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YaHS: yet another Hi-C scaffolding tool
Zhou, Chenxi, McCarthy, Shane A, Durbin, Richard
Published in Bioinformatics (Oxford, England) (01.01.2023)
Published in Bioinformatics (Oxford, England) (01.01.2023)
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining
Lee, Jinhyuk, Yoon, Wonjin, Kim, Sungdong, Kim, Donghyeon, Kim, Sunkyu, So, Chan Ho, Kang, Jaewoo
Published in Bioinformatics (15.02.2020)
Published in Bioinformatics (15.02.2020)
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ProteinBERT: a universal deep-learning model of protein sequence and function
Brandes, Nadav, Ofer, Dan, Peleg, Yam, Rappoport, Nadav, Linial, Michal
Published in Bioinformatics (12.04.2022)
Published in Bioinformatics (12.04.2022)
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Chaumeil, Pierre-Alain, Mussig, Aaron J, Hugenholtz, Philip, Parks, Donovan H
Published in Bioinformatics (15.11.2019)
Published in Bioinformatics (15.11.2019)
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GraphDTA: predicting drug–target binding affinity with graph neural networks
Nguyen, Thin, Le, Hang, Quinn, Thomas P, Nguyen, Tri, Le, Thuc Duy, Venkatesh, Svetha
Published in Bioinformatics (23.05.2021)
Published in Bioinformatics (23.05.2021)
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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
Kozlov, Alexey M, Darriba, Diego, Flouri, Tomáš, Morel, Benoit, Stamatakis, Alexandros
Published in Bioinformatics (01.11.2019)
Published in Bioinformatics (01.11.2019)
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Identifying and removing haplotypic duplication in primary genome assemblies
Guan, Dengfeng, McCarthy, Shane A, Wood, Jonathan, Howe, Kerstin, Wang, Yadong, Durbin, Richard
Published in Bioinformatics (01.05.2020)
Published in Bioinformatics (01.05.2020)
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KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
Aramaki, Takuya, Blanc-Mathieu, Romain, Endo, Hisashi, Ohkubo, Koichi, Kanehisa, Minoru, Goto, Susumu, Ogata, Hiroyuki
Published in Bioinformatics (01.04.2020)
Published in Bioinformatics (01.04.2020)
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TISIDB: an integrated repository portal for tumor–immune system interactions
Ru, Beibei, Wong, Ching Ngar, Tong, Yin, Zhong, Jia Yi, Zhong, Sophia Shek Wa, Wu, Wai Chung, Chu, Ka Chi, Wong, Choi Yiu, Lau, Chit Ying, Chen, Ian, Chan, Nam Wai, Zhang, Jiangwen
Published in Bioinformatics (15.10.2019)
Published in Bioinformatics (15.10.2019)
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PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations
Kamat, Mihir A, Blackshaw, James A, Young, Robin, Surendran, Praveen, Burgess, Stephen, Danesh, John, Butterworth, Adam S, Staley, James R
Published in Bioinformatics (01.11.2019)
Published in Bioinformatics (01.11.2019)
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DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Ji, Yanrong, Zhou, Zhihan, Liu, Han, Davuluri, Ramana V
Published in Bioinformatics (Oxford, England) (09.08.2021)
Published in Bioinformatics (Oxford, England) (09.08.2021)
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VarSome: the human genomic variant search engine
Kopanos, Christos, Tsiolkas, Vasilis, Kouris, Alexandros, Chapple, Charles E, Albarca Aguilera, Monica, Meyer, Richard, Massouras, Andreas
Published in Bioinformatics (Oxford, England) (01.06.2019)
Published in Bioinformatics (Oxford, England) (01.06.2019)
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ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
Gustavsson, Emil K, Zhang, David, Reynolds, Regina H, Garcia-Ruiz, Sonia, Ryten, Mina
Published in Bioinformatics (02.08.2022)
Published in Bioinformatics (02.08.2022)
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PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files
Zhang, Chi, Dong, Shan-Shan, Xu, Jun-Yang, He, Wei-Ming, Yang, Tie-Lin
Published in Bioinformatics (15.05.2019)
Published in Bioinformatics (15.05.2019)
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igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
Robinson, James T, Thorvaldsdottir, Helga, Turner, Douglass, Mesirov, Jill P
Published in Bioinformatics (Oxford, England) (01.01.2023)
Published in Bioinformatics (Oxford, England) (01.01.2023)
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