojo, Olugbenga O. Oluwagbemi, Tolulope Adeoye, Itunuoluwa Ewejobi, Marion O. Adebiyi, Ezekiel F. Adebiyi, Clement Bewaji, Oyekanmi Nashiru. Computational Biology and Bioinformatics in Nigeria
0 -- 0Kirill Serkh, Daniel B. Forger. Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment
0 -- 0Florent Meyniel, Lou Safra, Mathias Pessiglione. How the Brain Decides When to Work and When to Rest: Dissociation of Implicit-Reactive from Explicit-Predictive Computational Processes
0 -- 0Harriet L. Mills, Steven Riley. The Spatial Resolution of Epidemic Peaks
0 -- 0Michelle D. Brazas, Fran Lewitter, Maria Victoria Schneider, Celia W. G. van Gelder, Patricia M. Palagi. A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences
0 -- 0Margarete Boos, Johannes Pritz, Simon Lange, Michael Belz. Leadership in Moving Human Groups
0 -- 0Alyssa Goodman, Alberto Pepe, Alexander W. Blocker, Christine L. Borgman, Kyle Cranmer, Mercè Crosas, Rosanne Di Stefano, Yolanda Gil, Paul T. Groth, Margaret Hedstrom, David W. Hogg, Vinay Kashyap, Ashish Mahabal, Aneta Siemiginowska, Aleksandra Slavkovic. Ten Simple Rules for the Care and Feeding of Scientific Data
0 -- 0Lander Willem, Sean Stijven, Ekaterina Vladislavleva, Jan Broeckhove, Philippe Beutels, Niel Hens. Active Learning to Understand Infectious Disease Models and Improve Policy Making
0 -- 0Man Chon U, Eric Talevich, Samiksha Katiyar, Khaled Rasheed, Natarajan Kannan. Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers
0 -- 0. Correction: Learning Gene Networks under SNP Perturbations Using eQTL Datasets
0 -- 0Wan Yang, Alicia Karspeck, Jeffrey Shaman. Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics
0 -- 0Justin S. Hogg, Leonard A. Harris, Lori J. Stover, Niketh S. Nair, James R. Faeder. Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
0 -- 0. Correction: Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
0 -- 0Felix Campelo, Michael M. Kozlov. Sensing Membrane Stresses by Protein Insertions
0 -- 0Gerard J. P. van Westen, Anna Gaulton, John P. Overington. Chemical, Target, and Bioactive Properties of Allosteric Modulation
0 -- 0David A. Rasmussen, Erik M. Volz, Katia Koelle. Phylodynamic Inference for Structured Epidemiological Models
0 -- 0Ke Tang, Jinfeng Zhang, Jie Liang. Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method
0 -- 0Paul J. McMurdie, Susan Holmes. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
0 -- 0Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, Wei Wang. Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
0 -- 0. Correction: Task-Based Core-Periphery Organization of Human Brain Dynamics
0 -- 0Thomas Walenda, Thomas Stiehl, Hanna Braun, Julia Fröbel, Anthony D. Ho, Thomas Schroeder, Tamme W. Goecke, Björn Rath, Ulrich Germing, Anna Marciniak-Czochra, Wolfgang Wagner. Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis
0 -- 0Dávid Samu, Anil K. Seth, Thomas Nowotny. Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity
0 -- 0Bertrand Fontaine, José Luis Peña, Romain Brette. In Vivo
0 -- 0Aleksej Zelezniak, Steven Sheridan, Kiran Raosaheb Patil. Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes
0 -- 0David J. McIver, John S. Brownstein. Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time
0 -- 0Laetitia Canini, Jessica M. Conway, Alan S. Perelson, Fabrice Carrat. Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study
0 -- 0Hao Bai, Matthew D. Rolfe, Wenjing Jia, Simon Coakley, Robert K. Poole, Jeffrey Green, Mike Holcombe. Escherichia coli
0 -- 0Lars Boukharta, Hugo Gutiérrez-de-Terán, Johan Åqvist. Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors
0 -- 0Bram Vrancken, Andrew Rambaut, Marc A. Suchard, Alexei J. Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, Philippe Lemey. The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates
0 -- 0Bailu Si, Sandro Romani, Misha Tsodyks. Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells
0 -- 0Remco R. Bouckaert, Joseph Heled, Denise Kühnert, Timothy G. Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
0 -- 0Hamed Nili, Cai Wingfield, Alexander Walther, Li Su, William D. Marslen-Wilson, Nikolaus Kriegeskorte. A Toolbox for Representational Similarity Analysis
0 -- 0Vincent Frappier, Rafael J. Najmanovich. A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations
0 -- 0Roland F. Schwarz, Anne Trinh, Botond Sipos, James D. Brenton, Nick Goldman, Florian Markowetz. Phylogenetic Quantification of Intra-tumour Heterogeneity
0 -- 0Matteo Farinella, Daniel T. Ruedt, Padraig Gleeson, Frederic Lanore, R. Angus Silver. In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model
0 -- 0Andrea Insabato, Laura Dempere-Marco, Mario Pannunzi, Gustavo Deco, Ranulfo Romo. The Influence of Spatiotemporal Structure of Noisy Stimuli in Decision Making
0 -- 0Ambuj Kumar, Rituraj Purohit. Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs
0 -- 0Thomas S. B. Schmidt, João F. Matias Rodrigues, Christian von Mering. Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
0 -- 0Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A. Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick E. Hubbard, S. David Morley. rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
0 -- 0Wes Maciejewski, Feng Fu, Christoph Hauert. Evolutionary Game Dynamics in Populations with Heterogenous Structures
0 -- 0Franco M. Neri, Alex R. Cook, Gavin J. Gibson, Tim R. Gottwald, Christopher A. Gilligan. Bayesian Analysis for Inference of an Emerging Epidemic: Citrus Canker in Urban Landscapes
0 -- 0Thomas D. Cuypers, Paulien Hogeweg. A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation
0 -- 0Robert Brown, Bogdan Pasaniuc. Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
0 -- 0Bram Kuijper, Rufus A. Johnstone, Stuart Townley. The Evolution of Multivariate Maternal Effects
0 -- 0Qing-Miao Nie, Akio Togashi, Takeshi N. Sasaki, Mitsunori Takano, Masaki Sasai, Tomoki P. Terada. Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin
0 -- 0Marjet Elemans, Arnaud Florins, Luc Willems, Becca Asquith. Rates of CTL Killing in Persistent Viral Infection In Vivo
0 -- 0Daniel Machado, Markus J. Herrgård. Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Volume 10, Issue 3

0 -- 0Hazem Toutounji, Gordon Pipa. Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations
0 -- 0Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider. Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies
0 -- 0Teresa Szczepinska, Jan Kutner, Michal Kopczynski, Krzysztof Pawlowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski, Maga Rowicka. Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
0 -- 0Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel. Viral Quasispecies Assembly via Maximal Clique Enumeration
0 -- 0James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David Gavaghan, Stephen Emmott, Charlotte M. Deane. Ten Simple Rules for Effective Computational Research
0 -- 0Megan A. Cummins, Pavan J. Dalal, Marco Bugana, Stefano Severi, Eric A. Sobie. Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence
0 -- 0Saurabh Gombar, Thomas MacCarthy, Aviv Bergman. Epigenetics Decouples Mutational from Environmental Robustness. Did It Also Facilitate Multicellularity?
0 -- 0András György, Domitilla Del Vecchio. Modular Composition of Gene Transcription Networks
0 -- 0Chase Cockrell, Scott Christley, Gary An. Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT)
0 -- 0Noah C. Benson, Omar H. Butt, David H. Brainard, Geoffrey K. Aguirre. Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy
0 -- 0Alexandra Jilkine, Ryan N. Gutenkunst. Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell-Driven Cancers
0 -- 0Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
0 -- 0Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq. Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing
0 -- 0Michael Pargett, Ann E. Rundell, Gregery T. Buzzard, David M. Umulis. Drosophila Germline Stem Cell Regulation
0 -- 0Fabian Konrath, Johannes Witt, Thomas Sauter, Dagmar Kulms. Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach
0 -- 0Jian Zhou, Olga G. Troyanskaya. Global Quantitative Modeling of Chromatin Factor Interactions
0 -- 0Jean Peccoud. If You Can't Measure It, You Can't Manage It
0 -- 0Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten. Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating
0 -- 0Alexandros Goulas, Matteo Bastiani, Gleb Bezgin, Harry B. M. Uylings, Alard Roebroeck, Peter Stiers. Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain
0 -- 0Md. Abul Hassan Samee, Saurabh Sinha. Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence
0 -- 0Lit-Hsin Loo, Danai Laksameethanasan, Yi-Ling Tung. Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins
0 -- 0Sebastian J. Schultheiß, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean, Magali Michaut. Crossing Borders for Science
0 -- 0Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yufang Jin. Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map
0 -- 0Navneet Bung, Meenakshi Pradhan, Harini Srinivasan, Gopalakrishnan Bulusu. E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane
0 -- 0James Lu, Katrin Hübner, M. Nazeem Nanjee, Eliot A. Brinton, Norman A. Mazer. In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway
0 -- 0. Correction: A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
0 -- 0Lars Ole Schwen, Markus Krauss, Christoph Niederalt, Felix Gremse, Fabian Kiessling, Andrea Schenk, Tobias Preusser, Lars Kuepfer. Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver
0 -- 0Nico J. D. Nagelkerke, Paul Arora, Prabhat Jha, Brian Williams, Lyle McKinnon, Sake J. de Vlas. The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling
0 -- 0Jörn-Philipp Lies, Ralf M. Häfner, Matthias Bethge. Slowness and Sparseness Have Diverging Effects on Complex Cell Learning
0 -- 0Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford. An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding
0 -- 0Samanthe M. Lyons, Wenlong Xu, June Medford, Ashok Prasad. Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems
0 -- 0David Kappel, Bernhard Nessler, Wolfgang Maass. STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning
0 -- 0Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford. Universal Count Correction for High-Throughput Sequencing
0 -- 0Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya. Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects
0 -- 0Partha S. Bhagavatula, Charles Claudianos, Michael R. Ibbotson, Mandyam V. Srinivasan. Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars
0 -- 0Arnaud Messé, David Rudrauf, Habib Benali, Guillaume Marrelec. Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities
0 -- 0Wondimu Teka, Toma M. Marinov, Fidel Santamaría. Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model
0 -- 0Florian Klimm, Danielle S. Bassett, Jean M. Carlson, Peter J. Mucha. Resolving Structural Variability in Network Models and the Brain
0 -- 0Colin J. Worby, Marc Lipsitch, William P. Hanage. Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data
0 -- 0Vladimir Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab. Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains
0 -- 0Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger. HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data
0 -- 0Sepp Kollmorgen, Richard H. R. Hahnloser. Dynamic Alignment Models for Neural Coding
0 -- 0Ewa Szczurek, Niko Beerenwinkel. Modeling Mutual Exclusivity of Cancer Mutations
0 -- 0Yili Zhang, Paul Smolen, Douglas A. Baxter, John H. Byrne. Computational Analyses of Synergism in Small Molecular Network Motifs
0 -- 0Mingming Chen, Daqing Guo, Tiebin Wang, Wei Jing, Yang Xia, Peng Xu, Cheng Luo, Pedro A. Valdes-Sosa, Dezhong Yao. Bidirectional Control of Absence Seizures by the Basal Ganglia: A Computational Evidence
0 -- 0Andrey Rzhetsky, Steven C. Bagley, Kanix Wang, Christopher S. Lyttle, Edwin H. Cook Jr., Russ B. Altman, Robert D. Gibbons. Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability

Volume 10, Issue 2

0 -- 0Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, Rona G. Giffard. Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia
0 -- 0Katherine C. H. Amrine, Wesley D. Swingley, David H. Ardell. tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria
0 -- 0Thomas Garcia, Leonardo Gregory Brunnet, Silvia De Monte. Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups
0 -- 0Chung-Jung Tsai, Ruth Nussinov. A Unified View of "How Allostery Works"
0 -- 0Markku Nurhonen, Kari Auranen. Optimal Serotype Compositions for Pneumococcal Conjugate Vaccination under Serotype Replacement
0 -- 0Peilin Jia, Zhongming Zhao. VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data
0 -- 0Oliver W. Layton, N. Andrew Browning. A Unified Model of Heading and Path Perception in Primate MSTd
0 -- 0Shyam Srinivasan, Jia-Sheng Hu, D. Spencer Currle, Ernest S. Fung, Wayne B. Hayes, Arthur D. Lander, Edwin S. Monuki. A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain
0 -- 0Tapesh Santra, Walter Kolch, Boris N. Kholodenko. Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration
0 -- 0Frederick A. Matsen IV, Christopher T. Small, Khanh Soliven, Gregory A. Engel, Mostafa M. Feeroz, Xiaoxing Wang, Karen L. Craig, M. Kamrul Hasan, Michael Emerman, Maxine L. Linial, Lisa Jones-Engel. A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
0 -- 0Florian Lesaint, Olivier Sigaud, Shelly B. Flagel, Terry E. Robinson, Mehdi Khamassi. Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations
0 -- 0Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas. k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
0 -- 0Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino, Michele Caselle. A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes
0 -- 0Kerstin Hünniger, Teresa Lehnert, Kristin Bieber, Ronny Martin, Marc Thilo Figge, Oliver Kurzai. Candida albicans Immune Escape in Human Blood
0 -- 0Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson. The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery
0 -- 0Oscar Lao, Fan Liu, Andreas Wollstein, Manfred Kayser. GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans
0 -- 0Elad Noor, Arren Bar-Even, Avi I. Flamholz, Ed Reznik, Wolfram Liebermeister, Ron Milo. Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
0 -- 0Katrina Pavelin, Sangya Pundir, Jennifer A. Cham. Ten Simple Rules for Running Interactive Workshops
0 -- 0Zeina Shreif, Vipul Periwal. A Network Characteristic That Correlates Environmental and Genetic Robustness
0 -- 0Chad Liu, Chuan-Yuan Li, Fan Yuan. Mathematical Modeling of the Phoenix Rising Pathway
0 -- 0Yu Hu, Joel Zylberberg, Eric Shea-Brown. The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes
0 -- 0Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas. Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species
0 -- 0Alan E. Bilsland, Katrina Stevenson, Yu Liu, Stacey Hoare, Claire J. Cairney, Jon Roffey, W. Nicol Keith. Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms
0 -- 0Saliha Ece Acuner Ozbabacan, Attila Gürsoy, Ruth Nussinov, Ozlem Keskin. The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer
0 -- 0Cristina Savin, Peter Dayan, Máté Lengyel. Optimal Recall from Bounded Metaplastic Synapses: Predicting Functional Adaptations in Hippocampal Area CA3
0 -- 0Pascal Carrivain, Maria Barbi, Jean-Marc Victor. In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics
0 -- 0Lingxue Zhang, Seyoung Kim. Learning Gene Networks under SNP Perturbations Using eQTL Datasets
0 -- 0Germán Enciso, Douglas R. Kellogg, Arturo Vargas. Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint
0 -- 0James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux. Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations
0 -- 0Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker. Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor
0 -- 0Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen. Combining Experiments and Simulations Using the Maximum Entropy Principle
0 -- 0Segun A. Fatumo, Sayane Shome, Geoff Macintyre. Workshops: A Great Way to Enhance and Supplement a Degree

Volume 10, Issue 12

0 -- 0Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray. Protein-Protein Docking with Dynamic Residue Protonation States
0 -- 0Gilad Wallach, Jules Lallouette, Nitzan Herzog, Maurizio De Pittà, Eshel Ben-Jacob, Hugues Berry, Yael Hanein. Glutamate Mediated Astrocytic Filtering of Neuronal Activity
0 -- 0Adviti Naik, Damjana Rozman, Ales Belic. SteatoNet: The First Integrated Human Metabolic Model with Multi-layered Regulation to Investigate Liver-Associated Pathologies
0 -- 0Sven Jahnke, Raoul-Martin Memmesheimer, Marc Timme. Oscillation-Induced Signal Transmission and Gating in Neural Circuits
0 -- 0Ganesh Shahane, Chirag Parsania, Durba Sengupta, Manali Joshi. 2-Adrenergic Receptor
0 -- 0Avital Brodt, Maya Botzman, Eyal David, Irit Gat-Viks. Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast
0 -- 0Niklas Hübel, Markus A. Dahlem. Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs
0 -- 0. Correction: Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle
0 -- 0Bratislav Misic, Joaquín Goñi, Richard F. Betzel, Olaf Sporns, Anthony Randal McIntosh. A Network Convergence Zone in the Hippocampus
0 -- 0Ofri Raviv, Itay Lieder, Yonatan Loewenstein, Merav Ahissar. Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception
0 -- 0Julijana Gjorgjieva, Rebecca A. Mease, William J. Moody, Adrienne L. Fairhall. Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks
0 -- 0Roman Bauer, Frédéric Zubler, Sabina S. Pfister, Andreas Hauri, Michael Pfeiffer, Dylan R. Muir, Rodney J. Douglas. Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks
0 -- 0Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink. Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation
0 -- 0Norman E. Davey, Venkata P. Satagopam, Salvador Santiago-Mozos, Carlos Villacorta-Martin, Tanmay A. M. Bharat, Reinhard Schneider 0002, John A. G. Briggs. The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data
0 -- 0Benjamin Lansdell, Kevin Ford, J. Nathan Kutz. A Reaction-Diffusion Model of Cholinergic Retinal Waves
0 -- 0. Correction: Limits of Feedback Control in Bacterial Chemotaxis
0 -- 0Jacopo Marino, Melanie I. Stefan, Sarah Blackford. Ten Simple Rules for Finishing Your PhD
0 -- 0Christoph Zechner, Heinz Koeppl. Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
0 -- 0Songting Li, Nan Liu, Xiao-Hui Zhang, Douglas Zhou, David Cai. Bilinearity in Spatiotemporal Integration of Synaptic Inputs
0 -- 0Christoph A. Haselwandter, Ned S. Wingreen. The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices
0 -- 0. k-mer Features
0 -- 0Robert Ietswaart, Florian Szardenings, Kenn Gerdes, Martin Howard. Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid
0 -- 0Gergely Boza, András Szilágyi, Ádám Kun, Mauro Santos, Eörs Szathmáry. Evolution of the Division of Labor between Genes and Enzymes in the RNA World
0 -- 0Natalia Zabzina, Audrey Dussutour, Richard P. Mann, David J. T. Sumpter, Stamatios C. Nicolis. Symmetry Restoring Bifurcation in Collective Decision-Making
0 -- 0A. Sofia F. Oliveira, João M. Damas, António M. Baptista, Cláudio M. Soares. c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site
0 -- 0Larissa Albantakis, Arend Hintze, Christof Koch, Christoph Adami, Giulio Tononi. Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity
0 -- 0Eline Boghaert, Derek C. Radisky, Celeste M. Nelson. In Situ Suggests Rules for Breast Cancer Progression to an Invasive State
0 -- 0Pablo Sartori, Léo Granger, Chiu Fan Lee, Jordan M. Horowitz. Thermodynamic Costs of Information Processing in Sensory Adaptation
0 -- 0Kelly C. Chang, Jason D. Bayer, Natalia A. Trayanova. Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation
0 -- 0Adrian J. de Froment, Daniel I. Rubenstein, Simon A. Levin. An Extra Dimension to Decision-Making in Animals: The Three-way Trade-off between Speed, Effort per-Unit-Time and Accuracy
0 -- 0Charles F. Cadieu, Ha Hong, Daniel Yamins, Nicolas Pinto, Diego Ardila, Ethan A. Solomon, Najib J. Majaj, James J. DiCarlo. Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition
0 -- 0Marnix H. Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A. Fischbach. A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis
0 -- 0Matt J. Whitfield, Jonathon P. Luo, Wendy E. Thomas. Yielding Elastic Tethers Stabilize Robust Cell Adhesion
0 -- 0Paraskevi Gkeka, Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia. Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion
0 -- 0Yang Ding, Meng Wang, Yao He, Adam Yongxin Ye, Xiaoxu Yang, Fenglin Liu, Yuqi Meng, Ge Gao, Liping Wei. "Bioinformatics: Introduction and Methods, " a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education
0 -- 0James F. Denton, Jose Lugo-Martinez, Abraham E. Tucker, Daniel R. Schrider, Wesley C. Warren, Matthew W. Hahn. Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
0 -- 0Lakshmi Krishnan, Mounya Elhilali, Shihab A. Shamma. Segregating Complex Sound Sources through Temporal Coherence
0 -- 0Jean-Pierre Rospars, Alexandre Grémiaux, David Jarriault, Antoine Chaffiol, Christelle Monsempes, Nina Deisig, Sylvia Anton, Philippe Lucas, Dominique Martinez. Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons
0 -- 0Yana Gofman, Charlotta Schärfe, Debora S. Marks, Turkan Haliloglu, Nir Ben-Tal. Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel
0 -- 0Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond. Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration
0 -- 0Mayu Sugiyama, Takashi Saitou, Hiroshi Kurokawa, Asako Sakaue-Sawano, Takeshi Imamura, Atsushi Miyawaki, Tadahiro Iimura. Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development
0 -- 0Christiaan H. van Dorp, Michiel van Boven, Rob J. De Boer. Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution
0 -- 0Lin Chen, Javad Noorbakhsh, Rhys M. Adams, Joseph Samaniego-Evans, Germaine Agollah, Dmitry Nevozhay, Jennie Kuzdzal-Fick, Pankaj Mehta, Gábor Balázsi. Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation
0 -- 0Evandro Ferrada. The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets
0 -- 0Hua Cheng, R. Dustin Schaeffer, Yuxing Liao, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V. Grishin. ECOD: An Evolutionary Classification of Protein Domains
0 -- 0Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph. Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
0 -- 0Xiaolin Tang, Mourad Bendjennat, Saveez Saffarian. Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models
0 -- 0Alex N. Nguyen Ba, Bob Strome, Jun Jie Hua, Jonathan Desmond, Isabelle Gagnon-Arsenault, Eric L. Weiss, Christian R. Landry, Alan M. Moses. Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences
0 -- 0Axel Kammerer, Christian Leibold. Hippocampal Remapping Is Constrained by Sparseness rather than Capacity
0 -- 0Tadashi Ando, Jeffrey Skolnick. Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models
0 -- 0Ritwik K. Niyogi, Peter Shizgal, Peter Dayan. Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure
0 -- 0Krzysztof Puszynski, Alberto Gandolfi, Alberto d'Onofrio. The Pharmacodynamics of the p53-Mdm2 Targeting Drug Nutlin: The Role of Gene-Switching Noise
0 -- 0Bill R. Miller III, Carol A. Parish, Eugene Y. Wu. Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
0 -- 0Marie Devaine, Guillaume Hollard, Jean Daunizeau. The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?
0 -- 0Ina Bisha, Alex Rodriguez, Alessandro Laio, Alessandra Magistrato. + Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT

Volume 10, Issue 11

0 -- 0Klas H. Pettersen, Henrik Lindén, Tom Tetzlaff, Gaute T. Einevoll. Power Laws from Linear Neuronal Cable Theory: Power Spectral Densities of the Soma Potential, Soma Membrane Current and Single-Neuron Contribution to the EEG
0 -- 0Michael Mak, Roger D. Kamm, Muhammad H. Zaman. Impact of Dimensionality and Network Disruption on Microrheology of Cancer Cells in 3D Environments
0 -- 0Junaid Hassan, Linda L. Bergaust, I. David Wheat, Lars R. Bakken. nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification
0 -- 0Zhongyao Sun, Xiaofen Jin, Réka Albert, Sarah M. Assmann. Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought
0 -- 0Marcin J. Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
0 -- 0Anya L. Goodman, Alex Dekhtyar. Teaching Bioinformatics in Concert
0 -- 0Helmut Schmidt, George Petkov, Mark P. Richardson, John R. Terry. Dynamics on Networks: The Role of Local Dynamics and Global Networks on the Emergence of Hypersynchronous Neural Activity
0 -- 0Lei Huang, Dongsung Kim, Xiaojing Liu, Christopher R. Myers, Jason W. Locasale. Estimating Relative Changes of Metabolic Fluxes
0 -- 0Eran Elhaik, Dan Graur. A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes
0 -- 0Aurélie Carlier, Nick van Gastel, Liesbet Geris, Geert Carmeliet, Hans Van Oosterwyck. In Silico Approach for the Treatment of Critical Size Bone Defects
0 -- 0Yasser Iturria-Medina, Roberto C. Sotero, Paule-Joanne Toussaint, Alan C. Evans. Epidemic Spreading Model to Characterize Misfolded Proteins Propagation in Aging and Associated Neurodegenerative Disorders
0 -- 0Jennifer L. Martin. Ten Simple Rules to Achieve Conference Speaker Gender Balance
0 -- 0Stefan Fürtinger, Joel C. Zinn, Kristina Simonyan. A Neural Population Model Incorporating Dopaminergic Neurotransmission during Complex Voluntary Behaviors
0 -- 0Thomas R. Caulfield, Fabienne C. Fiesel, Elisabeth L. Moussaud-Lamodière, Daniel F. A. R. Dourado, Samuel Flores, Wolfdieter Springer. Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin
0 -- 0Ivan V. Kazbanov, Richard H. Clayton, Martyn P. Nash, Chris P. Bradley, David J. Paterson, Martin P. Hayward, Peter Taggart, Alexander V. Panfilov. Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart
0 -- 0Ryan Tasseff, Anjali Bheda-Malge, Teresa DiColandrea, Charles C. Bascom, Robert J. Isfort, Richard Gelinas. Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators
0 -- 0Frederik Graw, Ashwin Balagopal, Abraham J. Kandathil, Stuart C. Ray, David L. Thomas, Ruy M. Ribeiro, Alan S. Perelson. Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes
0 -- 0Samuel Gershman, Angela Radulescu, Kenneth A. Norman, Yael Niv. Statistical Computations Underlying the Dynamics of Memory Updating
0 -- 0Mahdi Shafiei, Katherine A. Dunn, Hugh A. Chipman, Hong Gu, Joseph P. Bielawski. BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities
0 -- 0. Correction: Reactive Searching and Infotaxis in Odor Source Localization
0 -- 0Arne Weigenand, Michael Schellenberger Costa, Hong-Viet Victor Ngo, Jens Christian Claussen, Thomas Martinetz. Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model
0 -- 0. Correction: Exploring the miRNA Regulatory Network Using Evolutionary Correlations
0 -- 0Ken Nakae, Yuji Ikegaya, Tomoe Ishikawa, Shigeyuki Oba, Hidetoshi Urakubo, Masanori Koyama, Shin Ishii. A Statistical Method of Identifying Interactions in Neuron-Glia Systems Based on Functional Multicell Ca2+ Imaging
0 -- 0Flávio L. Pinheiro, Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco. Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas
0 -- 0Varsha Dhankani, J. Nathan Kutz, Joshua T. Schiffer. Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons
0 -- 0V. V. Hemanth Giri Rao, Shachi Gosavi. In the Multi-domain Protein Adenylate Kinase, Domain Insertion Facilitates Cooperative Folding while Accommodating Function at Domain Interfaces
0 -- 0Tarja Äijänen, Artturi Koivuniemi, Matti Javanainen, Sami Rissanen, Tomasz Róg, Ilpo Vattulainen. How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations
0 -- 0Veronika Boskova, Sebastian Bonhoeffer, Tanja Stadler. Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
0 -- 0Ricardo Pinho, Victor Garcia, Manuel Irimia, Marcus W. Feldman. Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks
0 -- 0. In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway
0 -- 0Rava Azeredo da Silveira, Michael J. Berry II. High-Fidelity Coding with Correlated Neurons
0 -- 0. Correction: Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression
0 -- 0Luca Ferreri, Mario Giacobini, Paolo Bajardi, Luigi Bertolotti, Luca Bolzoni, Valentina Tagliapietra, Annapaola Rizzoli, Roberto Rosà. Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens
0 -- 0Xavier Laurent, Nicolas Renault, Amaury Farce, Philippe Chavatte, Eric Henon. Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics Simulations
0 -- 0. Correction: A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges
0 -- 0Leonardo Abdala Elias, Renato Naville Watanabe, André Fabio Kohn. Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model
0 -- 0Seyed-Mahdi Khaligh-Razavi, Nikolaus Kriegeskorte. Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation
0 -- 0Amir Rubinstein, Benny Chor. Computational Thinking in Life Science Education
0 -- 0Sathej Gopalakrishnan, Hesam Montazeri, Stephan Menz, Niko Beerenwinkel, Wilhelm Huisinga. Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data
0 -- 0Nicholas Generous, Geoffrey Fairchild, Alina Deshpande, Sara Y. Del Valle, Reid Priedhorsky. Global Disease Monitoring and Forecasting with Wikipedia

Volume 10, Issue 10

0 -- 0Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson. Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach
0 -- 0Allen Cheung. Estimating Location without External Cues
0 -- 0Tanggis Bohnuud, Dima Kozakov, Sandor Vajda. Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces
0 -- 0François Bertaux, Szymon Stoma, Dirk Drasdo, Grégory Batt. Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance
0 -- 0Adiel Statman, Maya Kaufman, Amir Minerbi, Noam E. Ziv, Naama Brenner. Synaptic Size Dynamics as an Effectively Stochastic Process
0 -- 0Bahman Nasseroleslami, Christopher J. Hasson, Dagmar Sternad. Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos
0 -- 0Benedikt Obermayer, Erel Levine. Exploring the miRNA Regulatory Network Using Evolutionary Correlations
0 -- 0. Correction: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
0 -- 0Mary Hongying Cheng, Ivet Bahar. Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
0 -- 0Nathalie Poupin, François Mariotti, Jean-François Huneau, Dominique Hermier, Hélène Fouillet. Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis
0 -- 0José A. Seoane, Colin Campbell, Ian N. M. Day, Juan P. Casas, Tom R. Gaunt. Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery
0 -- 0Sophia Rudorf, Michael Thommen, Marina V. Rodnina, Reinhard Lipowsky. In Vitro
0 -- 0Markus Rehberg, Joachim B. Ritter, Udo Reichl. Glycolysis Is Governed by Growth Regime and Simple Enzyme Regulation in Adherent MDCK Cells
0 -- 0Nicole Voges, Antoine Chaffiol, Philippe Lucas, Dominique Martinez. Reactive Searching and Infotaxis in Odor Source Localization
0 -- 0. Correction: Inferring on the Intentions of Others by Hierarchical Bayesian Learning
0 -- 0Mariliis Tark-Dame, Hansjoerg Jerabek, Erik M. M. Manders, Dieter W. Heermann, Roel van Driel. Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
0 -- 0Frédéric Crevecoeur, Stephen H. Scott. Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections
0 -- 0Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Wolfgang Wurst, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabe de Angelis. Fast Synchronization of Ultradian Oscillators Controlled by Delta-Notch Signaling with Cis-Inhibition
0 -- 0David Higgins, Michael Graupner, Nicolas Brunel. Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity
0 -- 0Marco Mauri, Stefan Klumpp. A Model for Sigma Factor Competition in Bacterial Cells
0 -- 0Christian Lohse, Danielle S. Bassett, Kelvin O. Lim, Jean M. Carlson. Resolving Anatomical and Functional Structure in Human Brain Organization: Identifying Mesoscale Organization in Weighted Network Representations
0 -- 0Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, Leonid A. Mirny. Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
0 -- 0Dirk De Vos, Kris Vissenberg, Jan Broeckhove, Gerrit T. S. Beemster. Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root?
0 -- 0Nikola Ojkic, Javier López-Garrido, Kit Pogliano, Robert G. Endres. Bacillus subtilis by a Zipper Mechanism in Absence of the Cell Wall
0 -- 0Nicole Dölker, Maria W. Górna, Ludovico Sutto, Antonio S. Torralba, Giulio Superti-Furga, Francesco L. Gervasio. The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion
0 -- 0Paraskevi Gkeka, Thomas Evangelidis, Maria Pavlaki, Vasiliki Lazani, Savvas Christoforidis, Bogos Agianian, Zoe Cournia. PIK3CA Wild-Type and H1047R Oncogenic Mutant
0 -- 0Stinus Lindgreen, Sinan Ugur Umu, Alicia Sook-Wei Lai, Hisham Eldai, Wenting Liu, Stephanie McGimpsey, Nicole E. Wheeler, Patrick J. Biggs, Nick R. Thomson, Lars Barquist, Anthony M. Poole, Paul P. Gardner. Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling
0 -- 0Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell. Improving Contact Prediction along Three Dimensions
0 -- 0Roger C. Young, Peter Barendse. Linking Myometrial Physiology to Intrauterine Pressure; How Tissue-Level Contractions Create Uterine Contractions of Labor
0 -- 0Seth D. Axen, Onur Erbilgin, Cheryl A. Kerfeld. A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
0 -- 0Rebecca Batorsky, Rinat A. Sergeev, Igor M. Rouzine. The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations
0 -- 0Srivas Chennu, Paola Finoia, Evelyn Kamau, Judith Allanson, Guy B. Williams, Martin M. Monti, Valdas Noreika, Aurina Arnatkeviciute, Andrés Canales-Johnson, Francisco Olivares, Daniela Cabezas-Soto, David K. Menon, John D. Pickard, Adrian M. Owen, Tristan A. Bekinschtein. Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness
0 -- 0Heidi Koldsø, David Shorthouse, Jean Hélie, Mark S. P. Sansom. Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers
0 -- 0Gang Peng, Yu Fan, Wenyi Wang. FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units
0 -- 0Shuai Liu, Pengfei Cai, Xianyu Piao, Nan Hou, Xiaosu Zhou, Chuang Wu, Heng Wang, Qijun Chen. Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets
0 -- 0Robert A. Legenstein, Wolfgang Maass. Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment
0 -- 0Rafael Tapia-Rojo, Juan José Mazo, José Ángel Hernández, María Luisa Peleato, María F. Fillat, Fernando Falo. Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters
0 -- 0Inhae Kim, Heetak Lee, Seong Kyu Han, Sanguk Kim. Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks
0 -- 0Calvin J. Schneider, Hermann Cuntz, Ivan Soltesz. Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations
0 -- 0Andrew J. Fritz, Branislav Stojkovic, Hu Ding, Jinhui Xu, Sambit Bhattacharya, Ronald Berezney. Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle
0 -- 0Jinhua Liu, Xuelong Wang, Juan Li, Haifang Wang, Gang Wei, Jun Yan. Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain
0 -- 0Yue Li, Minggao Liang, Zhaolei Zhang. Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia
0 -- 0Matthew N. Benedict, Michael B. Mundy, Christopher S. Henry, Nicholas Chia, Nathan D. Price. Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
0 -- 0Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli. Hydrophobic Compounds Reshape Membrane Domains
0 -- 0Michael J. Prerau, Katie E. Hartnack, Gabriel Obregon-Henao, Aaron Sampson, Margaret Merlino, Karen Gannon, Matt T. Bianchi, Jeffrey M. Ellenbogen, Patrick L. Purdon. Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics
0 -- 0. Correction: Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections
0 -- 0Hai Fang. dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
0 -- 0Mary A. Rohrdanz, Wenwei Zheng, Bradley Lambeth, Jocelyne Vreede, Cecilia Clementi. Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble
0 -- 0Diana Clausznitzer, Gabriele Micali, Silke Neumann, Victor Sourjik, Robert G. Endres. Predicting Chemical Environments of Bacteria from Receptor Signaling
0 -- 0Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne. Ten Simple Rules for Writing a PLOS Ten Simple Rules Article
0 -- 0Amos Korman, Efrat Greenwald, Ofer Feinerman. Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups
0 -- 0Christian L. Althaus, Beda Joos, Alan S. Perelson, Huldrych F. Günthard. Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells
0 -- 0Avinash Kumar Shanmugam, Geoff Macintyre. Establishing and Managing a Global Student Network
0 -- 0. Correction: Environmental Statistics and Optimal Regulation
0 -- 0Kei Moritsugu, Tohru Terada, Akinori Kidera. Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling
0 -- 0Munia Amin, Varun B. Kothamachu, Elisenda Feliu, Birgit E. Scharf, Steven L. Porter, Orkun S. Soyer. Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices
0 -- 0Roy Malka, Francisco Feijó Delgado, Scott R. Manalis, John M. Higgins. In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells
0 -- 0Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari. A Reappraisal of How to Build Modular, Reusable Models of Biological Systems

Volume 10, Issue 1

0 -- 0Jayanthi Santhanam, Lars Råberg, Andrew F. Read, Nicholas Jon Savill. Immune-Mediated Competition in Rodent Malaria Is Most Likely Caused by Induced Changes in Innate Immune Clearance of Merozoites
0 -- 0Jean Daunizeau, Vincent Adam, Lionel Rigoux. VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data
0 -- 0Yi-Fei Huang, Geoffrey Brian Golding. Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures
0 -- 0Aidan I. Brown, Peter K. Kim, Andrew D. Rutenberg. PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes
0 -- 0Biswa Sengupta, Simon Barry Laughlin, Jeremy Edward Niven. Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency
0 -- 0Joshua E. Auerbach, Josh C. Bongard. Environmental Influence on the Evolution of Morphological Complexity in Machines
0 -- 0Devin L. O'Connor, Adam Runions, Aaron Sluis, Jennifer Bragg, John P. Vogel, Przemyslaw Prusinkiewicz, Sarah Hake. A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses
0 -- 0Shelly Mahlab, Michal Linial. Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective
0 -- 0Ruth Nussinov. The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead
0 -- 0W. Garrett Jenkinson, John K. Goutsias. Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching
0 -- 0Claude Gérard, Didier Gonze, Frédéric Lemaigre, Béla Novák. A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches
0 -- 0David J. Klinke II. Induction of Wnt-Inducible Signaling Protein-1 Correlates with Invasive Breast Cancer Oncogenesis and Reduced Type 1 Cell-Mediated Cytotoxic Immunity: A Retrospective Study
0 -- 0Aaron C. Miller, Linnea A. Polgreen, Philip Polgreen. Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting
0 -- 0Kasper Jensen, Gianni Panagiotou, Irene Kouskoumvekaki. Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level
0 -- 0Jacqueline M. Fulvio, C. Shawn Green, Paul R. Schrater. Task-Specific Response Strategy Selection on the Basis of Recent Training Experience
0 -- 0Ran Darshan, Arthur Leblois, David Hansel. Interference and Shaping in Sensorimotor Adaptations with Rewards
0 -- 0Bratislav Misic, Olaf Sporns, Anthony Randal McIntosh. Communication Efficiency and Congestion of Signal Traffic in Large-Scale Brain Networks
0 -- 0Roberta Santoro, Michelle Moerel, Federico De Martino, Rainer Goebel, Kamil Ugurbil, Essa Yacoub, Elia Formisano. Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex
0 -- 0Paul Verbruggen, Tim Heinemann, Erik M. M. Manders, Gesa von Bornstaedt, Roel van Driel, Thomas Höfer. Robustness of DNA Repair through Collective Rate Control
0 -- 0Matthias Rupp, Matthias R. Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M. Boeckler, Gisbert Schneider. Machine Learning Estimates of Natural Product Conformational Energies
0 -- 0Rosalyn J. Moran, Mkael Symmonds, Raymond J. Dolan, Karl J. Friston. The Brain Ages Optimally to Model Its Environment: Evidence from Sensory Learning over the Adult Lifespan
0 -- 0Jia Chen, Haicen Yue, Qi Ouyang. Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model
0 -- 0Axel von Kamp, Steffen Klamt. Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks
0 -- 0Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský. PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
0 -- 0Behruz Bozorg, Pawel Krupinski, Henrik Jönsson. Stress and Strain Provide Positional and Directional Cues in Development
0 -- 0Weixiong Zhang. Ten Simple Rules for Writing Research Papers
0 -- 0Reeta Rani Singhania, Dhatri Madduru, Pranathi Pappu, Sameera Panchangam, Renuka Suravajhala, Mohanalatha Chandrasekharan. The Making of the Women in Biology Forum (WiB) at Bioclues
0 -- 0Kavisha Ramdayal, Miranda D. Stobbe, Tarun Mishra, Magali Michaut. Building the Future of Bioinformatics through Student-Facilitated Conferencing
0 -- 0Mehdi Adibi, James Scott McDonald, Colin W. G. Clifford, Ehsan Arabzadeh. Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses
0 -- 0Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil M. Ferguson. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
0 -- 0Jonathan D. Drover. Timing over Tuning: Overcoming the Shortcomings of a Line Attractor during a Working Memory Task
0 -- 0Thomas A. Dunton, Joseph E. Goose, David J. Gavaghan, Mark S. P. Sansom, James M. Osborne. The Free Energy Landscape of Dimerization of a Membrane Protein, NanC
0 -- 0Zoltan Palmai, Christian Seifert, Frauke Gräter, Erika Balog. An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis
0 -- 0Isabel Marques, Paulo Almeida, Renato J. Alves, Maria João Dias, Ana Godinho, José B. Pereira-Leal. Bioinformatics Projects Supporting Life-Sciences Learning in High Schools
0 -- 0Zsuzsa Ákos, Róbert Beck, Mate Nagy, Tamás Vicsek, Enikö Kubinyi. Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs
0 -- 0Nicole Bohme Carnegie, Rui Wang, Vladimir A. Novitsky, Victor De Gruttola. Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data
0 -- 0Gesham Magombedze, Shigetoshi Eda, Vitaly V. Ganusov. paratuberulosis Infection in Ruminants
0 -- 0Michela Riz, Matthias Braun, Morten Gram Pedersen. β-Cells
0 -- 0Areum Han, Peter Stoilov, Anthony J. Linares, Yu Zhou, Xiang-Dong Fu, Douglas L. Black. De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function
0 -- 0Marc-Oliver Gewaltig, Robert C. Cannon. Current Practice in Software Development for Computational Neuroscience and How to Improve It
0 -- 0Moritz Helias, Tom Tetzlaff, Markus Diesmann. The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics
0 -- 0Sean T. Kelly, Jens Kremkow, Jianzhong Jin, Yushi Wang, Qi Wang, Jose-Manuel Alonso, Garrett B. Stanley. The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity
0 -- 0Bin Hu, Hua-Xin Liao, S. Munir Alam, Byron Goldstein. Estimating the Probability of Polyreactive Antibodies 4E10 and 2F5 Disabling a gp41 Trimer after T Cell-HIV Adhesion
0 -- 0Omar Gutierrez-Arenas, Olivia Eriksson, Jeanette Hellgren Kotaleski. Segregation and Crosstalk of D1 Receptor-Mediated Activation of ERK in Striatal Medium Spiny Neurons upon Acute Administration of Psychostimulants
0 -- 0Federico Comoglio, Renato Paro. Drosophila
0 -- 0Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter. Fast Reconstruction of Compact Context-Specific Metabolic Network Models
0 -- 0John G. Koland. Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation
0 -- 0Jacob G. Scott, Anita B. Hjelmeland, Prakash Chinnaiyan, Alexander R. A. Anderson, David Basanta. Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity
0 -- 0Gasper Tkacik, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, Michael J. Berry II. Searching for Collective Behavior in a Large Network of Sensory Neurons
0 -- 0Geoffrey L. Johnston, Peter W. Gething, Simon I. Hay, David L. Smith, David A. Fidock. Plasmodium falciparum Transmission and Prospects for Malaria Elimination
0 -- 0Guillem Casanovas, Anashua Banerji, Flavia d'Alessio, Martina U. Muckenthaler, Stefan Legewie. A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis
0 -- 0Geetu Tuteja, Karen Betancourt Moreira, Tisha Chung, Jenny Chen, Aaron M. Wenger, Gill Bejerano. Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data
0 -- 0Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés. Global Patterns of Protein Domain Gain and Loss in Superkingdoms