Software

PAPipe

  • Park N, Kim H, Oh J, Kim J, Heo C, Kim J, PAPipe: a pipeline for comprehensive population genetic analysis, Molecular Biology and Evolution, msae040, 2024
  • Source code

msPIPE

  • Kim H, Sim M, Park N, Kwon K, Kim J, Kim J, msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data, BMC Bioinformatics, 2022
  • Source code

DLEB

  • Wy S, Kwon D, Kwon K, Kim J, DLEB: a web application for building deep learning models in biological research, Nucleic Acids Research, 2022
  • Website

PLR-GEN

  • Sim M, Lee J, Wy S, Park N, Lee D, Kwon D, Kim J, Generation and application of pseudo-long reads for metagenome assembly, GigaScience, 2022
  • Source code

TAMA

  • Sim M, Lee J, Lee D, Kwon D, Kim J, TAMA: Improved metagenomic sequence classification through meta-analysis, BMC Bioinformatics, 21:185, 2020
  • Source code

IMAP

  • Song G, Lee J, Kim J, Kang S, Lee H, Kwon D, Lee D, Lang G, Cherry M, Kim J, Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies, PLoS ONE, 14(8): e0221858, 2019
  • Source code

GMASS

  • Kwon D, Lee J, Kim J, GMASS: a novel measure for genome assembly structural similarity, BMC Bioinformatics, 20:147, 2019
  • Source code

mySyntenyPortal

  • Lee J, Lee D, Sim M, Kwon D, Kim J, Ko Y, Kim J, mySyntenyPortal: an application package to construct websites for synteny block analysis, BMC Bioinformatics, 19:216, doi: 10.1186/s12859-018-2219-x, 2018
  • Source code

INTERSPIA

  • Kwon D, Lee D, Kim J, Lee J, Sim M, and Kim J, INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species, Nucleic Acids Research, gky378​, doi:10.1093/nar/gky378, 2018
  • Website

DESCHRAMBLER

  • Kim J, Farré M, Auvil L, Capitanu B, Larkin DM, Ma J, and Lewin HA, Reconstruction and evolutionary history of eutherian chromosomes, PNAS, published ahead of print, doi:10.1073/pnas.1702012114, 2017
  • Source code​

Synteny Portal

  • Lee J, Hong WY, Cho M, Sim M, Lee D, Ko Y, and Kim J, Synteny Portal: a web-based application portal for synteny block analysis, Nucleic Acids Research, 44(W1):W35-W40;doi:10.1093/nar/gkw310, 2016
  • Website

AGB (Ancestral Genome Browser)​

  • Lee D, Lee J, Hong WY, Jang E, and Kim J, AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes, Journal of KIISE, 42(12):1584-1589, 2015
  • Website

FCMM

  • Lee J, Lee H, Hong WY, Jang E and Kim J, FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples. Journal of Microbiological Methods, 115:121-128, 2015
  • Website

PSAR-Align

  • Kim J and Ma J, PSAR-Align: improving multiple sequence alignment using probabilistic sampling. Bioinformatics, 30(7):1010-1012, 2014
  • Source code
  • Supplementary data

RACA

  • Kim J, Larkin DM, Cai Q, Asan, Zhang Y, Ge R, Auvil L, Capitanu B, Zhang G, Lewin HA, and Ma J, Reference-Assisted Chromosome Assembly. PNAS, 110(5):1785-90, 2013
  • Source code
  • Supplementary website

PSAR

  • Kim J and Ma J, PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Research, 39(15):6359-68, 2011
  • Source code
  • Supplementary data

Indelign

  • Kim J and Sinha S, Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics, 23(3):289-97, 2007
  • Source code
Intelligent Bioinformatics Computing Laboratory since 2012
Dept. of Biomedical Science and Engineering, Konkuk University
Room 406-1 Animal Science Bldg. 120 Neungdong-ro, Gwangjin-gu, Seoul 05029 Korea