| 2319 | -- | 2327 | Jonathan Raad, Georgina Stegmayer, Diego H. Milone. Complexity measures of the mature miRNA for improving pre-miRNAs prediction |
| 2328 | -- | 2336 | Chuanyi Zhang, Idoia Ochoa. VEF: a variant filtering tool based on ensemble methods |
| 2337 | -- | 2344 | Gleb Goussarov, Ilse Cleenwerck, Mohamed Mysara, Natalie Leys, Pieter Monsieurs, Guillaume Tahon, Aurélien Carlier, Peter Vandamme, Rob Van Houdt. PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing |
| 2345 | -- | 2351 | Xinyan Zhang, Nengjun Yi. Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data |
| 2352 | -- | 2358 | Guodong Yang, Aiqun Ma, Zhaohui S. Qin, Li Chen. Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules |
| 2359 | -- | 2364 | Pasi Rastas. Lep-Anchor: automated construction of linkage map anchored haploid genomes |
| 2365 | -- | 2374 | Xiaqiong Wang, Yalu Wen. A U-statistics for integrative analysis of multilayer omics data |
| 2375 | -- | 2384 | Akhilesh Mishra, Sahil Dhanda, Priyanka Siwach, Shruti Aggarwal, B. Jayaram. A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics |
| 2385 | -- | 2392 | Shilpa Garg, John Aach, Heng Li 0002, Isaac Sebenius, Richard Durbin, George M. Church. A haplotype-aware de novo assembly of related individuals using pedigree sequence graph |
| 2393 | -- | 2400 | Haitao Yu, Zhiming Dai. SANPolyA: a deep learning method for identifying Poly(A) signals |
| 2401 | -- | 2409 | Nils Strodthoff, Patrick Wagner, Markus Wenzel 0002, Wojciech Samek. UDSMProt: universal deep sequence models for protein classification |
| 2410 | -- | 2416 | Thomas Bradley, Simon Moxon. FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals |
| 2417 | -- | 2428 | Tobias Brinkjost, Christiane Ehrt, Oliver Koch, Petra Mutzel. SCOT: Rethinking the classification of secondary structure elements |
| 2429 | -- | 2437 | Xiaoqiang Huang, Wei Zheng, Robin Pearce, Yang Zhang. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function |
| 2438 | -- | 2442 | Yiwei Cao, Sang-Jun Park, Akul Y. Mehta, Richard D. Cummings, Wonpil Im. GlyMDB: Glycan Microarray Database and analysis toolset |
| 2443 | -- | 2450 | Jun Liu, Xiao-gen Zhou, Yang Zhang 0040, Gui-jun Zhang. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm |
| 2451 | -- | 2457 | Louis Becquey, Eric Angel, Fariza Tahi. BiORSEO: a bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules |
| 2458 | -- | 2465 | Isak Johansson-Åkhe, Claudio Mirabello, Björn Wallner. InterPep2: global peptide-protein docking using interaction surface templates |
| 2466 | -- | 2473 | Jiao Sun, Jae-Woong Chang, Teng Zhang, Jeongsik Yong, Rui Kuang, Wei Zhang 0076. Platform-integrated mRNA isoform quantification |
| 2474 | -- | 2485 | Zhan-Ying Feng, Xianwen Ren, Yuan Fang, Yining Yin, Chutian Huang, Yimin Zhao, Yong Wang. scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization |
| 2486 | -- | 2491 | Serin Zhang, Jiang Shao, Disa Yu, Xing Qiu, Jinfeng Zhang. MatchMixeR: a cross-platform normalization method for gene expression data integration |
| 2492 | -- | 2499 | Yifan Ji, Chang Yu, Hong Zhang. contamDE-lm: linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples |
| 2500 | -- | 2505 | Gittu George, Sushrima Gan, Yu Huang, Philip Appleby, A. S. Nar, Radha Venkatesan, Viswanathan Mohan, Colin N. A. Palmer, Alex S. F. Doney. PheGWAS: a new dimension to visualize GWAS across multiple phenotypes |
| 2506 | -- | 2514 | Jingsi Ming, Tao Wang, Can Yang. LPM: a latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations |
| 2515 | -- | 2521 | Kristina Buschur, Maria Chikina, Panayiotis V. Benos. Causal network perturbations for instance-specific analysis of single cell and disease samples |
| 2522 | -- | 2529 | Rasmus Magnusson, Mika Gustafsson. LiPLike: towards gene regulatory network predictions of high certainty |
| 2530 | -- | 2537 | Hui-Zeng Sun, Mi Zhou, Ou Wang, Yanhong Chen, Jian-xin Liu, Le Luo Guan. Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows |
| 2538 | -- | 2546 | Jin Li, Sai Zhang, Tao Liu, Chenxi Ning, Zhuoxuan Zhang, Wei Zhou. Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction |
| 2547 | -- | 2553 | Mayank Baranwal, Abram Magner, Paolo Elvati, Jacob Saldinger, Angela Violi, Alfred Hero. A deep learning architecture for metabolic pathway prediction |
| 2554 | -- | 2560 | Xiaohui Yao, Shan Cong, Jingwen Yan, Shannon L. Risacher, Andrew J. Saykin, Jason H. Moore, Li Shen 0001. Regional imaging genetic enrichment analysis |
| 2561 | -- | 2568 | Xia-an Bi, Yingchao Liu, Yiming Xie, Xi Hu, Qinghua Jiang. Morbigenous brain region and gene detection with a genetically evolved random neural network cluster approach in late mild cognitive impairment |
| 2569 | -- | 2571 | Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manu Molina, Toni Gabaldón. HaploTypo: a variant-calling pipeline for phased genomes |
| 2572 | -- | 2574 | Soumitra Pal 0001, Teresa M. Przytycka. Bioinformatics pipeline using JUDI: Just Do It! |
| 2575 | -- | 2577 | Swadha Anand, Bhusan K. Kuntal, Anwesha Mohapatra, Vineet Bhatt, Sharmila S. Mande. FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information |
| 2578 | -- | 2580 | Yu Li 0006, Sheng Wang 0001, Chongwei Bi, Zhaowen Qiu, Mo Li 0005, Xin Gao 0001. DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing |
| 2581 | -- | 2583 | Sophia C. Tintori, Patrick Golden, Bob Goldstein. Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets |
| 2584 | -- | 2586 | Dominika Labudová, Jirí Hon, Matej Lexa. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm |
| 2587 | -- | 2588 | Christopher M. Ward, Thu-Hien To, Stephen M. Pederson. ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files |
| 2589 | -- | 2591 | Lorraine A. K. Ayad, Panagiotis Charalampopoulos, Solon P. Pissis. SMART: SuperMaximal approximate repeats tool |
| 2592 | -- | 2594 | Deren A. R. Eaton, Isaac Overcast. ipyrad: Interactive assembly and analysis of RADseq datasets |
| 2595 | -- | 2598 | Bianka Farkas, Georgina Csizmadia, Eszter Katona, Gábor E. Tusnády, Tamás Hegedüs. MemBlob database and server for identifying transmembrane regions using cryo-EM maps |
| 2599 | -- | 2601 | Tomasz Magdziarz, Karolina Mitusinska, Maria Bzówka, Agata Raczynska, Agnieszka Stanczak, Michal Banas, Weronika Bagrowska, Artur Góra. AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective |
| 2602 | -- | 2604 | Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George M. Spyrou. ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing |
| 2605 | -- | 2607 | Gui-Yan Xie, Meng Xuan Xia, Ya-Ru Miao, Mei Luo, Qiong Zhang, An-Yuan Guo. FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human |
| 2608 | -- | 2610 | Aritro Nath, Jeremy Chang, R. Stephanie Huang. iMIRAGE: an R package to impute microRNA expression using protein-coding genes |
| 2611 | -- | 2613 | Thang V. Pham, Alex A. Henneman, Connie R. Jimenez. iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics |
| 2614 | -- | 2615 | Palle Duun Rohde, Izel Fourie Sørensen, Peter Sørensen. qgg: an R package for large-scale quantitative genetic analyses |
| 2616 | -- | 2617 | Andre Schultz, Rehan Akbani. SAMMI: a semi-automated tool for the visualization of metabolic networks |
| 2618 | -- | 2619 | César Parra-Rojas, Esteban A. Hernández-Vargas. PDEparams: parameter fitting toolbox for partial differential equations in python |
| 2620 | -- | 2622 | Irina Balaur, Ludovic Roy, Alexander Mazein, S. Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Yu. Zinovyev. cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats |
| 2623 | -- | 2625 | Thomas C. Keaty, Paul A. Jensen. Gapsplit: efficient random sampling for non-convex constraint-based models |
| 2626 | -- | 2627 | Corentin Molitor, Matt Brember, Fady R. Mohareb. VarGen: an R package for disease-associated variant discovery and annotation |
| 2628 | -- | 2629 | Steven X. Ge, Dongmin Jung, Runan Yao. ShinyGO: a graphical gene-set enrichment tool for animals and plants |
| 2630 | -- | 2631 | Alexander Keller 0006, Sonja Hohlfeld, Andreas Kolter, Jörg Schultz, Birgit Gemeinholzer, Markus J. Ankenbrand. BCdatabaser: on-the-fly reference database creation for (meta-)barcoding |
| 2632 | -- | 2633 | Francesco Ceccarelli, Denes Turei, Attila Gabor, Julio Saez-Rodriguez. Bringing data from curated pathway resources to Cytoscape with OmniPath |
| 2634 | -- | 2635 | Sébastien Tosi, Lídia Bardia, Maria Jose Filgueira, Alexandre Calon, Julien Colombelli. LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data |
| 2636 | -- | 2642 | Rachel Drysdale, Charles E. Cook, Robert Petryszak, Vivienne Baillie Gerritsen, Mary Barlow, Elisabeth Gasteiger, Franziska Gruhl, Jürgen Haas, Jerry Lanfear, Rodrigo Lopez, Nicole Redaschi, Heinz Stockinger, Daniel Teixeira, Aravind Venkatesan, Alex Bateman, Alan Bridge, Guy Cochrane, Robert D. Finn, Frank Oliver Glöckner, Marc Hanauer, Thomas M. Keane, Andrew Leach, Luana Licata, Per Oksvold, Sandra E. Orchard, Christine A. Orengo, Helen E. Parkinson, Bengt Persson, Pablo Porras, Jordi Rambla, Ana Rath, Charlotte Rodwell, Ugis Sarkans, Dietmar Schomburg, Ian Sillitoe, Dylan Spalding, Mathias Uhlén, Sameer Velankar, Juan Antonio Vizcaíno, Kalle von Feilitzen, Christian von Mering, Andrew D. Yates, Niklas Blomberg, Christine Durinx, Johanna R. McEntyre. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences |
| 2643 | -- | 0 | Nils Koelling, Marie Bernkopf, Eduardo Calpena, Geoffrey J. Maher, Kerry A. Miller, Hannah K. Ralph, Anne Goriely, Andrew O. M. Wilkie. amplimap: a versatile tool to process and analyze targeted NGS data |
| 2644 | -- | 0 | Rui Liu 0009, Pei Chen, Luonan Chen. Corrigendum to: Single-sample landscape entropy reveals the imminent phase transition during disease progression |
| 2645 | -- | 0 | Aleksandr Ianevski, Liye He, Tero Aittokallio, Jing Tang 0002. SynergyFinder: a web application for analyzing drug combination dose-response matrix data |
| 2646 | -- | 0 | Sergey V. Tarlachkov, Taras V. Shevchuk, Maria del Carmen Montero-Calasanz, Irina P. Starodumova. Diversity of rhodopsins in cultivated bacteria of the family Geodermatophilaceae associated with non-aquatic environments |
| 2647 | -- | 0 | Gabriel Studer, Christine Rempfer, Andrew Waterhouse, Rafal Gumienny, Juergen Haas, Torsten Schwede. QMEANDisCo - distance constraints applied on model quality estimation |