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K. Chougule · SciRah

Researcher profile · Semantic Scholar

K. Chougule

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K. Chougule — researcher profile on SciRah

h-index: 21
Works: 53
Citations: 4,362

Most-cited papers

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Shujun Ou, Weija Su, Yi Liao, K. Chougule +9 more
2019Genome Biology1,366 citations Open access
Semantic Scholar
Ensembl 2024
P. Harrison, M. Amode, Olanrewaju Austine-Orimoloye, A. Azov +94 more
2023Nucleic Acids Research622 citations Open access
Semantic Scholar
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
M. Hufford, Arun S. Seetharam, M. Woodhouse, K. Chougule +42 more
2021Science568 citations Open access
Semantic Scholar
Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
J. Stein, Yeisoo Yu, D. Copetti, D. Zwickl +61 more
2018Nature Genetics474 citations Open access
Semantic Scholar
Rapid evolution of protein diversity by de novo origination in Oryza
Li Zhang, Yan Ren, Tao Yang, Guang-Wei Li +18 more
2019Nature Ecology & Evolution169 citations
Semantic Scholar
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
Andrew D. Yates, James E. Allen, R. Amode, A. Azov +61 more
2021Nucleic Acids Res.153 citations Open access
Semantic Scholar
Gramene 2018: unifying comparative genomics and pathway resources for plant research
M. Tello-Ruiz, S. Naithani, J. Stein, Parul Gupta +35 more
2017Nucleic Acids Res.138 citations Open access
Semantic Scholar
Gramene 2016: comparative plant genomics and pathway resources
M. Tello-Ruiz, J. Stein, Sharon Wei, Justin Preece +28 more
2015Nucleic Acids Res.133 citations Open access
Semantic Scholar
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
M. Tello-Ruiz, S. Naithani, Parul Gupta, Andrew C. Olson +25 more
2020Nucleic Acids Res.101 citations Open access
Semantic Scholar
Gapless assembly of maize chromosomes using long-read technologies
Jianing Liu, Arun S. Seetharam, K. Chougule, Shujun Ou +14 more
2020Genome Biology77 citations Open access
Semantic Scholar
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Yong Zhou, Zhichao Yu, D. Chebotarov, K. Chougule +21 more
2023Nature Communications67 citations Open access
Semantic Scholar
Gramene Database: Navigating Plant Comparative Genomics Resources
Parul Gupta, S. Naithani, M. Tello-Ruiz, K. Chougule +18 more
2016Current Plant Biology56 citations Open access
Semantic Scholar
Effect of sequence depth and length in long-read assembly of the maize inbred NC358
Shujun Ou, Jianing Liu, K. Chougule, A. Fungtammasan +20 more
2020Nature Communications53 citations Open access
Semantic Scholar
Double triage to identify poorly annotated genes in maize: The missing link in community curation
M. Tello-Ruiz, C. Marco, Fei-Man Hsu, R. Khangura +14 more
2019bioRxiv47 citations Open access
Semantic Scholar
SorghumBase: a web-based portal for sorghum genetic information and community advancement
Nicholas Gladman, Andrew C. Olson, Sharon Wei, K. Chougule +16 more
2022Planta38 citations Open access
Semantic Scholar
Era of Gapless Plant Genomes: Innovations in Sequencing and Mapping Technologies Revolutionize Genomics and Breeding
Nicholas Gladman, S. Goodwin, K. Chougule, W. R. McCombie +1 more
2023Current Opinion in Biotechnology35 citations Open access
Semantic Scholar
Gapless assembly of maize chromosomes using long-read technologies
Jianing Liu, Arun S. Seetharam, K. Chougule, Shujun Ou +14 more
2020Genome Biology30 citations Open access
Semantic Scholar
Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length
D. Bhatia, R. Wing, Yeisoo Yu, K. Chougule +4 more
2018Euphytica29 citations
Semantic Scholar
Variant phasing and haplotypic expression from long-read sequencing in maize
Bo Wang, Elizabeth Tseng, P. Baybayan, K. Eng +7 more
2020Communications Biology28 citations Open access
Semantic Scholar
A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset
Yong Zhou, N. Kathiresan, Zhichao Yu, Luis F. Rivera +15 more
2024BMC Biology25 citations Open access
Semantic Scholar
Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes
Bo Wang, Yinping Jiao, K. Chougule, Andrew J. Olson +14 more
2021bioRxiv22 citations Open access
Semantic Scholar
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
Jonathan Cahn, Michael Regulski, J. Lynn, Evan Ernst +18 more
2024bioRxiv17 citations Open access
Semantic Scholar
Sorghum root epigenetic landscape during limiting phosphorus conditions
Nicholas Gladman, B. Hufnagel, M. Regulski, Zhi-Gang Liu +5 more
2021bioRxiv17 citations Open access
Semantic Scholar
Engineering homoeologs provide a fine scale for quantitative traits in polyploid
Eun Song Lee, Jung-Soo Heo, Young-Bang Woo, K. Chougule +23 more
2023Plant Biotechnology Journal15 citations Open access
Semantic Scholar
Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Shujun Ou, Weijia Su, Y. Liao, K. Chougule +9 more
2022Genome Biology12 citations Open access
Semantic Scholar
Gene disruption by structural mutations drives selection in US rice breeding over the last century
Justin N. Vaughn, W. Korani, J. Stein, Jeremy D. Edwards +8 more
2020bioRxiv11 citations Open access
Semantic Scholar
Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes
William G. Voelker, K. Krishnan, K. Chougule, Louie C Alexander +8 more
2022bioRxiv10 citations Open access
Semantic Scholar
Guidelines for gene and genome assembly nomenclature
Ethalinda K. S. Cannon, David C. Molik, Adam J. Wright, Hui-Ting Zhang +3 more
2025Genetics9 citations Open access
Semantic Scholar
Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research.
Andrew C. Olson, S. Kumari, Xuehong Wei, K. Chougule +27 more
2025Nucleic Acids Research9 citations Open access
Semantic Scholar
Low-phosphate-selected Auxenochlorella protothecoides redirects phosphate to essential pathways while producing more biomass
Sang-Hyuck Park, J. Kyndt, K. Chougule, Jeong-Jin Park +1 more
2018PLoS ONE7 citations Open access
Semantic Scholar
Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
J. Stein, Yeisoo Yu, D. Copetti, D. Zwickl +61 more
2018Nature Genetics7 citations Open access
Semantic Scholar
Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud
Fabrice Ntakirutimana, C. Tranchant-Dubreuil, P. Cubry, K. Chougule +5 more
2023G35 citations Open access
Semantic Scholar
High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436.
Bo Wang, K. Chougule, Yin-Ping Jiao, Andrew C. Olson +16 more
2024NAR Genomics and Bioinformatics4 citations Open access
Semantic Scholar
SorghumBase: a knowledgebase for sorghum genomics, phenomics, and stakeholder engagement.
Nicholas Gladman, Andrew C. Olson, S. Kumari, Sharon Wei +20 more
2026Genetics3 citations Open access
Semantic Scholar
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data
Sharon Wei, K. Chougule, Andrew C. Olson, Zhen-Yuan Lu +8 more
2025Database J. Biol. Databases Curation3 citations Open access
Semantic Scholar
Genome sequence assembly and annotation of MATA and MATB strains of Yarrowia lipolytica
Narges Zali, Osama El Demerdash, K. Chougule, Zhen-Yuan Lu +2 more
2025bioRxiv3 citations Open access
Semantic Scholar
The PanOryza pangene catalog of Asian cultivated rice
B. Contreras-Moreira, Eshan Sharma, Shradha Saraf, G. Naamati +25 more
2025Genome Research3 citations Open access
Semantic Scholar
Variant Phasing and Haplotypic Expression from Single-molecule Long-read Sequencing in Maize
Bo Wang, Elizabeth Tseng, P. Baybayan, K. Eng +7 more
2019bioRxiv3 citations Open access
Semantic Scholar
Improved RNA‐seq Workflows Using CyVerse Cyberinfrastructure
K. Chougule, Liya Wang, J. Stein, Xiao-Fei Wang +3 more
2018Current Protocols in Bioinformatics3 citations
Semantic Scholar
A pan-gene catalogue of Asian cultivated rice
B. Contreras-Moreira, Eshan Sharma, Shradha Saraf, G. Naamati +25 more
2025bioRxiv1 citations Open access
Semantic Scholar
HPC-based genome variant calling workflow (HPC-GVCW)
Yong Zhou, N. Kathiresan, Zhichao Yu, L. Rivera +13 more
2023bioRxiv1 citations Open access
Semantic Scholar
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)
Yong Zhou, Zhichao Yu, D. Chebotarov, K. Chougule +21 more
2022bioRxiv1 citations Open access
Semantic Scholar
Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358
Shujun Ou, Jianing Liu, K. Chougule, A. Fungtammasan +20 more
2019bioRxiv1 citations Open access
Semantic Scholar
Unlocking the black pericarp sorghum (Sorghum bicolor (L.) Moench) trait through genome assembly and integrated omics analysis of key genes in 3-deoxyanthocyanidin biosynthesis
Brooklyn C. Schumaker, K. Chougule, Zhen-Yuan Lu, Michael Regulski +4 more
2026BMC Genomics0 citations Open access
Semantic Scholar
Author Correction: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
Jonathan Cahn, Michael Regulski, J. Lynn, Evan Ernst +18 more
2025Nature Communications0 citations Open access
Semantic Scholar
Correction: Double triage to identify poorly annotated genes in maize: The missing link in community curation
M. Tello-Ruiz, Cristina F. Marco, Fei-Man Hsu, R. Khangura +14 more
2024PLoS ONE0 citations Open access
Semantic Scholar
HuffordLab/NAM-genomes: publication.prerelease
M. Hufford, Arun S. Seetharam, M. Woodhouse, K. Chougule +42 more
20210 citations
Semantic Scholar
Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length
D. Bhatia, R. Wing, Yeisoo Yu, K. Chougule +4 more
2018Euphytica0 citations
Semantic Scholar
of and wild rice relatives highlight genetic conservation, turnover and innovation across the genus
J. Stein, Yeisoo Yu, D. Copetti, D. Zwickl +49 more
20180 citations
Semantic Scholar
Tello-RuizGramene2016Comparative.pdf
M. Tello-Ruiz, J. Stein, Sharon Wei, Justin Preece +28 more
20170 citations
Semantic Scholar

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