Sotabase

Career

· Professor, University of Cincinnati2023–
· Associate Professor, University of Cincinnati2018–2023
· Online Master Of Science In Sport Administration (MSSA) Program Coordinator, University of Cincinnati2017–
· Asst. Professor Sport Administration, University of Cincinnati2013–2018
· Annual Adj. Professor, University of Cincinnati2009–2013

Publications (65)

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Nature Protocols · 2012
11,688
cited
A whole-genome assembly of the domestic cow, Bos taurus
Genome Biology · 2009
1,123
cited
Effective gene expression prediction from sequence by integrating long-range interactions
Nature Methods · 2021
990
cited
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
bioRxiv · 2015
906
cited
Quake: quality-aware detection and correction of sequencing errors
Genome Biology · 2010
628
cited
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Genome Research · 2011
545
cited
Transposable elements reveal a stem cell-specific class of long noncoding RNAs
Genome Biology · 2012
507
cited
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
Nature Structural &Molecular Biology · 2014
501
cited
Sequential regulatory activity prediction across chromosomes with convolutional neural networks
bioRxiv · 2017
453
cited
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
Cell · 2013
437
cited
Long noncoding RNAs regulate adipogenesis
Proceedings of the National Academy of Sciences of the United States of America · 2013
406
cited
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
BMC Genomics · 2008
303
cited
Predicting 3D genome folding from DNA sequence with Akita
Nature Methods · 2020
237
cited
Widespread RNA binding by chromatin-associated proteins
Genome Biology · 2016
227
cited
Cross-species regulatory sequence activity prediction
bioRxiv · 2019
203
cited
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning.
Cell Systems · 2020
185
cited
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation
bioRxiv · 2023
175
cited
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
Nucleic Acids Research · 2011
174
cited
Topological Organization of Multi-chromosomal Regions by Firre
Nature Structural & Molecular Biology · 2014
162
cited
Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
Genome Research · 2019
158
cited
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David Kelley | Researcher Profile | Sotabase | Sotabase