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M. Vaughn · SciRah

Researcher profile · Semantic Scholar

M. Vaughn

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M. Vaughn — researcher profile on SciRah

h-index: 34
Works: 103
Citations: 9,568

Most-cited papers

The B73 Maize Genome: Complexity, Diversity, and Dynamics
P. Schnable, D. Ware, R. Fulton, J. Stein +153 more
2009Science3,949 citations
Semantic Scholar
Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
R. K. Slotkin, M. Vaughn, M. Tanurdžić, Filipe Borges +3 more
2009Cell1,036 citations Open access
Semantic Scholar
The iPlant Collaborative: Cyberinfrastructure for Plant Biology
S. Goff, M. Vaughn, S. McKay, E. Lyons +61 more
2011Frontiers in Plant Science478 citations Open access
Semantic Scholar
The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences
N. Merchant, Eric Lyons, S. Goff, M. Vaughn +3 more
2016PLoS Biology305 citations Open access
Semantic Scholar
Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations[C][W]
S. Eichten, R. Briskine, Jawon Song, Qing Li +9 more
2013The Plant Cell235 citations Open access
Semantic Scholar
Argonaute Slicing Is Required for Heterochromatic Silencing and Spreading
D. V. Irvine, M. Zaratiegui, N. Tolia, Derek B. Goto +4 more
2006Science230 citations
Semantic Scholar
RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome
Qing Li, J. Gent, Gregory J. Zynda, Jawon Song +10 more
2015Proceedings of the National Academy of Sciences of the United States of America210 citations Open access
Semantic Scholar
Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm[W]
A. Waters, I. Makarevitch, S. Eichten, Ruth A. Swanson-Wagner +6 more
2011The Plant Cell208 citations Open access
Semantic Scholar
Jetstream: a self-provisioned, scalable science and engineering cloud environment
C. Stewart, Timothy M. Cockerill, Ian T Foster, David Y. Hancock +8 more
2015Extreme Science and Engineering Discovery Environment207 citations Open access
Semantic Scholar
Araport: the Arabidopsis Information Portal
V. Krishnakumar, M. Hanlon, S. Contrino, Erik S. Ferlanti +13 more
2014Nucleic Acids Res.203 citations Open access
Semantic Scholar
Genetic Perturbation of the Maize Methylome[W]
Qing Li, S. Eichten, Peter Hermanson, Virginia Zaunbrecher +15 more
2014The Plant Cell190 citations Open access
Semantic Scholar
Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons
S. Eichten, N. Ellis, I. Makarevitch, C. Yeh +8 more
2012PLoS Genetics176 citations Open access
Semantic Scholar
Heritable Epigenetic Variation among Maize Inbreds
S. Eichten, Ruth A. Swanson-Wagner, James C. Schnable, A. Waters +9 more
2011PLoS Genetics166 citations Open access
Semantic Scholar
MicroRNA-Targeted and Small Interfering RNA–Mediated mRNA Degradation Is Regulated by Argonaute, Dicer, and RNA-Dependent RNA Polymerase in Arabidopsis[W][OA]
M. Ronemus, M. Vaughn, R. Martienssen
2006The Plant Cell Online164 citations Open access
Semantic Scholar
Genomic Distribution of H3K9me2 and DNA Methylation in a Maize Genome
P. West, Qing Li, Lexiang Ji, S. Eichten +4 more
2014PLoS ONE147 citations Open access
Semantic Scholar
Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species
A. Waters, Paul Bilinski, S. Eichten, M. Vaughn +3 more
2013Proceedings of the National Academy of Sciences of the United States of America130 citations Open access
Semantic Scholar
S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription.
Fei Lan, M. Zaratiegui, J. Villén, M. Vaughn +7 more
2007Molecules and Cells116 citations Open access
Semantic Scholar
Jetstream2: Accelerating cloud computing via Jetstream
David Y. Hancock, Jeremy Fischer, John Michael Lowe, Winona Snapp-Childs +8 more
2021Practice and Experience in Advanced Research Computing115 citations Open access
Semantic Scholar
Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27[W]
I. Makarevitch, S. Eichten, R. Briskine, A. Waters +5 more
2013The Plant Cell101 citations Open access
Semantic Scholar
CENP-B preserves genome integrity at replication forks paused by Retrotransposon LTR
M. Zaratiegui, M. Vaughn, D. V. Irvine, Derek B. Goto +4 more
2010Nature96 citations Open access
Semantic Scholar
Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State
Tae-Jin Lee, Pete E. Pascuzzi, Sharon B. Settlage, Randall W. Shultz +12 more
2010PLoS Genetics82 citations Open access
Semantic Scholar
Software-as-a-Service: The iPlant Foundation API
R. Dooley, M. Vaughn, D. Stanzione, Steve Terry +1 more
201278 citations
Semantic Scholar
Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize1[OPEN]
Qing Li, Jawon Song, P. West, Gregory J. Zynda +3 more
2015Plant Physiology66 citations Open access
Semantic Scholar
Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis.
Faye M. Rosin, N. Watanabe, J. Cacas, Naohiro Kato +10 more
2008The Plant Journal58 citations Open access
Semantic Scholar
Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing.
D. V. Irvine, Derek B. Goto, M. Vaughn, Y. Nakaseko +3 more
2009Genome Research53 citations Open access
Semantic Scholar
An ‘eFP‐Seq Browser’ for visualizing and exploring RNA sequencing data
Alexander Joo-Hyun Sullivan, P. Purohit, Nowlan H. Freese, A. Pasha +13 more
2019The Plant Journal50 citations Open access
Semantic Scholar
Variation in DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues
S. Eichten, M. Vaughn, Peter Hermanson, Nathan M. Springer
201340 citations Open access
Semantic Scholar
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery
V. Krishnakumar, S. Contrino, Chia-Yi Cheng, I. Belyaeva +6 more
2016Plant and Cell Physiology39 citations Open access
Semantic Scholar
Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs
Vamsi Kundeti, S. Rajasekaran, H. Dinh, M. Vaughn +1 more
2010BMC Bioinformatics38 citations Open access
Semantic Scholar
Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips[OPEN]
E. Wear, Jawon Song, Gregory J. Zynda, Chantal LeBlanc +10 more
2017The Plant Cell37 citations Open access
Semantic Scholar
The Fission Yeast Jmj2 Reverses Histone H3 Lysine 4 Trimethylation*
Maite Huarte, Fei Lan, Taesoo Kim, M. Vaughn +4 more
2007Journal of Biological Chemistry36 citations Open access
Semantic Scholar
It's a Small RNA World, After All
M. Vaughn, R. Martienssen
2005Science36 citations
Semantic Scholar
Genomic Distribution of H 3 K 9 me 2 and DNA Methylation in a Maize Genome
P. West, Qing Li, Lexiang Ji, S. Eichten +4 more
201435 citations
Semantic Scholar
Genome-Wide Analysis of the Arabidopsis Replication Timing Program1[OPEN]
L. Concia, A. Brooks, E. Wheeler, Gregory J. Zynda +9 more
2018Plant Physiology34 citations Open access
Semantic Scholar
CyVerse: Cyberinfrastructure for open science
T. Swetnam, P. Antin, Ryan P. Bartelme, Alexander Bucksch +45 more
2023bioRxiv30 citations Open access
Semantic Scholar
Large-scale design and refinement of stable proteins using sequence-only models
Jed Singer, Scott Novotney, D. Strickland, Hugh K. Haddox +20 more
2021bioRxiv30 citations Open access
Semantic Scholar
Finding the right template: RNA Pol IV, a plant-specific RNA polymerase.
M. Vaughn, R. Martienssen
2005Molecules and Cells28 citations Open access
Semantic Scholar
In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts[W][OPEN]
Pete E. Pascuzzi, M. Flores-Vergara, Tae-Jin Lee, B. Sosinski +4 more
2014The Plant Cell23 citations Open access
Semantic Scholar
Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways
Sarah N. Anderson, Gregory J. Zynda, Jawon Song, Zhao-Xue Han +3 more
2018G3: Genes, Genomes, Genetics21 citations Open access
Semantic Scholar
Repliscan: a tool for classifying replication timing regions
Gregory J. Zynda, Jawon Song, L. Concia, E. Wear +3 more
2017BMC Bioinformatics19 citations Open access
Semantic Scholar
Prediction of Whole-Cell Transcriptional Response with Machine Learning
Mohammed Eslami, Amin Espah Borujeni, Hamid Doosthosseini, M. Vaughn +17 more
2021bioRxiv18 citations Open access
Semantic Scholar
Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors
L. Koesterke, J. Koltes, N. Weeks, K. Milfeld +3 more
2014Concurrency and Computation18 citations
Semantic Scholar
iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology
B. Bolduc, Olivier Zablocki, Jia-Rong Guo, A. Zayed +9 more
2021ISME Communications17 citations Open access
Semantic Scholar
Integrating Jupyter into Research Computing Ecosystems: Challenges and Successes in Architecting JupyterHub for Collaborative Research Computing Ecosystems
Joe Stubbs, Julia Looney, Marjo Poindexter, E. Chalhoub +5 more
2020Practice and Experience in Advanced Research Computing16 citations
Semantic Scholar
Optimizing the PCIT algorithm on stampede's Xeon and Xeon Phi processors for faster discovery of biological networks
L. Koesterke, K. Milfeld, M. Vaughn, D. Stanzione +3 more
2013Extreme Science and Engineering Discovery Environment15 citations
Semantic Scholar
Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment[OA]
F. Berger, Xiao-Feng Cao, V. Chandler, L. Dennis +26 more
2012The Plant Cell15 citations Open access
Semantic Scholar
Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop
Breschine Cummins, Justin D. Vrana, Robert C. Moseley, Hamed Eramian +28 more
2022bioRxiv14 citations Open access
Semantic Scholar
Leveraging the national cyberinfrastructure for biomedical research
Richard D. LeDuc, M. Vaughn, John M. Fonner, Michael Sullivan +4 more
2013J. Am. Medical Informatics Assoc.14 citations Open access
Semantic Scholar
Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin1[OPEN]
E. Wheeler, A. Brooks, L. Concia, Daniel L. Vera +8 more
2020Plant Physiology13 citations Open access
Semantic Scholar
The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology1
J. Friesner, S. Assmann, R. Bastow, J. Bailey-Serres +35 more
2017Plant Physiology13 citations Open access
Semantic Scholar

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S. Eichten×11
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Gregory J. Zynda

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