Daehwan Kim

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Steven SalzbergBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at jhu.edu
Chanhee ParkAmazon Web ServicesVerified email at amazon.com
Geo PerteaData/Software Engineer, Lieber Institute for Brain DevelopmentVerified email at jhu.edu
Cole TrapnellAssociate Professor, Dept. of Genome Sciences, University of WashingtonVerified email at uw.edu
Harold PimentelAssistant Professor, UCLAVerified email at ucla.edu
Joseph M. PaggiMIT, PostdocVerified email at mit.edu
Ben LangmeadProfessor of Computer Science, Johns Hopkins UniversityVerified email at cs.jhu.edu
Adam RobertsGoogle DeepMindVerified email at google.com
Lior PachterBren Professor of Computational Biology, CaltechVerified email at caltech.edu
David R KelleyCalico LabsVerified email at calicolabs.com
Loyal A. GoffJohns Hopkins Institute of Genetic MedicineVerified email at jhmi.edu
John RinnProfessor University of Colorado Boulder BioFrontiersVerified email at colorado.edu
Mihaela PerteaAssociate Professor, Johns Hopkins UniversityVerified email at jhu.edu
Jeff LeekChief Data Officer, VP, and J Orin Edson Foundation Professor, Fred Hutchinson Cancer CenterVerified email at fredhutch.org
Li SongDepartment of Biomedical Data Science, Dartmouth CollegeVerified email at dartmouth.edu
Micah ThorntonAssistant Professor of Mathematics, Texas Woman's UniversityVerified email at smu.edu
Yun (Leo) ZhangModernaVerified email at modernatx.com
Florian P BreitwieserPrincipal Software Engineer at SOPHiA GeneticsVerified email at jhu.edu
Lenette LuUTSWVerified email at utsouthwestern.edu
Pei LuThe University of Texas Southwestern Medical CenterVerified email at utsouthwestern.edu

Daehwan Kim

Omphalos Lifesciences Inc

Verified email at omphaloslifesci.com - Homepage

L++Human Code E. coli Code Life Design Life Sciences


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HISAT: a fast spliced aligner with low memory requirements D Kim, B Langmead, SL Salzberg Nature methods 12 (4), 357-360, 2015	22393	2015
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions D Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, SL Salzberg Genome biology 14 (4), R36, 2013	14137	2013
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ... Nature protocols 7 (3), 562-578, 2012	13863	2012
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype D Kim, JM Paggi, C Park, C Bennett, SL Salzberg Nature biotechnology 37 (8), 907-915, 2019	13127	2019
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown M Pertea, D Kim, GM Pertea, JT Leek, SL Salzberg Nature protocols 11 (9), 1650-1667, 2016	6483	2016
Centrifuge: rapid and sensitive classification of metagenomic sequences D Kim, L Song, FP Breitwieser, SL Salzberg Genome research 26 (12), 1721-1729, 2016	1613	2016
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts D Kim, SL Salzberg Genome biology 12 (8), R72, 2011	958	2011
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N Y Zhang, C Park, C Bennett, M Thornton, D Kim Genome Research 31 (7), 1290-1295, 2021	304	2021
BNT162b2-induced neutralizing and non-neutralizing antibody functions against SARS-CoV-2 diminish with age TA Bates, P Lu, YJ Kang, D Schoen, M Thornton, SK McBride, C Park, ... Cell reports 41 (4), 2022	40	2022
HISAT2: graph-based alignment of next-generation sequencing reads to a population of genomes D Kim, B Langmead, S Salzberg	28	2017
Hisat-genotype: Next generation genomic analysis platform on a personal computer D Kim, JM Paggi, S Salzberg BioRxiv, 266197, 2018	25	2018
HISAT: hierarchical indexing for spliced alignment of transcripts D Kim, B Langmead, SL Salzberg BioRxiv, 012591, 2014	13	2014
Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms A Cox, C Park, P Koduru, K Wilson, O Weinberg, W Chen, R García, ... Bioinformatics 38 (5), 1420-1426, 2022	12	2022
Graph-based 683 genome alignment and genotyping with HISAT2 and HISAT-genotype D Kim, JM Paggi, C Park, C Bennett, SL Salzberg Nat. 684 Biotechnol 37 (907-915), 685, 2019	11	2019
Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia A Pallavajjala, D Kim, T Li, G Ghiaur, RJ Jones, KH Burns, SL Salzberg, ... Leukemia & lymphoma 59 (5), 1231-1238, 2018	11	2018
The novel fusion transcript NR5A2‐KLHL29FT is generated by an insertion at the KLHL29 locus Z Sun, X Ke, SL Salzberg, D Kim, V Antonescu, Y Cheng, B Huang, ... Cancer 123 (9), 1507-1515, 2017	6	2017
HISAT-3N: a rapid and accurate three-nucleotide sequence aligner Y Zhang, C Park, C Bennett, M Thornton, D Kim bioRxiv, 2020.12. 15.422906, 2020	4	2020
SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers C Bennett, M Thornton, C Park, G Henry, Y Zhang, V Malladi, D Kim Bioinformatics 38 (7), 1830-1837, 2022	3	2022
MultiQC: summarize analysis results for multiple tools and samples in a single report D Kim, JM Paggi, C Park, C Bennett, SL Salzberg Nat Biotechnol 37, 907-15, 2019	3	2019
TReNCo: Topologically associating domain (TAD) aware regulatory network construction VM Christopher Bennett, Viren Amin, Daehwan Kim, Murat Cobanoglu F1000Research 11 (426), 2022		2022

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