| 985 | -- | 989 | Galo A. Goig, Manuela Torres-Puente, Carla Mariner-Llicer, Luis M. Villamayor, Álvaro Chiner-Oms, Ana Gil-Brusola, Rafael Borrás, Iñaki Comas Espadas. Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics |
| 990 | -- | 993 | Luis Sánchez-Pulido, Chris P. Ponting. Hexa-Longin domain scaffolds for inter-Rab signalling |
| 994 | -- | 999 | Qian Zhu, Xavier Tekpli, Olga G. Troyanskaya, Vessela N. Kristensen. Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations |
| 1000 | -- | 1006 | Kang Jin Kim, Jaehyun Park, Sang-Chul Park, Sungho Won. Phylogenetic tree-based microbiome association test |
| 1007 | -- | 1013 | Gaia Ceddia, Liuba Nausicaa Martino, Alice C. L. Parodi, Piercesare Secchi, Stefano Campaner, Marco Masseroli. Association rule mining to identify transcription factor interactions in genomic regions |
| 1014 | -- | 1021 | Arif Harmanci, Akdes Serin Harmanci, Jyothishmathi Swaminathan, Vidya Gopalakrishnan. EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements |
| 1022 | -- | 1029 | Deepank R. Korandla, Jacob M. Wozniak, Anaamika Campeau, David J. Gonzalez, Erik S. Wright. AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions |
| 1030 | -- | 1036 | Ziwei Li, Bo He, Weixing Feng. Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases |
| 1037 | -- | 1043 | Zengyan Hong, Xiangxiang Zeng, Leyi Wei, Xiangrong Liu. Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism |
| 1044 | -- | 1051 | Yichao Li, Yating Liu, David Juedes, Frank Drews, Razvan Bunescu, Lonnie R. Welch. Set cover-based methods for motif selection |
| 1052 | -- | 1056 | Xue-qing, Meng Wang, Gerrit Karssen, Patricia Bucki, Wim Bert, Sigal Braun-Miyara. PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes |
| 1057 | -- | 1065 | Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song. DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites |
| 1066 | -- | 1073 | Sen Liu, Yuping Wang, Wuning Tong, Shiwei Wei. A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment |
| 1074 | -- | 1081 | Bin Yu, Wenying Qiu, Cheng Chen, Anjun Ma, Jing Jiang, Hongyan Zhou, Qin Ma 0003. SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting |
| 1082 | -- | 1090 | Camir Ricketts, Daniel Seidman, Victoria Popic, Fereydoun Hormozdiari, Serafim Batzoglou, Iman Hajirasouliha. Meltos: multi-sample tumor phylogeny reconstruction for structural variants |
| 1091 | -- | 1098 | Tianqi Wu, Jie Hou, Badri Adhikari, Jianlin Cheng. Analysis of several key factors influencing deep learning-based inter-residue contact prediction |
| 1099 | -- | 1106 | Amélie Barozet, Kevin Molloy, Marc Vaisset, Thierry Siméon, Juan Cortés. A reinforcement-learning-based approach to enhance exhaustive protein loop sampling |
| 1107 | -- | 1113 | Jack Hanson, Thomas Litfin, Kuldip K. Paliwal, Yaoqi Zhou. Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning |
| 1114 | -- | 1120 | Min Zeng, Fuhao Zhang, Fang-Xiang Wu, Yaohang Li, Jianxin Wang, Min Li 0007. Protein-protein interaction site prediction through combining local and global features with deep neural networks |
| 1121 | -- | 1128 | Tanvir Alam, Meshari Alazmi, Rayan Naser, Franceline Huser, Afaque A. Momin, Veronica Astro, SeungBeom Hong, Katarzyna W. Walkiewicz, Christian G. Canlas, Raphaël Huser, Amal J. Ali, Jasmeen Merzaban, Antonio Adamo, Mariusz Jaremko, Lukasz Jaremko, Vladimir B. Bajic, Xin Gao, Stefan T. Arold. Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs |
| 1129 | -- | 1134 | Mariusz Popenda, Joanna Miskiewicz, Joanna Sarzynska, Tomasz Zok, Marta Szachniuk. Topology-based classification of tetrads and quadruplex structures |
| 1135 | -- | 1142 | Xiaoqiang Huang, Robin Pearce, Yang Zhang. EvoEF2: accurate and fast energy function for computational protein design |
| 1143 | -- | 1149 | Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang, Qin Ma 0003. QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data |
| 1150 | -- | 1158 | Abha S. Bais, Dennis Kostka. scds: computational annotation of doublets in single-cell RNA sequencing data |
| 1159 | -- | 1166 | Christopher R. John, David Watson, Michael R. Barnes, Costantino Pitzalis, Myles J. Lewis. Spectrum: fast density-aware spectral clustering for single and multi-omic data |
| 1167 | -- | 1173 | Wilson H. McKerrow, David Fenyö. L1EM: a tool for accurate locus specific LINE-1 RNA quantification |
| 1174 | -- | 1181 | Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei. bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data |
| 1182 | -- | 1190 | Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham. Metric learning on expression data for gene function prediction |
| 1191 | -- | 1197 | María Bogaerts-Márquez, Maite G. Barrón, Anna-Sophie Fiston-Lavier, Pol Vendrell-Mir, Raúl Castanera, Josep M. Casacuberta, Josefa González. T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data |
| 1198 | -- | 1207 | Mahdi Shafiee Kamalabad, Marco Grzegorczyk. Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters |
| 1208 | -- | 1212 | Rex Parsons, Richard Parsons, Nicholas Garner, Henrik Oster, Oliver Rawashdeh. CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms |
| 1213 | -- | 1218 | Yuanyue Li, Michael Kuhn 0004, Anne-Claude Gavin, Peer Bork. Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features |
| 1219 | -- | 1225 | Saman Salike, Nirav Bhatt. Thermodynamically consistent estimation of Gibbs free energy from data: data reconciliation approach |
| 1226 | -- | 1233 | Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su. Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts |
| 1234 | -- | 1240 | Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, Jaewoo Kang. BioBERT: a pre-trained biomedical language representation model for biomedical text mining |
| 1241 | -- | 1251 | Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy 0001, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun. Graph embedding on biomedical networks: methods, applications and evaluations |
| 1252 | -- | 1259 | Ruijie Yao, Jiaqiang Qian, Qiang Huang. Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules |
| 1260 | -- | 1261 | David Porubsky, Ashley D. Sanders, Aaron Taudt, Maria Colomé-Tatché, Peter M. Lansdorp, Victor Guryev. breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data |
| 1262 | -- | 1264 | Congting Ye, Qian Zhou, Xiaohui Wu, Chen Yu, Guoli Ji, Daniel R. Saban, Qingshun Quinn Li. scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data |
| 1265 | -- | 1266 | Marina Marcet-Houben, Toni Gabaldón. EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes |
| 1267 | -- | 1269 | Davide Bolognini, Ashley D. Sanders, Jan O. Korbel, Alberto Magi, Vladimir Benes, Tobias Rausch. VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing |
| 1270 | -- | 1272 | Hongjian Jin, Lawryn H. Kasper, Jon D. Larson, Gang Wu, Suzanne J. Baker, Jinghui Zhang, Yiping Fan. ChIPseqSpikeInFree: a ChIP-seq normalization approach to reveal global changes in histone modifications without spike-in |
| 1273 | -- | 1274 | Ignacio Ferrés, Pablo Fresia, Gregorio Iraola. simurg: simulate bacterial pangenomes in R |
| 1275 | -- | 1276 | Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, Claire Lemaitre. SimkaMin: fast and resource frugal de novo comparative metagenomics |
| 1277 | -- | 1278 | Jun Wang, Pu-Feng Du, Xin-Yu Xue, Guang-Ping Li, Yuan-Ke Zhou, Wei Zhao, Hao Lin, Wei Chen. VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences |
| 1279 | -- | 1280 | Guillermo Serrano, Elizabeth Guruceaga, Victor Segura. DeepMSPeptide: peptide detectability prediction using deep learning |
| 1281 | -- | 1282 | Zhenhua Yu, Fang Du, Xuehong Sun, Ao Li. SCSsim: an integrated tool for simulating single-cell genome sequencing data |
| 1283 | -- | 1285 | Zeynep Baskurt, Scott Mastromatteo, Jiafen Gong, Richard F. Wintle, Stephen W. Scherer, Lisa J. Strug. VikNGS: a C++ variant integration kit for next generation sequencing association analysis |
| 1286 | -- | 1288 | Adrián A. Davín, Théo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J. Szöllosi. Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages |
| 1289 | -- | 1290 | Patrick H. Bradley, Katherine S. Pollard. phylogenize: correcting for phylogeny reveals genes associated with microbial distributions |
| 1291 | -- | 1292 | Conrad Stork, Gerd Embruch, Martin Sícho, Christina de Bruyn Kops, Ya Chen, Daniel Svozil, Johannes Kirchmair. NERDD: a web portal providing access to in silico tools for drug discovery |
| 1293 | -- | 1295 | Chao Fang, Zhaoyu Li, Dong Xu 0002, Yi Shang. MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns |
| 1296 | -- | 1297 | Julian Bender, Carla Schmidt. The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments |
| 1298 | -- | 1299 | António Cruz, Penousal Machado, Joel P. Arrais. CroP - Coordinated Panel visualization for biological networks analysis |
| 1300 | -- | 1302 | A. Trullo, J. Dufourt, M. Lagha. MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos |
| 1303 | -- | 1304 | Florian P. Breitwieser, Steven L. Salzberg. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification |
| 1305 | -- | 1306 | Grégoire Versmée, Laura Versmée, Mikaël Dusenne, Niloofar Jalali, Paul Avillach. dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP) |
| 1307 | -- | 1308 | Anthony Federico, Stefano Monti. hypeR: an R package for geneset enrichment workflows |
| 1309 | -- | 1310 | Kevin McDonnell, Nicholas Waters, Enda Howley, Florence Abram. Chordomics: a visualization tool for linking function to phylogeny in microbiomes |
| 1311 | -- | 1313 | Marcela Aguilera Flores, Iulia M. Lazar. XMAn v2 - a database of Homo sapiens mutated peptides |
| 1314 | -- | 1316 | Pablo Vicente-Munuera, Pedro Gómez-Gálvez, Robert J. Tetley, Cristina Forja, Antonio Tagua, Marta Letrán, Melda Tozluoglu, Yanlan Mao, Luis M. Escudero. EpiGraph: an open-source platform to quantify epithelial organization |