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Showing results 1 to 28 of 28

Issue Date	Title / Author(s) / Citation	File
2005-07	jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences Jeon, Yoon-Seong; Chung, Hwanwon; Park, Sunyoung; Hur, Inae; Lee, Jae-Hak; Chun, Jongsik Bioinformatics, Vol.21 No.14, pp.3171-3173	DOI
2011-12	O-18-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry Kim, Jong-Seo; Fillmore, Thomas L.; Liu, Tao; Robinson, Errol; Hossain, Mahmud; Champion, Boyd L.; Moore, Ronald J.; Camp, David G., II; Smith, Richard D.; Qian, Wei-Jun Molecular and Cellular Proteomics, Vol.10 No.12, p. M110.007302	DOI
2012-04	Genome sequence of extracellular-protease-producing Alishewanella jeotgali Isolated from traditional Korean fermented seafood Jung, Jaejoon; Chun, Jongsik; Park, Woojun Journal of Bacteriology, Vol.194 No.8, pp.2097-2097	DOI
2012-10	The co-regulation mechanism of transcription factors in the human gene regulatory network Kim, Junil; Choi, Minsoo; Kim, Jeong-Rae; Jin, Hua; Kim, V. Narry; Cho, Kwang-Hyun Nucleic Acids Research, Vol.40 No.18, pp.8849-8861	DOI
2013	Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain CrmT (= DSM 23852T) Hyun, Dong-Wook; Whon, Tae Woong; Cho, Yong-Joon; Chun, Jongsik; Kim, Min-Soo; Jung, Mi-Ja; Shin, Na-Ri; Kim, Joon-Yong; Kim, Pil Soo; Yun, Ji-Hyun; Lee, Jina; Oh, Sei Joon; Bae, Jin-Woo Standards in Genomic Sciences, Vol.8 No.2, pp.255-263	view file DOI
2013-01	MiRGator v3.0: A microRNA portal for deep sequencing, expression profiling and mRNA targeting Cho, Sooyoung; Jang, Insu; Jun, Yukyung; Yoon, Suhyeon; Ko, Minjeong; Kwon, Yeajee; Choi, Ikjung; Chang, Hyeshik; Ryu, Daeun; Lee, Byungwook; Kim, V. Narry; Kim, Wankyu; Lee, Sanghyuk Nucleic Acids Research, Vol.41 No.D1, pp.D252-D257	DOI
2014	Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8T Yun, Ji-Hyun; Cho, Yong-Joon; Chun, Jongsik; Hyun, Dong-Wook; Bae, Jin-Woo Standards in Genomic Sciences, Vol.9 No.3, pp.495-504	view file DOI
2014-03	Genome sequence of type strain of Staphylococcus aureus subsp aureus Kim, Bong-Soo; Yi, Hana; Chun, Jongsik; Cha, Chang-Jun Gut Pathogens, Vol.6, p. 6	DOI
2015-10	Complete genome sequence of Mycobacterium tuberculosis K from a Korean high school outbreak, belonging to the Beijing family Han, Seung Jung; Song, Taeksun; Cho, Yong-Joon; Kim, Jong-Seok; Choi, Soo Young; Bang, Hye-Eun; Chun, Jongsik; Bai, Gill-Han; Cho, Sang-Nae; Shin, Sung Jae Standards in Genomic Sciences, Vol.10, p. 78	view file DOI
2018-03	hc-OTU: A fast and accurate method for clustering operational taxonomic units based on homopolymer compaction Park, Seunghyun; Choi, Hyun-soo; Lee, Byunghan; Chun, Jongsik; Won, Joong-Ho; Yoon, Sungroh IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.15 No.2, pp.441-451	DOI
2018-04	UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction Na, Seong-In; Kim, Yeong Ouk; Yoon, Seok-Hwan; Ha, Sung-min; Baek, Inwoo; Chun, Jongsik The Journal of Microbiology, Vol.56 No.4, pp.280-285	DOI
2018-07	HFSP: high speed homology-driven function annotation of proteins Mahlich, Yannick; Steinegger, Martin; Rost, Burkhard; Bromberg, Yana Bioinformatics, Vol.34 No.13, pp.304-312	DOI
2019-03	Genomic characterization of Nocardia seriolae strains isolated from diseased fish Han, Hyun-Ja; Kwak, Min-Jung; Ha, Sung-Min; Yang, Seung-Jo; Kim, Lin Do; Cho, Kyoung-Hee; Kim, Tae-Wook; Cho, Mi Young; Kim, Byung-Yong; Jung, Sung-Hee; Chun, Jongsik MicrobiologyOpen, Vol.8 No.3, p. 656	view file DOI
2019-09	HH-suite3 for fast remote homology detection and deep protein annotation Steinegger, Martin; Meier, Markus; Mirdita, Milot; Voehringer, Harald; Haunsberger, Stephan J.; Soeding, Johannes BMC Bioinformatics, Vol.20 No.1, p. 473	DOI
2019-11	Application of the Whole Genome-Based Bacterial Identification System, TrueBac ID, Using Clinical Isolates That Were Not Identified With Three Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems Ha, Sung-Min; Kim, Chang Ki; Roh, Juhye; Byun, Jung-Hyun; Yang, Seung-Jo; Choi, Seon-Bin; Chun, Jongsik; Yong, Dongeun Annals of Laboratory Medicine, Vol.39 No.6, pp.530-536	view file DOI
2020-05	Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank Steinegger, Martin; Salzberg, Steven L. Genome Biology, Vol.21 No.1, p. 115	DOI
2020-11	Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation Park, Sein; Steinegger, Martin; Cho, Ho-Seong; Chun, Jongsik Frontiers in Microbiology, Vol.11, p. 585622	DOI
2021-05	Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity Kim, Dongwook; Park, Sein; Chun, Jongsik The Journal of Microbiology, Vol.59 No.5, pp.476-480	DOI
2021-07	PredictProtein - Predicting Protein Structure and Function for 29 Years Bernhofer, Michael; Dallago, Christian; Karl, Tim; Satagopam, Venkata; Heinzinger, Michael; Littmann, Maria; Olenyi, Tobias; Qiu, Jiajun; Schuetze, Konstantin; Yachdav, Guy; Ashkenazy, Haim; Ben-Tal, Nir; Bromberg, Yana; Goldberg, Tatyana; Kajan, Laszlo; O'Donoghue, Sean; Sander, Chris; Schafferhans, Andrea; Schlessinger, Avner; Vriend, Gerrit; Mirdita, Milot; Gawron, Piotr; Gu, Wei; Jarosz, Yohan; Trefois, Christophe; Steinegger, Martin; Schneider, Reinhard; Rost, Burkhard Nucleic Acids Research, Vol.49 No.W1, pp.W535-W540	DOI
2021-08	Taxonomic composition and variation in the gut microbiota of laboratory mice Yang, Junwon; Chun, Jongsik Mammalian Genome, Vol.32 No.4, pp.297-310	DOI
2021-09	VicPred: A Vibrio cholerae Genotype Prediction Tool Lee, Imchang; Ha, Sung-Min; Baek, Min-gyung; Kim, Dong Wook; Yi, Hana; Chun, Jongsik Frontiers in Microbiology, Vol.12	DOI
2022-11	Nearest neighbor search on embeddings rapidly identifies distant protein relations Schuetze, Konstantin; Heinzinger, Michael; Steinegger, Martin; Rost, Burkhard Frontiers in Bioinformatics, Vol.2, p. 1033775	DOI
2022-12	Structure-guided isoform identification for the human transcriptome Sommer, Markus J.; Cha, Sooyoung; Varabyou, Ales; Rincon, Natalia; Park, Sukhwan; Minkin, Ilia; Pertea, Mihaela; Steinegger, Martin; Salzberg, Steven L. eLife, Vol.11	DOI
2022-12	Metagenome analysis using the Kraken software suite Lu, Jennifer; Rincon, Natalia; Wood, Derrick E.; Breitwieser, Florian P.; Pockrandt, Christopher; Langmead, Ben; Salzberg, Steven L.; Steinegger, Martin Nature Protocols, Vol.17 No.12, pp.2815-2839	DOI
2023-02	AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms Bordin, Nicola; Sillitoe, Ian; Nallapareddy, Vamsi; Rauer, Clemens; Lam, Su Datt; Waman, Vaishali P.; Sen, Neeladri; Heinzinger, Michael; Littmann, Maria; Kim, Stephanie; Velankar, Sameer; Steinegger, Martin; Rost, Burkhard; Orengo, Christine Communications Biology, Vol.6 No.1, p. 160	DOI
2023-05	Cross-phyla protein annotation by structural prediction and alignment Ruperti, Fabian; Papadopoulos, Nikolaos; Musser, Jacob M.; Mirdita, Milot; Steinegger, Martin; Arendt, Detlev Genome Biology, Vol.24 No.1, p. 113	DOI
2023-10	Clustering predicted structures at the scale of the known protein universe Barrio-Hernandez, Inigo; Yeo, Jingi; Jänes, Jürgen; Mirdita, Milot; Gilchrist, Cameron L. M.; Wein, Tanita; Varadi, Mihaly; Velankar, Sameer; Beltrao, Pedro; Steinegger, Martin Nature, Vol.622 No.7983, pp.637-645	DOI
2024-02	Fast and accurate protein structure search with Foldseek van Kempen, Michel; Kim, Stephanie S.; Tumescheit, Charlotte; Mirdita, Milot; Lee, Jeongjae; Gilchrist, Cameron L. M.; Soeding, Johannes; Steinegger, Martin Nature Biotechnology, Vol.42 No.2, pp.243-246	DOI