| 0 | -- | 0 | Pang Wei Koh, Emma Pierson, Anshul Kundaje. Denoising genome-wide histone ChIP-seq with convolutional neural networks |
| 0 | -- | 0 | Kymberleigh A. Pagel, Vikas Pejaver, Guan Ning Lin, Hyun-Jun Nam, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants |
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| 0 | -- | 0 | Mark A. Hallen, Bruce Randall Donald. CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions |
| 0 | -- | 0 | Mirco Michel, David Menéndez Hurtado, Karolis Uziela, Arne Elofsson. Large-scale structure prediction by improved contact predictions and model quality assessment |
| 0 | -- | 0 | . ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE |
| 0 | -- | 0 | Lila Rieber, Shaun Mahony. miniMDS: 3D structural inference from high-resolution Hi-C data |
| 0 | -- | 0 | Xiaoke Hao, Chanxiu Li, Jingwen Yan, Xiaohui Yao, Shannon L. Risacher, Andrew J. Saykin, Li Shen 0001, Daoqiang Zhang. Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis |
| 0 | -- | 0 | Lin Zhu 0008, Hong-Bo Zhang, De-Shuang Huang. Direct AUC optimization of regulatory motifs |
| 0 | -- | 0 | Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Robert Patro. Improved data-driven likelihood factorizations for transcript abundance estimation |
| 0 | -- | 0 | Lei Ding, Daniel J. McDonald. Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression |
| 0 | -- | 0 | Omer Weissbrod, Elior Rahmani, Regev Schweiger, Saharon Rosset, Eran Halperin. Association testing of bisulfite-sequencing methylation data via a Laplace approximation |
| 0 | -- | 0 | Anupama Jha, Matthew R. Gazzara, Yoseph Barash. Integrative deep models for alternative splicing |
| 0 | -- | 0 | Michael Estrin, Haim J. Wolfson. SnapDock - template-based docking by Geometric Hashing |
| 0 | -- | 0 | Juraj Michalik, Hélène Touzet, Yann Ponty. Efficient approximations of RNA kinetics landscape using non-redundant sampling |
| 0 | -- | 0 | . Author Index |
| 0 | -- | 0 | Min Xu, Xiaoqi Chai, Hariank Muthakana, Xiaodan Liang, Ge Yang, Tzviya Zeev-Ben-Mordehai, Eric P. Xing. Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms |
| 0 | -- | 0 | Francesca Petralia, Vasily N. Aushev, Kalpana Gopalakrishnan, Maya Kappil, Nyan W. Khin, Jia Chen, Susan L. Teitelbaum, Pei Wang. A new method to study the change of miRNA-mRNA interactions due to environmental exposures |
| 0 | -- | 0 | Prashant Pandey, Michael A. Bender, Rob Johnson, Robert Patro. deBGR: an efficient and near-exact representation of the weighted de Bruijn graph |
| 0 | -- | 0 | Martina Fischer, Benjamin Strauch, Bernhard Y. Renard. Abundance estimation and differential testing on strain level in metagenomics data |
| 0 | -- | 0 | Atefeh Kazeroonian, Fabian J. Theis, Jan Hasenauer. A scalable moment-closure approximation for large-scale biochemical reaction networks |
| 0 | -- | 0 | Niko Beerenwinkel, Yana Bromberg. ISMB/ECCB 2017 proceedings |
| 0 | -- | 0 | Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford. Improving the performance of minimizers and winnowing schemes |
| 0 | -- | 0 | Jing Guo, Jie Zheng. HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape |
| 0 | -- | 0 | Yoichiro Nakatani, Aoife McLysaght. Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes |
| 0 | -- | 0 | Ishita K. Khan, Mansurul Bhuiyan, Daisuke Kihara. DextMP: deep dive into text for predicting moonlighting proteins |
| 0 | -- | 0 | Gizem Sogancioglu, Hakime Öztürk, Arzucan Özgür. BIOSSES: a semantic sentence similarity estimation system for the biomedical domain |
| 0 | -- | 0 | Xiongtao Ruan, Christoph Wülfing, Robert F. Murphy. Image-based spatiotemporal causality inference for protein signaling networks |
| 0 | -- | 0 | Clément-Marie Train, Natasha Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz. Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference |
| 0 | -- | 0 | Stefan Avey, Subhasis Mohanty, Jean Wilson, Heidi Zapata, Samit R. Joshi, Barbara Siconolfi, Sui Tsang, Albert C. Shaw, Steven H. Kleinstein. Multiple network-constrained regressions expand insights into influenza vaccination responses |
| 0 | -- | 0 | Maryam Habibi, Leon Weber, Mariana L. Neves, David Luis Wiegandt, Ulf Leser. Deep learning with word embeddings improves biomedical named entity recognition |
| 0 | -- | 0 | Pinar Kavak, Yen-Yi Lin, Ibrahim Numanagic, Hossein Asghari, Tunga Güngör, Can Alkan, Faraz Hach. Discovery and genotyping of novel sequence insertions in many sequenced individuals |
| 0 | -- | 0 | Eugenio Cinquemani, Valérie Laroute, Muriel Cocaign-Bousquet, Hidde de Jong, Delphine Ropers. Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data |
| 0 | -- | 0 | C.-H. Lee, Eleazar Eskin, Buhm Han. Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects |
| 0 | -- | 0 | Dennis Pischel, Kai Sundmacher, Robert J. Flassig. Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems |
| 0 | -- | 0 | Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri. popFBA: tackling intratumour heterogeneity with Flux Balance Analysis |
| 0 | -- | 0 | Djork-Arné Clevert, Thomas Unterthiner, Gundula Povysil, Sepp Hochreiter. Rectified factor networks for biclustering of omics data |
| 0 | -- | 0 | Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang, Jianyang Zeng. TITER: predicting translation initiation sites by deep learning |
| 0 | -- | 0 | Gryte Satas, Benjamin J. Raphael. Tumor phylogeny inference using tree-constrained importance sampling |
| 0 | -- | 0 | Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang. Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding |
| 0 | -- | 0 | Sean Robinson, Jaakko Nevalainen, Guillaume Pinna, Anna Campalans, J. Pablo Radicella, Laurent Guyon. Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields |
| 0 | -- | 0 | Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul, Eleazar Eskin. Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes |
| 0 | -- | 0 | Yohei Rosen, Jordan Eizenga, Benedict Paten. Modelling haplotypes with respect to reference cohort variation graphs |
| 0 | -- | 0 | Mingfu Shao, Jianzhu Ma, Sheng Wang 0001. DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields |
| 0 | -- | 0 | Yang Yang, Ruochi Zhang, Shashank Singh 0005, Jian Ma. Exploiting sequence-based features for predicting enhancer-promoter interactions |
| 0 | -- | 0 | Marinka Zitnik, Jure Leskovec. Predicting multicellular function through multi-layer tissue networks |
| 0 | -- | 0 | M. Altenbuchinger, P. Schwarzfischer, T. Rehberg, J. Reinders, Ch. W. Kohler, W. Gronwald, J. Richter, M. Szczepanowski, N. Masqué-Soler, W. Klapper, Peter J. Oefner, R. Spang. Molecular signatures that can be transferred across different omics platforms |
| 0 | -- | 0 | Vipin Vijayan, Dominic Critchlow, Tijana Milenkovic. Alignment of dynamic networks |
| 2071 | -- | 2077 | Erik L. Clarke, Sesh A. Sundararaman, Stephanie N. Seifert, Frederic D. Bushman, Beatrice H. Hahn, Dustin Brisson. swga: a primer design toolkit for selective whole genome amplification |
| 2078 | -- | 2081 | Shudong Wang, Sicheng He, Fayou Yuan, Xinjie Zhu. Tagging SNP-set selection with maximum information based on linkage disequilibrium structure in genome-wide association studies |
| 2082 | -- | 2088 | Lorian Schaeffer, Harold Pimentel, Nicolas Bray, Páll Melsted, Lior Pachter. Pseudoalignment for metagenomic read assignment |
| 2089 | -- | 2096 | Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E. Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen. RNAscClust: clustering RNA sequences using structure conservation and graph based motifs |
| 2097 | -- | 2105 | Zhen Gao, Jianhua Ruan. Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning |
| 2106 | -- | 2113 | Luciano Censoni, Heloisa dos Santos Muniz, Leandro Martínez. A network model predicts the intensity of residue-protein thermal coupling |
| 2114 | -- | 2122 | Amélie Héliou, Dominik Budday, Rasmus Fonseca, Henry van den Bedem. Fast, clash-free RNA conformational morphing using molecular junctions |
| 2123 | -- | 2130 | Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei. QRank: a novel quantile regression tool for eQTL discovery |
| 2131 | -- | 2139 | Musheng Li, Xueying Xie, Jing Zhou, Mengying Sheng, Xiaofeng Yin, Eun-A Ko, Tong Zhou, Wanjun Gu. Quantifying circular RNA expression from RNA-seq data using model-based framework |
| 2140 | -- | 2147 | Lin Wang, Silvia Liu, Ying Ding, Shin-sheng Yuan, Yen-Yi Ho, George C. Tseng. Meta-analytic framework for liquid association |
| 2148 | -- | 2155 | Jade Yu Cheng, Thomas Mailund, Rasmus Nielsen. Fast admixture analysis and population tree estimation for SNP and NGS data |
| 2156 | -- | 2164 | Nil Mamano, Wayne B. Hayes. SANA: simulated annealing far outperforms many other search algorithms for biological network alignment |
| 2165 | -- | 2172 | Mojdeh Faraji, Eberhard O. Voit. Stepwise inference of likely dynamic flux distributions from metabolic time series data |
| 2173 | -- | 2181 | Zengmiao Wang, Huaying Fang, Nelson L. S. Tang, Minghua Deng. VCNet: vector-based gene co-expression network construction and its application to RNA-seq data |
| 2182 | -- | 2190 | Murad Megjhani, Pedro Correa de Sampaio, Julienne Leigh Carstens, Raghu Kalluri, Badrinath Roysam. Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy |
| 2191 | -- | 2193 | Charles Curnin, Assaf Gordon, Yaniv Erlich. DNA Compass: a secure, client-side site for navigating personal genetic information |
| 2194 | -- | 2196 | Matthias Monfort, Eileen E. M. Furlong, Charles Girardot. Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets |
| 2197 | -- | 2198 | Asher Haug-Baltzell, Sean A. Stephens, Sean Davey, Carlos Eduardo Scheidegger, Eric Lyons. SynMap2 and SynMap3D: web-based whole-genome synteny browsers |
| 2199 | -- | 2201 | Koon-Kiu Yan, Galip Gürkan Yardimci, Chengfei Yan, William S. Noble, Mark Gerstein. HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps |
| 2202 | -- | 2204 | Gregory W. Vurture, Fritz J. Sedlazeck, Maria Nattestad, Charles J. Underwood, Han Fang, James Gurtowski, Michael C. Schatz. GenomeScope: fast reference-free genome profiling from short reads |
| 2205 | -- | 2206 | Konstantin S. Yarygin, Boris Kovarsky, Tanya Bibikova, Damir Melnikov, Alexander V. Tyakht, Dmitry G. Alexeev. ResistoMap - online visualization of human gut microbiota antibiotic resistome |
| 2207 | -- | 2208 | Robert D. Stewart, Mick Watson. poRe GUIs for parallel and real-time processing of MinION sequence data |
| 2209 | -- | 2211 | Felix Simkovic, Jens M. H. Thomas, Daniel J. Rigden. ConKit: a python interface to contact predictions |
| 2212 | -- | 2213 | Sandrine Perrin, Cyril Firmo, Sophie Lemoine, Stéphane Le Crom, Laurent Jourdren. Aozan: an automated post-sequencing data-processing pipeline |
| 2214 | -- | 2215 | Qi Wu, Zu-Guo Yu, Jianyi Yang. DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method |
| 2216 | -- | 2217 | Jinkai Wang, Yang Pan, Shihao Shen, Lan Lin, Yi Xing. rMATS-DVR: rMATS discovery of differential variants in RNA |
| 2218 | -- | 2220 | Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brazma. The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data |
| 2221 | -- | 2223 | Thomas O. McDonald, Franziska Michor. SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution |
| 2224 | -- | 2225 | Christopher Heffelfinger, Christopher A. Fragoso, Mathias Lorieux. Constructing linkage maps in the genomics era with MapDisto 2.0 |
| 2226 | -- | 2228 | Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone. MaBoSS 2.0: an environment for stochastic Boolean modeling |
| 2229 | -- | 2231 | Sascha Herzinger, Wei Gu, Venkata P. Satagopam, Serge Eifes, Kavita Rege, Adriano Barbosa-Silva, Reinhard Schneider 0002, On behalf of the eTRIKS Consortium. SmartR: an open-source platform for interactive visual analytics for translational research data |
| 2232 | -- | 2234 | Daniel Schlauch, Joseph N. Paulson, Albert Young, Kimberly Glass, John Quackenbush. Estimating gene regulatory networks with pandaR |
| 2235 | -- | 2237 | Zhiwei Zhou, Xin Xiong, Zheng-Jiang Zhu. MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics |
| 2238 | -- | 2240 | Istemi Bahceci, Ugur Dogrusoz, Konnor C. La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz. PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data |
| 2241 | -- | 2242 | Clemens Messerschmidt, Manuel Holtgrewe, Dieter Beule. HLA-MA: simple yet powerful matching of samples using HLA typing results |
| 2243 | -- | 2244 | Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev |
| 2245 | -- | 2246 | Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner |
| 2247 | -- | 2248 | Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock |
| 2249 | -- | 2250 | Christiana N. Fogg, Diane E. Kovats, Bonnie Berger. Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter |