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J. Drenkow · SciRah

Researcher profile · Semantic Scholar

J. Drenkow

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J. Drenkow — researcher profile on SciRah

h-index: 26
Works: 60
Citations: 38K

Most-cited papers

STAR: ultrafast universal RNA-seq aligner
A. Dobin, Carrie A. Davis, F. Schlesinger, J. Drenkow +5 more
2013Bioinform.22K citations Open access
Semantic Scholar
Landscape of transcription in human cells
S. Djebali, Carrie A. Davis, A. Merkel, A. Dobin +81 more
2012Nature4,999 citations Open access
Semantic Scholar
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
P. Kapranov, Jill Cheng, S. Dike, David A. Nix +18 more
2007Science2,541 citations
Semantic Scholar
A Comparative Encyclopedia of DNA Elements in the Mouse Genome
Feng Yue, Yong Cheng, A. Breschi, J. Vierstra +133 more
2014Nature1,636 citations Open access
Semantic Scholar
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
Jill Cheng, P. Kapranov, J. Drenkow, S. Dike +15 more
2005Science1,206 citations
Semantic Scholar
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.
S. Cawley, S. Bekiranov, H. Ng, P. Kapranov +16 more
2004Cell1,156 citations Open access
Semantic Scholar
Large-Scale Transcriptional Activity in Chromosomes 21 and 22
P. Kapranov, S. Cawley, J. Drenkow, S. Bekiranov +3 more
2002Science877 citations
Semantic Scholar
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.
D. Kampa, Jill Cheng, P. Kapranov, Mark Yamanaka +8 more
2004Genome Research554 citations Open access
Semantic Scholar
Reprogramming of the Macrophage Transcriptome in Response to Interferon-γ and Mycobacterium tuberculosis
S. Ehrt, D. Schnappinger, S. Bekiranov, J. Drenkow +5 more
2001Journal of Experimental Medicine477 citations Open access
Semantic Scholar
Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays.
P. Kapranov, J. Drenkow, Jill Cheng, J. Long +3 more
2005Genome Research315 citations Open access
Semantic Scholar
Comparing genomes within the species Mycobacterium tuberculosis.
M. Kato-Maeda, Jeanne T. Rhee, T. Gingeras, H. Salamon +3 more
2001Genome Research291 citations Open access
Semantic Scholar
University of Birmingham Comparative analysis of the transcriptome across distant species
M. Gerstein, J. Rozowsky, Koon-Kiu Yan, Daifeng Wang +93 more
284 citations
Semantic Scholar
Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays.
T. Gingeras, Ghassan Ghandour, Eugene Wang, A. Berno +6 more
1998Genome Research271 citations Open access
Semantic Scholar
Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells
S. Djebali, J. Lagarde, P. Kapranov, V. Lacroix +34 more
2012PLoS ONE234 citations Open access
Semantic Scholar
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
F. Denoeud, P. Kapranov, C. Ucla, A. Frankish +22 more
2007Genome Research211 citations Open access
Semantic Scholar
Structured RNAs in the ENCODE selected regions of the human genome.
Stefan Washietl, J. S. Pedersen, J. Korbel, Claudia Stocsits +20 more
2007Genome Research195 citations Open access
Semantic Scholar
Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery
Xiaosa Xu, M. Crow, Brian R. Rice, Forrest Li +18 more
2020Developmental Cell188 citations Open access
Semantic Scholar
MyD88 Primes Macrophages for Full-Scale Activation by Interferon-γ yet Mediates Few Responses to Mycobacterium tuberculosis
Shuangping Shi, C. Nathan, D. Schnappinger, J. Drenkow +8 more
2003Journal of Experimental Medicine166 citations Open access
Semantic Scholar
The transcriptional responses of respiratory epithelial cells to Bordetella pertussis reveal host defensive and pathogen counter-defensive strategies.
Christopher E. Belcher, J. Drenkow, Bettina Kehoe, T. Gingeras +4 more
2000Proceedings of the National Academy of Sciences of the United States of America166 citations Open access
Semantic Scholar
Temporal gene regulation during HIV-1 infection of human CD4+ T cells.
Jacques Corbeil, Dennis A. Sheeter, D. Genini, S. Rought +11 more
2001Genome Research117 citations Open access
Semantic Scholar
Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
D. Pervouchine, S. Djebali, A. Breschi, Carrie A. Davis +19 more
2015Nature Communications86 citations Open access
Semantic Scholar
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
J. Rozowsky, Jia-Hao Gao, Beatrice Borsari, Yucheng T. Yang +99 more
2022bioRxiv76 citations Open access
Semantic Scholar
Detection of deleted genomic DNA using a semiautomated computational analysis of GeneChip data.
H. Salamon, M. Kato-Maeda, P. Small, J. Drenkow +1 more
2000Genome Research74 citations Open access
Semantic Scholar
Efficient targeted transcript discovery via array-based normalization of RACE libraries
S. Djebali, P. Kapranov, S. Foissac, J. Lagarde +18 more
2008Nature Methods48 citations Open access
Semantic Scholar
A limited set of transcriptional programs define major cell types
A. Breschi, Manuel Muñoz-Aguirre, Valentin Wucher, Carrie A. Davis +14 more
2019Genome Research35 citations Open access
Semantic Scholar
Dynamics of microRNA expression during mouse prenatal development
Sorena Rahmanian, R. Murad, A. Breschi, Weihua Zeng +17 more
2018Genome Research28 citations Open access
Semantic Scholar
Wet Electrons at the H 2 O / TiO 2 ( 110 ) Surface
Jill Cheng, P. Kapranov, J. Drenkow, S. Dike +15 more
200823 citations
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
Transcriptional Maps of 10 Human Chromosomes at
Jill Cheng, P. Kapranov, J. Drenkow, S. Dike +15 more
200820 citations
Semantic Scholar
Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.
A. Willingham, Sujit Dike, Jill Cheng, J. Manak +14 more
2006Cold Spring Harbor Symposia on Quantitative Biology20 citations Open access
Semantic Scholar
HIV regulation of the IL‐7R: a viral mechanism for enhancing HIV‐1 replication in human macrophages in vitro
Ming-Jie Zhang, J. Drenkow, Carla S. R. Lankford, D. M. Frucht +6 more
2006Journal of Leukocyte Biology19 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
SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
Mikio Shiga, S. Seno, Makoto Onizuka, H. Matsuda +313 more
2020bioRxiv15 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
A limited set of transcriptional programs define major histological types and provide the molecular basis for a cellular taxonomy of the human body
A. Breschi, Manuel Muñoz-Aguirre, Valentin Wucher, Carrie A. Davis +14 more
2019bioRxiv3 citations Open access
Semantic Scholar
SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data
Liya Wang, Zhen-Yuan Lu, M. Delabastide, P. Van Buren +17 more
2019bioRxiv3 citations Open access
Semantic Scholar
Magnitude and specificity of temporal gene expression during HIV-1 infection of a CD4+ T cell
Jacques Corbeil, Dennis Sheeter, Steffney Rought, Pin-Yi Du +7 more
1999Nature Genetics3 citations
Semantic Scholar
Multi-tissue integrative analysis of personal epigenomes
J. Rozowsky, J. Drenkow, Yucheng T. Yang, Gamze Gursoy +107 more
20212 citations
Semantic Scholar
Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud
Liya Wang, Zhen-Yuan Lu, M. Delabastide, P. Van Buren +17 more
2020Frontiers in Plant Science2 citations Open access
Semantic Scholar
Enhanced Transcriptome Maps from Multiple Mouse Tissues Reveal Evolutionary Constraint in Gene Expression for Thousands of Genes
D. Pervouchine, S. Djebali, A. Breschi, Carrie A. Davis +19 more
2014bioRxiv2 citations Open access
Semantic Scholar
Transcriptome of Human Chromosomes 21 and 22 Novel RNAs Identified From an In-Depth Analysis of the data
D. Kampa, Jill Cheng, P. Kapranov, Mark Yamanaka +8 more
20042 citations
Semantic Scholar
Evidence for transcript networks composed of chimeric RNAs in human cells
S. Djebali, J. Lagarde, P. Kapranov, V. Lacroix +38 more
20171 citations
Semantic Scholar
Variation in Novel Exons (RACEfrags) of the MECP2 Gene in Rett Syndrome Patients and Controls
P. Makrythanasis, P. Kapranov, L. Bartoloni, A. Reymond +11 more
2009Human Mutation1 citations Open access
Semantic Scholar
Global mapping of functionally-important and regulatory regions on human chromosomes 21 and 22 reveal novel regulatory networks in the human genome
D. Kampa, P. Kapranov, S. Cawley, S. Bekiranov +14 more
20031 citations
Semantic Scholar
tuberculosis Mycobacterium Comparing Genomes within the Species
M. Kato-Maeda, Jeanne T. Rhee, T. Gingeras, H. Salamon +3 more
20011 citations
Semantic Scholar
Magnitude and specificity of temporal gene expression during HIV-1 infection of a CD4+ T cell
J. Corbeil, Dennis A. Sheeter, S. Rought, Pin-Yi Du +7 more
19991 citations
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
Author Correction: Perspectives on ENCODE
F. Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian +496 more
2022Nature0 citations Open access
Semantic Scholar
Multi-tissue integrative analysis of personal epigenomes
J. Rozowsky, J. Drenkow, Yucheng T. Yang, Gamze Gursoy +91 more
20210 citations
Semantic Scholar
Decision letter: A δ-cell subpopulation with a pro-β-cell identity contributes to efficient age-independent recovery in a zebrafish model of diabetes
Claudio Andrès Carril Pardo, L. Massoz, M. Dupont, D. Bergemann +216 more
20210 citations Open access
Semantic Scholar

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