An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters

by Stephen A. Ramsey
Published 2016-10-01

An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters

by Stephen A. Ramsey
Published 2015-01-01

Predicting chemotherapy response using a variational autoencoder approach

by Qi Wei, Stephen A. Ramsey
Published 2021-09-01

Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference.

by Meghamala Sinha, Prasad Tadepalli, Stephen A Ramsey
Published 2021-01-01

CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features

by Yao Yao, Zheng Liu, Qi Wei, Stephen A. Ramsey
Published 2019-02-01

Control of signaling in a MAP-kinase pathway by an RNA-binding protein.

by Susanne Prinz, Christine Aldridge, Stephen A Ramsey, R James Taylor, Timothy Galitski
Published 2007-02-01

Vitamin E Deficiency Disrupts Gene Expression Networks during Zebrafish Development

by Brian Head, Stephen A. Ramsey, Chrissa Kioussi, Robyn L. Tanguay, Maret G. Traber
Published 2021-01-01

Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists

by Xiaoxi Dong, Anatoly Yambartsev, Stephen A. Ramsey, Lina D Thomas, Natalia Shulzhenko, Andrey Morgun
Published 2015-01-01

Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists

by Xiaoxi Dong, Anatoly Yambartsev, Stephen A. Ramsey, Lina D Thomas, Natalia Shulzhenko, Andrey Morgun
Published 2015-04-01

Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation.

by Peter S Askovich, Stephen A Ramsey, Alan H Diercks, Kathleen A Kennedy, Theo A Knijnenburg, Alan Aderem
Published 2017-01-01

Prospective evaluation of the lymph node proteome in dogs with multicentric lymphoma supplemented with sulforaphane

by Cyril Parachini‐Winter, Shay Bracha, Stephen A. Ramsey, Liping Yang, Emily Ho, Haley J. Leeper, Kaitlin M. Curran
Published 2020-09-01

Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway.

by Stephen A Ramsey, Yuliya Vengrenyuk, Prashanthi Menon, Irina Podolsky, Jonathan E Feig, Alan Aderem, Edward A Fisher, Elizabeth S Gold
Published 2014-12-01

Urokinase plasminogen activator induces pro-fibrotic/m2 phenotype in murine cardiac macrophages.

by Jessica Meznarich, Laura Malchodi, Deri Helterline, Stephen A Ramsey, Kate Bertko, Tabitha Plummer, Abigail Plawman, Elizabeth Gold, April Stempien-Otero
Published 2013-01-01

An approach for open multivariate analysis of integrated clinical and environmental exposures data

by Karamarie Fecho, Perry Haaland, Ashok Krishnamurthy, Bo Lan, Stephen A. Ramsey, Patrick L. Schmitt, Priya Sharma, Meghamala Sinha, Hao Xu
Published 2021-01-01

Elucidating the transcriptional program of feline injection-site sarcoma using a cross-species mRNA-sequencing approach

by Qi Wei, Stephen A. Ramsey, Maureen K. Larson, Noah E. Berlow, Donasian Ochola, Christopher Shiprack, Amita Kashyap, Bernard Séguin, Charles Keller, Christiane V. Löhr
Published 2019-04-01

Exosomal proteomic signatures correlate with drug resistance and carboplatin treatment outcome in a spontaneous model of canine osteosarcoma

by Marcus A. Weinman, Stephen A. Ramsey, Haley J. Leeper, Jacqueline V. Brady, Andrew Schlueter, Stanislau Stanisheuski, Claudia S. Maier, Tasha Miller, Carl E. Ruby, Shay Bracha
Published 2021-05-01

A Preliminary Proteomic Investigation of Circulating Exosomes and Discovery of Biomarkers Associated with the Progression of Osteosarcoma in a Clinical Model of Spontaneous Disease

by Jacqueline V. Brady, Ryan M. Troyer, Stephen A. Ramsey, Haley Leeper, Liping Yang, Claudia S. Maier, Cheri P. Goodall, Carl E. Ruby, Hassan A.M. Albarqi, Oleh Taratula, Shay Bracha
Published 2018-10-01

Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis

by Amita Kashyap, Adelaide Rhodes, Brent Kronmiller, Josie Berger, Ashley Champagne, Edward W. Davis, Mitchell V. Finnegan, Matthew Geniza, David A. Hendrix, Christiane V. Löhr, Vanessa M. Petro, Thomas J. Sharpton, Jackson Wells, Clinton W. Epps, Pankaj Jaiswal, Brett M. Tyler, Stephen A. Ramsey
Published 2020-02-01

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.

by Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich
Published 2008-03-01

Correction: Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.

by Stephen A. Ramsey, Sandy L. Klemm, Daniel E. Zak, Kathleen A. Kennedy, Vesteinn Thorsson, Bin Li, Mark Gilchrist, Elizabeth S. Gold, Carrie D. Johnson, Vladimir Litvak, Garnet Navarro, Jared C. Roach, Carrie M. Rosenberger, Alistair G. Rust, Natalya Yudkovsky, Alan Aderem, Ilya Shmulevich
Published 2008-04-01