| 1989 | -- | 1993 | Qingsu Cheng, Bahram Parvin. Organoid model of mammographic density displays a higher frequency of aberrant colony formations with radiation exposure |
| 1994 | -- | 2000 | Kevin R. Amses, William J. Davis, Timothy Y. James. SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes |
| 2001 | -- | 2008 | Samuele Cancellieri, Matthew C. Canver, Nicola Bombieri, Rosalba Giugno, Luca Pinello. CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing |
| 2009 | -- | 2016 | Yi Yang, Xingjie Shi, Yuling Jiao, Jian Huang 0003, Min Chen, Xiang Zhou, Lei Sun, Xinyi Lin, Can Yang, Jin Liu 0011. CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies |
| 2017 | -- | 2024 | Weiwei Zhang, Ziyi Li, Nana Wei, Hua-Jun Wu, Xiaoqi Zheng. Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities |
| 2025 | -- | 2032 | Yuwei Zhang, Tianfei Yi, Huihui Ji, Guofang Zhao, Yang Xi, Changzheng Dong, Lina Zhang, Xiaohong Zhang, Jinshun Zhao, Qi Liao. Designing a general method for predicting the regulatory relationships between long noncoding RNAs and protein-coding genes based on multi-omics characteristics |
| 2033 | -- | 2039 | Junfeng Liu, Ziyang An, Jianjun Luo, Jing Li, Feifei Li, Zhihua Zhang. Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite |
| 2040 | -- | 2046 | Fabian Klötzl, Bernhard Haubold. Phylonium: fast estimation of evolutionary distances from large samples of similar genomes |
| 2047 | -- | 2052 | Ha-Young Kim, Dongsup Kim. Prediction of mutation effects using a deep temporal convolutional network |
| 2053 | -- | 2059 | Saket Choudhary, Wenzheng Li, Andrew D. Smith. Accurate detection of short and long active ORFs using Ribo-seq data |
| 2060 | -- | 2067 | Sam Friedman, Laura D. Gauthier, Yossi Farjoun, Eric Banks. Lean and deep models for more accurate filtering of SNP and INDEL variant calls |
| 2068 | -- | 2075 | Jing Xu, Han Zhang, Jinfang Zheng, Philippe Dovoedo, Yanbin Yin. eCAMI: simultaneous classification and motif identification for enzyme annotation |
| 2076 | -- | 2081 | Gabriele Orlando, Alexandra Silva 0004, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim F. Vranken. Accurate prediction of protein beta-aggregation with generalized statistical potentials |
| 2082 | -- | 2089 | Tomasz Marek Kowalski, Szymon Grabowski. PgRC: pseudogenome-based read compressor |
| 2090 | -- | 2097 | Zach Dinardo, Kiran Tomlinson, Anna M. Ritz, Layla Oesper. Distance measures for tumor evolutionary trees |
| 2098 | -- | 2104 | Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T. Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie von Dobschütz, Filip Claes, Scott H. Newman, Marc A. Suchard, Guy Baele, Marius Gilbert. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region |
| 2105 | -- | 2112 | Chengxin Zhang, Wei Zheng, S. M. Mortuza, Yang Li, Yang Zhang 0040. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins |
| 2113 | -- | 2118 | Xiao Wang, Genki Terashi, Charles Christoffer, Mengmeng Zhu, Daisuke Kihara. Protein docking model evaluation by 3D deep convolutional neural networks |
| 2119 | -- | 2125 | Zongyang Du, Shuo Pan, Qi Wu, Zhenling Peng, Jianyi Yang. CATHER: a novel threading algorithm with predicted contacts |
| 2126 | -- | 2133 | Ge Liu, Haoyang Zeng, Jonas Mueller, Brandon Carter 0001, Ziheng Wang, Jonas Schilz, Geraldine Horny, Michael E. Birnbaum, Stefan Ewert, David K. Gifford. Antibody complementarity determining region design using high-capacity machine learning |
| 2134 | -- | 2141 | Carlos Martí-Gómez, Enrique Lara Pezzi, Fátima Sánchez-Cabo. dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity |
| 2142 | -- | 2149 | Annika Jacobsen, Olga Ivanova, Saman Amini, Jaap Heringa, Patrick Kemmeren, K. Anton Feenstra. A framework for exhaustive modelling of genetic interaction patterns using Petri nets |
| 2150 | -- | 2156 | Likun Huang, Weiqi Tang, Suhong Bu, Weiren Wu. BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing |
| 2157 | -- | 2164 | Estelle Geffard, Sophie Limou, Alexandre Walencik, Michelle Daya, Harold Watson, Dara Torgerson, Kathleen C. Barnes, Anne Cesbron Gautier, Pierre-Antoine Gourraud, Nicolas Vince. Easy-HLA: a validated web application suite to reveal the full details of HLA typing |
| 2165 | -- | 2172 | F. Maggioli, Toni Mancini, Enrico Tronci. SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems |
| 2173 | -- | 2180 | Jui Wan Loh, Caitlin Guccione, Frances Di Clemente, Gregory Riedlinger, Shridar Ganesan, Hossein Khiabanian. All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data |
| 2181 | -- | 2188 | Marco S. Nobile, Giuseppina Votta, Roberta Palorini, Simone Spolaor, Humberto De Vitto, Paolo Cazzaniga, Francesca Ricciardiello, Giancarlo Mauri, Lilia Alberghina, Ferdinando Chiaradonna, Daniela Besozzi. Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells |
| 2189 | -- | 2194 | Lars Thielecke, Kerstin Cornils, Ingmar Glauche. genBaRcode: a comprehensive R-package for genetic barcode analysis |
| 2195 | -- | 2201 | Zhe Cui 0001, Jayaram Kancherla, Kyle W. Chang, Niklas Elmqvist, Héctor Corrada Bravo. Proactive visual and statistical analysis of genomic data in Epiviz |
| 2202 | -- | 2208 | Fabio Fabris, Daniel Palmer, Khalid M. Salama, João Pedro de Magalhães, Alex Alves Freitas. Using deep learning to associate human genes with age-related diseases |
| 2209 | -- | 2216 | Herty Liany, Anand Jeyasekharan, Vaibhav Rajan. Predicting synthetic lethal interactions using heterogeneous data sources |
| 2217 | -- | 2223 | Kathryn A. McGurk, Arianna Dagliati, Davide Chiasserini, Dave Lee, Darren Plant, Ivona Baricevic-Jones, Janet Kelsall, Rachael Eineman, Rachel Reed, Bethany Geary, Richard D. Unwin, Anna Nicolaou, Bernard D. Keavney, Anne Barton, Anthony D. Whetton, Nophar Geifman. The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination |
| 2224 | -- | 2228 | Raul Rodriguez-Esteban. Semantic persistence of ambiguous biomedical names in the citation network |
| 2229 | -- | 2236 | Fatima Zohra Smaili, Xin Gao 0001, Robert Hoehndorf. Formal axioms in biomedical ontologies improve analysis and interpretation of associated data |
| 2237 | -- | 2243 | Cyril F. Reboul, Simon Kiesewetter, Dominika Elmlund, Hans Elmlund. Point-group symmetry detection in three-dimensional charge density of biomolecules |
| 2244 | -- | 2250 | Wei Long, Yang Yang 0030, Hong-bin Shen. ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images |
| 2251 | -- | 2252 | Takuya Aramaki, Romain Blanc-Mathieu, Hisashi Endo, Koichi Ohkubo, Minoru Kanehisa, Susumu Goto, Hiroyuki Ogata. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold |
| 2253 | -- | 2255 | Jiang Hu, Junpeng Fan, Zongyi Sun, Shanlin Liu. NextPolish: a fast and efficient genome polishing tool for long-read assembly |
| 2256 | -- | 2257 | Readman Chiu, Ka Ming Nip, Inanç Birol. Fusion-Bloom: fusion detection in assembled transcriptomes |
| 2258 | -- | 2259 | Gurjit S. Randhawa, Kathleen A. Hill, Lila Kari. MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis |
| 2260 | -- | 2261 | Georgios Fotakis, Dietmar Rieder, Marlene Haider, Zlatko Trajanoski, Francesca Finotello. NeoFuse: predicting fusion neoantigens from RNA sequencing data |
| 2262 | -- | 2263 | Ahmed A. Quadeer, David Morales-Jiménez, Matthew R. McKay. RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins |
| 2264 | -- | 2265 | Mehari B. Zerihun, Fabrizio Pucci, Emanuel K. Peter, Alexander Schug. pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences |
| 2266 | -- | 2268 | Jimmy Caroli, Mattia Forcato, Silvio Bicciato. APTANI2: update of aptamer selection through sequence-structure analysis |
| 2269 | -- | 2271 | Snædís Kristmundsdóttir, Hannes P. Eggertsson, Gudny A. Arnadottir, Bjarni V. Halldórsson. popSTR2 enables clinical and population-scale genotyping of microsatellites |
| 2272 | -- | 2274 | Ammar Tareen, Justin B. Kinney. Logomaker: beautiful sequence logos in Python |
| 2275 | -- | 2277 | Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez. GABAC: an arithmetic coding solution for genomic data |
| 2278 | -- | 2279 | Ahmed A. Quadeer, Matthew R. McKay, John P. Barton, Raymond H. Y. Louie. MPF-BML: a standalone GUI-based package for maximum entropy model inference |
| 2280 | -- | 2281 | Sarah Lutteropp, Alexey M. Kozlov, Alexandros Stamatakis. A fast and memory-efficient implementation of the transfer bootstrap |
| 2282 | -- | 2283 | Jacques Ducasse, Visotheary Ung, Guillaume Lecointre, Aurélien Miralles. LIMES: a tool for comparing species partition |
| 2284 | -- | 2285 | Miguel Romero-Durana, Brian Jiménez-García, Juan Fernández-Recio. pyDockEneRes: per-residue decomposition of protein-protein docking energy |
| 2286 | -- | 2287 | Krisztian Adam, Zoltan Gyorgypal, Zoltan Hegedus. DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
| 2288 | -- | 2290 | Shian Su, Luyi Tian, Xueyi Dong, Peter F. Hickey, Saskia Freytag, Matthew E. Ritchie. CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods |
| 2291 | -- | 2292 | Saskia Freytag, Ryan Lister. schex avoids overplotting for large single-cell RNA-sequencing datasets |
| 2293 | -- | 2294 | Xiao Tan, Andrew Su, Minh Tran, Quan Nguyen. SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells |
| 2295 | -- | 2297 | Christina Nieuwoudt, Angela Brooks-Wilson, Jinko Graham. SimRVSequences: an R package to simulate genetic sequence data for pedigrees |
| 2298 | -- | 2299 | Laura M. Zingaretti, Gilles Renand, Diego P. Morgavi, Yuliaxis Ramayo-Caldas. Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities |
| 2300 | -- | 2302 | Maryam Nazarieh, Mohamed Hamed, Christian Spaniol, Thorsten Will, Volkhard Helms. TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks |
| 2303 | -- | 2305 | Junwei Han, Xudong Han, Qingfei Kong, Liang Cheng 0006. psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression |
| 2306 | -- | 2307 | Sergii Domanskyi, Carlo Piermarocchi, George Mias. PyIOmica: longitudinal omics analysis and trend identification |
| 2308 | -- | 2310 | Gongchao Jing, Yufeng Zhang, Ming Yang, Lu Liu, Jian Xu, Xiaoquan Su. Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level |
| 2311 | -- | 2313 | Roman Hillje, Pier Giuseppe Pelicci, Lucilla Luzi. Cerebro: interactive visualization of scRNA-seq data |
| 2314 | -- | 2315 | Jacobo de la Cuesta-Zuluaga, Ruth Ley, Nicholas Youngblut. Struo: a pipeline for building custom databases for common metagenome profilers |
| 2316 | -- | 2317 | Bilge Sürün, Charlotta P. I Schärfe, Mathew R. Divine, Julian Heinrich, Nora C. Toussaint, Lukas Zimmermann, Janina Beha, Oliver Kohlbacher. ClinVAP: a reporting strategy from variants to therapeutic options |