| 2975 | -- | 2979 | Zheng Zhang, Fen Yu, Yuanqiang Zou, Ye Qiu, Aiping Wu, Taijiao Jiang, Yousong Peng. Phage protein receptors have multiple interaction partners and high expressions |
| 2980 | -- | 2985 | Ilya M. Flyamer, Robert S. Illingworth, Wendy A. Bickmore. Coolpup.py: versatile pile-up analysis of Hi-C data |
| 2986 | -- | 2992 | Qiang Kang, Jun Meng, Jun Cui, Yushi Luan, Ming Chen. PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction |
| 2993 | -- | 3003 | Pavel Avdeyev, Nikita Alexeev, Yongwu Rong, Max A. Alekseyev. A unified ILP framework for core ancestral genome reconstruction problems |
| 3004 | -- | 3010 | Huang Xu, Xiang Li, Yaning Yang, Yi Li, Jose Pinheiro, Kate Sasser, Hisham Hamadeh, Xu Steven, Min Yuan. High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes |
| 3011 | -- | 3017 | Olga Mineeva, Mateo Rojas-Carulla, Ruth Ley, Bernhard Schölkopf, Nicholas Youngblut. DeepMAsED: evaluating the quality of metagenomic assemblies |
| 3018 | -- | 3027 | Chun-Qiu Xia, Xiaoyong Pan, Hong-bin Shen. Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data |
| 3028 | -- | 3034 | Xiangzheng Fu, Lijun Cai, Xiangxiang Zeng, Quan Zou 0001. StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency |
| 3035 | -- | 3042 | Shiwei Wei, Yuping Wang, Yuanchao Yang, Sen Liu. A path recorder algorithm for Multiple Longest Common Subsequences (MLCS) problems |
| 3043 | -- | 3048 | Michael A. Peabody, Wing Yin Venus Lau, Gemma Hoad, Baofeng Jia, Finlay Maguire, Kristen L. Gray, Robert G. Beiko, Fiona S. L. Brinkman. PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data |
| 3049 | -- | 3055 | Jae Yong Ryu, Mi-Young Lee, Jeong Hyun Lee, Byung Ho Lee, Kwang-Seok Oh. DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity |
| 3056 | -- | 3063 | Yuan Zhang, Xing Sui, Scott Stagg, Jinfeng Zhang. FTIP: an accurate and efficient method for global protein surface comparison |
| 3064 | -- | 3071 | Rostislav K. Skitchenko, Dmitrii Usoltsev, Mayya Uspenskaya, Andrey V. Kajava, Albert Guskov. Census of halide-binding sites in protein structures |
| 3072 | -- | 3076 | Elena Rivas, Jody Clements, Sean R. Eddy. Estimating the power of sequence covariation for detecting conserved RNA structure |
| 3077 | -- | 3083 | Wentao Shi, Jeffrey Mitchell Lemoine, Abd-El-Monsif A. Shawky, Manali Singha, Limeng Pu, Shuangyan Yang, J. Ramanujam, Michal Brylinski. BionoiNet: ligand-binding site classification with off-the-shelf deep neural network |
| 3084 | -- | 3092 | Luca Ponzoni, Daniel A. Peñaherrera, Zoltán N. Oltvai, Ivet Bahar. Rhapsody: predicting the pathogenicity of human missense variants |
| 3093 | -- | 3098 | Saeid Parvandeh, Hung-Wen Yeh, Martin P. Paulus, Brett A. McKinney. Consensus features nested cross-validation |
| 3099 | -- | 3106 | Burim Ramosaj, Lubna Amro, Markus Pauly. A cautionary tale on using imputation methods for inference in matched-pairs design |
| 3107 | -- | 3114 | Neo Christopher Chung. Statistical significance of cluster membership for unsupervised evaluation of cell identities |
| 3115 | -- | 3123 | Teng Fei, Tianwei Yu. scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment |
| 3124 | -- | 3130 | Wenfei Zhang, Ying Wei, Donghui Zhang, Ethan Y. Xu. ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data |
| 3131 | -- | 3138 | Ke Jin, Le Ou-Yang, Xing-Ming Zhao, Hong Yan 0001, Xiao-fei Zhang. scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation |
| 3139 | -- | 3147 | Junlin Xu, Lijun Cai, Bo Liao, Wen Zhu, Jialiang Yang. CMF-Impute: an accurate imputation tool for single-cell RNA-seq data |
| 3148 | -- | 3155 | David Bouyssié, Anne-Marie Hesse, Emmanuelle Mouton-Barbosa, Magali Rompais, Charlotte Macron, Christine Carapito, Anne Gonzalez de Peredo, Yohann Couté, Véronique Dupierris, Alexandre Burel, Jean-Philippe Menetrey, Andrea Kalaitzakis, Julie Poisat, Aymen Romdhani, Odile Burlet-Schiltz, Sarah Cianférani, Jerome Garin, Christophe Bruley. Proline: an efficient and user-friendly software suite for large-scale proteomics |
| 3156 | -- | 3161 | Chong Chen, Changjing Wu, Linjie Wu, Xiaochen Wang, Minghua Deng, Ruibin Xi. scRMD: imputation for single cell RNA-seq data via robust matrix decomposition |
| 3162 | -- | 3168 | Hong Zhang, Ni Zhao, Devan V. Mehrotra, Judong Shen. Composite Kernel Association Test (CKAT) for SNP-set joint assessment of genotype and genotype-by-treatment interaction in Pharmacogenetics studies |
| 3169 | -- | 3176 | Akio Onogi. Connecting mathematical models to genomes: joint estimation of model parameters and genome-wide marker effects on these parameters |
| 3177 | -- | 3184 | Eshan D. Mitra, William S. Hlavacek. Bayesian inference using qualitative observations of underlying continuous variables |
| 3185 | -- | 3191 | Edison Ong, Haihe Wang, Mei U. Wong, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He. Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens |
| 3192 | -- | 3199 | Stephen Kotiang, Ali Eslami. A probabilistic graphical model for system-wide analysis of gene regulatory networks |
| 3200 | -- | 3206 | Kavishwar B. Wagholikar, Hossein Estiri, Marykate Murphy, Shawn N. Murphy. Polar labeling: silver standard algorithm for training disease classifiers |
| 3207 | -- | 3214 | Rashmie Abeysinghe, Eugene W. Hinderer, Hunter N. B. Moseley, Licong Cui. SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology |
| 3215 | -- | 3224 | Katja Ovchinnikova, Lachlan Stuart, Alexander Rakhlin, Sergey I. Nikolenko, Theodore Alexandrov. ColocML: machine learning quantifies co-localization between mass spectrometry images |
| 3225 | -- | 3233 | Jie Shu, Jingxin Liu, YongMei Zhang, Hao Fu, Mohammad Ilyas, Giuseppe Faraci, Vincenzo Della Mea, Bozhi Liu, Guoping Qiu. Marker controlled superpixel nuclei segmentation and automatic counting on immunohistochemistry staining images |
| 3234 | -- | 3235 | Henry B. Zhang, Minji Kim, Jeffrey H. Chuang, Yijun Ruan. pyBedGraph: a python package for fast operations on 1D genomic signal tracks |
| 3236 | -- | 3238 | Wouter De Coster, Endre Bakken Stovner, Mojca Strazisar. Methplotlib: analysis of modified nucleotides from nanopore sequencing |
| 3239 | -- | 3241 | Zhencheng Fang, Jie Tan, Shufang Wu, Mo Li, Chunhui Wang, Yongchu Liu, Huaiqiu Zhu. PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning |
| 3242 | -- | 3243 | Samuel O'donnell, Gilles Fischer. MUM&Co: accurate detection of all SV types through whole-genome alignment |
| 3244 | -- | 3245 | Lisanna Paladin, Mathieu Schaeffer, Pascale Gaudet, Monique Zahn-Zabal, Pierre-André Michel, Damiano Piovesan, Silvio C. E. Tosatto, Amos Bairoch. The Feature-Viewer: a visualization tool for positional annotations on a sequence |
| 3246 | -- | 3247 | Václav Brázda, Jan Kolomazník, Jean-Louis Mergny, Jiri Stastny. G4Killer web application: a tool to design G-quadruplex mutations |
| 3248 | -- | 3250 | Marta Lovino, Maria Serena Ciaburri, Gianvito Urgese, Santa Di Cataldo, Elisa Ficarra. DEEPrior: a deep learning tool for the prioritization of gene fusions |
| 3251 | -- | 3253 | Congyu Lu, Zena Cai, Yuanqiang Zou, Zheng Zhang, Wenjun Chen, Lizong Deng, Xiangjun Du, Aiping Wu, Lei Yang 0002, Dayan Wang, Yuelong Shu, Taijiao Jiang, Yousong Peng. FluPhenotype - a one-stop platform for early warnings of the influenza A virus |
| 3254 | -- | 3256 | Hang Dai, Yongtao Guan. Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping |
| 3257 | -- | 3259 | Hao-Dong Xu, Ruifeng Hu 0004, Peilin Jia, Zhongming Zhao. 6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes |
| 3260 | -- | 3262 | Vladimir Perovic, Jeremy Y. Leclercq, Neven Sumonja, François D. Richard, Nevena Veljkovic, Andrey V. Kajava. Tally-2.0: upgraded validator of tandem repeat detection in protein sequences |
| 3263 | -- | 3265 | Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data |
| 3266 | -- | 3267 | Claudio Mirabello, Björn Wallner. InterLig: improved ligand-based virtual screening using topologically independent structural alignments |
| 3268 | -- | 3270 | Matteo P. Ferla, Alistair T. Pagnamenta, David R. Damerell, Jenny C. Taylor, Brian D. Marsden. MichelaNglo: sculpting protein views on web pages without coding |
| 3271 | -- | 3272 | Adrián García-Recio, Gemma Navarro, Rafael Franco, Mireia Olivella, Ramon Guixà-González, Arnau Cordomí. DIMERBOW: exploring possible GPCR dimer interfaces |
| 3273 | -- | 3275 | Elaine Y. Cao, John F. Ouyang, Owen J. L. Rackham. GeneSwitches: ordering gene expression and functional events in single-cell experiments |
| 3276 | -- | 3278 | Alemu Takele Assefa, Jo Vandesompele, Olivier Thas. SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data |
| 3279 | -- | 3280 | Arnaud Becheler, L. Lacey Knowles. Occupancy spectrum distribution: application for coalescence simulation with generic mergers |
| 3281 | -- | 3282 | Martin Scharm, Olaf Wolkenhauer, Mahdi Jalili, Ali Salehzadeh-Yazdi. GEMtractor: extracting views into genome-scale metabolic models |
| 3283 | -- | 3285 | Jinhwan Kim, Sora Yoon, Dougu Nam. netGO: R-Shiny package for network-integrated pathway enrichment analysis |
| 3286 | -- | 3287 | Evgeny Tankhilevich, Jonathan Ish-Horowicz, Tara Hameed, Elisabeth Roesch, Istvan Kleijn, Michael P. H. Stumpf, Fei He 0002. GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation |
| 3288 | -- | 3289 | Miroslav Kratochvíl, David Bednárek, Tomás Sieger, Karel Fiser, Jirí Vondrásek. ShinySOM: graphical SOM-based analysis of single-cell cytometry data |
| 3290 | -- | 3291 | Niall Beard, Finn Bacall, Aleksandra Nenadic, Milo Thurston, Carole A. Goble, Susanna-Assunta Sansone, Teresa K. Attwood. TeSS: a platform for discovering life-science training opportunities |
| 3292 | -- | 3294 | Zaki Hasnain, Andrew K. Fraser, Dan Georgess, Alex Choi, Paul Macklin, Joel S. Bader, Shelly R. Peyton, Andrew J. Ewald, Paul K. Newton. OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics |