| 4207 | -- | 4212 | Narciso M. Quijada, David Rodríguez-Lázaro, Jose María Eiros, Marta Hernández. TORMES: an automated pipeline for whole bacterial genome analysis |
| 4213 | -- | 4221 | Alberto Magi, Davide Bolognini, Niccoló Bartalucci, Alessandra Mingrino, Roberto Semeraro, Luna Giovannini, Stefania Bonifacio, Daniela Parrini, Elisabetta Pelo, Francesco Mannelli, Paola Guglielmelli, Alessandro Maria Vannucchi. Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data |
| 4222 | -- | 4228 | Tong Liu, Zheng Wang. HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data |
| 4229 | -- | 4238 | Ziye Wang, Zhengyang Wang, Yang Young Lu, Fengzhu Sun, Shanfeng Zhu. SolidBin: improving metagenome binning with semi-supervised normalized cut |
| 4239 | -- | 4246 | Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré. Graph analysis of fragmented long-read bacterial genome assemblies |
| 4247 | -- | 4254 | Takuya Moriyama, Seiya Imoto, Shuto Hayashi, Yuichi Shiraishi, Satoru Miyano, Rui Yamaguchi. A Bayesian model integration for mutation calling through data partitioning |
| 4255 | -- | 4263 | Mohammed Alser, Hasan Hassan, Akash Kumar 0001, Onur Mutlu, Can Alkan. Shouji: a fast and efficient pre-alignment filter for sequence alignment |
| 4264 | -- | 4271 | Juntao Liu, Xiangyu Liu, Xianwen Ren, Guojun Li. scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions |
| 4272 | -- | 4280 | Leyi Wei, Chen Zhou, Ran Su, Quan Zou 0001. PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning |
| 4281 | -- | 4289 | Jasmijn A. Baaijens, Alexander Schönhuth. Overlap graph-based generation of haplotigs for diploids and polyploids |
| 4290 | -- | 4297 | A. Oliva, S. Pulicani, Vincent Lefort, Laurent Bréhélin, Olivier Gascuel, Stéphane Guindon. Accounting for ambiguity in ancestral sequence reconstruction |
| 4298 | -- | 4306 | Max Ward, Hongying Sun, Amitava Datta, Michael J. Wise, David H. Mathews. Determining parameters for non-linear models of multi-loop free energy change |
| 4307 | -- | 4313 | Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev. Assessing reproducibility of matrix factorization methods in independent transcriptomes |
| 4314 | -- | 4320 | Ling-Yun Chen, Diego F. Morales-Briones, Courtney N. Passow, Ya Yang. Performance of gene expression analyses using de novo assembled transcripts in polyploid species |
| 4321 | -- | 4326 | Mark Abney, Aisha ElSherbiny. Kinpute: using identity by descent to improve genotype imputation |
| 4327 | -- | 4335 | Meiyue Wang, Shizhong Xu. A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies |
| 4336 | -- | 4343 | W. Jenny Shi, Yonghua Zhuang, Pamela H. Russell, Brian Hobbs, Margaret M. Parker, Peter J. Castaldi, Pratyaydipta Rudra, Brian Vestal, Craig P. Hersh, Laura M. Saba, Katerina Kechris. Unsupervised discovery of phenotype-specific multi-omics networks |
| 4344 | -- | 4349 | Yuwei Zhang, Yang Tao, Huihui Ji, Wei Li, Xingli Guo, Derry Minyao Ng, Maria Haleem, Yang Xi, Changzheng Dong, Jinshun Zhao, Lina Zhang, Xiaohong Zhang, Yangyang Xie, Xiaoyu Dai, Qi Liao. Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer |
| 4350 | -- | 4355 | Luis Vitores Valcarcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J. Planes. rMTA: robust metabolic transformation analysis |
| 4356 | -- | 4363 | Gaëlle Lefort, Laurence Liaubet, Cécile Canlet, Patrick Tardivel, Marie-Christine Père, Hélène Quesnel, Alain Paris, Nathalie Iannuccelli, Nathalie Vialaneix, Rémi Servien. ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra |
| 4364 | -- | 4371 | Jiajie Peng, Weiwei Hui, Qianqian Li, Bolin Chen, Jianye Hao, Qinghua Jiang, Xuequn Shang, Zhongyu Wei. A learning-based framework for miRNA-disease association identification using neural networks |
| 4372 | -- | 4380 | Jin-Dong Kim, Yue Wang, Toyofumi Fujiwara, Shujiro Okuda, Tiffany J. Callahan, K. Bretonnel Cohen. Open Agile text mining for bioinformatics: the PubAnnotation ecosystem |
| 4381 | -- | 4388 | Pengyuan Li 0001, Xiangying Jiang, Hagit Shatkay. Figure and caption extraction from biomedical documents |
| 4389 | -- | 4391 | Cory Y. McLean, Yeongwoo Hwang, Ryan Poplin, Mark A. DePristo. GenomeWarp: an alignment-based variant coordinate transformation |
| 4392 | -- | 4393 | Endre Bakken Stovner, Pål Sætrom. epic2 efficiently finds diffuse domains in ChIP-seq data |
| 4394 | -- | 4396 | Alexander T. Dilthey, Alexander J. Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb, Shabir A Madhi, Arang Rhie, Sergey Koren, Seiamak Bahram, Gil McVean, Adam M. Phillippy. HLA*LA - HLA typing from linearly projected graph alignments |
| 4397 | -- | 4399 | Stephanie U. Greer, Hanlee P. Ji. Structural variant analysis for linked-read sequencing data with gemtools |
| 4400 | -- | 4401 | Dapeng Wang. IntronDB: a database for eukaryotic intron features |
| 4402 | -- | 4404 | Carol L. Ecale Zhou, Stephanie Malfatti, Jeffrey Kimbrel, Casandra Philipson, Katelyn McNair, Theron Hamilton, Robert A. Edwards, Brian Souza. multiPhATE: bioinformatics pipeline for functional annotation of phage isolates |
| 4405 | -- | 4407 | Steven Monger, Michael Troup, Eddie Ip, Sally L. Dunwoodie, Eleni Giannoulatou. Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants |
| 4408 | -- | 4410 | Heng Li 0002. Identifying centromeric satellites with dna-brnn |
| 4411 | -- | 4412 | Vinhthuy Phan, Diem-Trang Pham, Caroline Melton, Adam J. Ramsey, Bernie J. Daigle Jr., Jennifer R. Mandel. icHET: interactive visualization of cytoplasmic heteroplasmy |
| 4413 | -- | 4418 | Mustafa Solmaz, Adam Lane, Bilal Gonen, Ogulsheker Akmamedova, Mehmet Hadi Gunes, Kakajan Komurov. Graphical data mining of cancer mechanisms with SEMA |
| 4419 | -- | 4421 | Sun-Ah Kim, Myriam Brossard, Delnaz Roshandel, Andrew D. Paterson, Shelley B. Bull, Yun Joo Yoo. gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks |
| 4422 | -- | 4423 | Yating Liu, Luke Sargent, Wilson Leung, Sarah C. R. Elgin, Jeremy Goecks. G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes |
| 4424 | -- | 4426 | Soohyun Lee, Jeremy Johnson, Carl Vitzthum, Koray Kirli, Burak Han Alver, Peter J. Park. Tibanna: software for scalable execution of portable pipelines on the cloud |
| 4427 | -- | 4429 | Andrea Ghelfi, Kenta Shirasawa, Hideki Hirakawa, Sachiko Isobe. Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants |
| 4430 | -- | 4432 | René L. Warren, Lauren Coombe, Hamid Mohamadi, Jessica Zhang, Barry Jaquish, Nathalie Isabel, Steven J. M. Jones, Jean Bousquet, Jörg Bohlmann, Inanç Birol. ntEdit: scalable genome sequence polishing |
| 4433 | -- | 4435 | Alessio Locallo, Davide Prandi, Tarcisio Fedrizzi, Francesca Demichelis. TPES: tumor purity estimation from SNVs |
| 4436 | -- | 4439 | Robert Müller, Cédric Chauve. HyAsP, a greedy tool for plasmids identification |
| 4440 | -- | 4441 | Romain Groux, Philipp Bucher. SPar-K: a method to partition NGS signal data |
| 4442 | -- | 4444 | Jia-Xing Yue, Gianni Liti. simuG: a general-purpose genome simulator |
| 4445 | -- | 4447 | Roberto Semeraro, Alberto Magi. PyPore: a python toolbox for nanopore sequencing data handling |
| 4448 | -- | 4450 | Shaun D. Jackman, Tatyana Mozgacheva, Susie Chen, Brendan O'Huiginn, Lance Bailey, Inanç Birol, Steven J. M. Jones. ORCA: a comprehensive bioinformatics container environment for education and research |
| 4451 | -- | 4452 | Robert Buels, Shihab Dider, Colin Diesh, James Robinson, Ian Holmes. Cram-JS: reference-based decompression in node and the browser |
| 4453 | -- | 4455 | Alexey M. Kozlov, Diego Darriba, Tomás Flouri, Benoit Morel, Alexandros Stamatakis. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference |
| 4456 | -- | 4458 | Maksim V. Shegay, Dmitry Suplatov, Nina N. Popova, Vytas Svedas, Vladimir V. Voevodin. parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems |
| 4459 | -- | 4461 | Sha Gong, Chengxin Zhang, Yang Zhang. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA |
| 4462 | -- | 4464 | Jordan H. Creed, Garrick Aden-Buie, Alvaro N. Monteiro, Travis A. Gerke. epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology |
| 4465 | -- | 4468 | Xin Gao, Yuan Zhong. FusionLearn: a biomarker selection algorithm on cross-platform data |
| 4469 | -- | 4471 | Kristoffer Vitting-Seerup, Albin Sandelin. IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences |
| 4472 | -- | 4473 | Páll Melsted, Vasilis Ntranos, Lior Pachter. The barcode, UMI, set format and BUStools |
| 4474 | -- | 4477 | Anjun Ma, Minxuan Sun, Adam McDermaid, Bingqiang Liu, Qin Ma 0003. MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome |
| 4478 | -- | 4479 | Juanjiangmeng Du, Monica Sudarsanam, Eduardo Pérez-Palma, Andrea Ganna, Laurent Francioli, Sumaiya Iqbal, Lisa-Marie Niestroj, Costin Leu, Ben Weisburd, Tim Poterba, Peter Nürnberg, Mark J. Daly, Aarno Palotie, Patrick May, Dennis Lal. Variant Score Ranker - a web application for intuitive missense variant prioritization |
| 4480 | -- | 4483 | Mathias Currat, Miguel Arenas, Claudio S. Quilodràn, Laurent Excoffier, Nicolas Ray. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal |
| 4484 | -- | 4487 | Pierre Millard, Baudoin Delépine, Matthieu Guionnet, Maud Heuillet, Floriant Bellvert, Fabien Létisse. IsoCor: isotope correction for high-resolution MS labeling experiments |
| 4488 | -- | 4489 | Clarice S. Groeneveld, Vinicius S. Chagas, Steven J. M. Jones, A. Gordon Robertson, Bruce A. J. Ponder, Kerstin B. Meyer, Mauro A. A. Castro. RTNsurvival: an R/Bioconductor package for regulatory network survival analysis |
| 4490 | -- | 4492 | Bence Ágg, Andrea Császár, Máté Szalay-Beko, Dániel V. Veres, Réka Mizsei, Péter Ferdinandy, Péter Csermely, István A. Kovács. The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks |
| 4493 | -- | 4495 | Michael Schubert. clustermq enables efficient parallelization of genomic analyses |
| 4496 | -- | 4498 | David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider 0002. MINERVA API and plugins: opening molecular network analysis and visualization to the community |
| 4499 | -- | 4500 | Adrien Rougny. sbgntikz - a TikZ library to draw SBGN maps |
| 4501 | -- | 4503 | Petar V. Todorov, Benjamin M. Gyori, John A. Bachman, Peter K. Sorger. INDRA-IPM: interactive pathway modeling using natural language with automated assembly |
| 4504 | -- | 4506 | Jennifer L. Wilson, Mike Wong, Ajinkya Chalke, Nicholas Stepanov, Dragutin Petkovic, Russ B. Altman. PathFXweb: a web application for identifying drug safety and efficacy phenotypes |
| 4507 | -- | 4508 | Geremy Clair, Sarah Reehl, Kelly G. Stratton, Matthew E. Monroe, Malak M. Tfaily, Charles Ansong, Jennifer E. Kyle. Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data |
| 4509 | -- | 4510 | Neil Pearson, Karim Malki, David Evans, Lewis Vidler, Cara Ruble, James Scherschel, Brian Eastwood, David A Collier. TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability |
| 4511 | -- | 4514 | Jan P. Buchmann, Edward C. Holmes. Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases |
| 4515 | -- | 4518 | Benjamin S. Glicksberg, Boris Oskotsky, Phyllis M. Thangaraj, Nicholas Giangreco, Marcus A. Badgeley, Kipp W. Johnson, Debajyoti Datta, Vivek A Rudrapatna, Nadav Rappoport, Mark M. Shervey, Riccardo Miotto, Theodore C. Goldstein, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel T. Dudley, Nicholas P. Tatonetti, Atul J. Butte. PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model |
| 4519 | -- | 4521 | Youssef Darzi, Yuta Yamate, Takuji Yamada. FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization |
| 4522 | -- | 4524 | Marcus D. Bloice, Peter M. Roth, Andreas Holzinger. Biomedical image augmentation using Augmentor |
| 4525 | -- | 4527 | Alex X. Lu, Taraneh Zarin, Ian Shenyen Hsu, Alan M. Moses. YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells |
| 4528 | -- | 4530 | Michael J. Whitehead, George A. McCanney, Hugh J. Willison, Susan C. Barnett. MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures |
| 4531 | -- | 4533 | David Wiesner, David Svoboda, Martin Maska, Michal Kozubek. CytoPacq: a web-interface for simulating multi-dimensional cell imaging |
| 4534 | -- | 0 | Enrico Siragusa, Niina Haiminen, Richard Finkers, Richard G. F. Visser, Laxmi Parida. Haplotype assembly of autotetraploid potato using integer linear programing |
| 4535 | -- | 0 | Pei-Hua Wang, Yi-shu Tu, Yufeng J. Tseng. PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors |
| 4536 | -- | 0 | Pay Giesselmann, Sara Hetzel, Franz-Josef Müller, Alexander Meissner, Helene Kretzmer. Nanopype: a modular and scalable nanopore data processing pipeline |