Publications by authors named "Christopher Bare"

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Profiling lamina specific pyramidal neurons using postmortem human formalin fixed paraffin embedded frontal cortex tissue in combination with digital spatial profiling.
Aleksandra Stanisavljevic, Kyrillos W Ibrahim, Philip H Stavrides, Christopher Bare, Melissa J Alldred

J Neurosci Methods· October 2025

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Hydrologic variation influences stream fish assemblage dynamics through flow regime and drought.
Daniel D Magoulick, Matthew P Dekar, Shawn W Hodges, Mandy K Scott, Michael R Rabalais, Christopher M Bare

Sci Rep· May 2021

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Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Anna Y Lee, Adam D Ewing, Kyle Ellrott, Yin Hu, Kathleen E Houlahan, J Christopher Bare

Genome Biol· November 2018

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Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci.
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Christopher Bare

Hum Mol Genet· June 2018

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Germline contamination and leakage in whole genome somatic single nucleotide variant detection.
Dorota H Sendorek, Cristian Caloian, Kyle Ellrott, J Christopher Bare, Takafumi N Yamaguchi

BMC Bioinformatics· January 2018

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Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci.
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Christopher Bare

Hum Mol Genet· May 2017

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Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.
Justin Guinney, Tao Wang, Teemu D Laajala, Kimberly Kanigel Winner, J Christopher Bare

Lancet Oncol· January 2017

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Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.
Genevera I Allen, Nicola Amoroso, Catalina Anghel, Venkat Balagurusamy, Christopher J Bare

Alzheimers Dement· June 2016

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DREAMTools: a Python package for scoring collaborative challenges.
Thomas Cokelaer, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M Bot

F1000Res· May 2016

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The mPower study, Parkinson disease mobile data collected using ResearchKit.
Brian M Bot, Christine Suver, Elias Chaibub Neto, Michael Kellen, Arno Klein, Christopher Bare

Sci Data· March 2016

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Erratum: Prediction of human population responses to toxic compounds by a collaborative competition.
Federica Eduati, Lara M Mangravite, Tao Wang, Hao Tang, J Christopher Bare

Nat Biotechnol· October 2015

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Prediction of human population responses to toxic compounds by a collaborative competition.
Federica Eduati, Lara M Mangravite, Tao Wang, Hao Tang, J Christopher Bare

Nat Biotechnol· September 2015

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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
Adam D Ewing, Kathleen E Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, J Christopher Bare

Nat Methods· July 2015

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Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting.
Elias Chaibub Neto, J Christopher Bare, Adam A Margolin

PLoS One· June 2015

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Global optimization of somatic variant identification in cancer genomes with a global community challenge.
Paul C Boutros, Adam D Ewing, Kyle Ellrott, Thea C Norman, Kristen K Dang, J Christopher Bare

Nat Genet· April 2014

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Network portal: a database for storage, analysis and visualization of biological networks.
Serdar Turkarslan, Elisabeth J Wurtmann, Wei-Ju Wu, Ning Jiang, J Christopher Bare

Nucleic Acids Res· January 2014

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Parallel evolution of transcriptome architecture during genome reorganization.
Sung Ho Yoon, David J Reiss, J Christopher Bare, Dan Tenenbaum, Min Pan

Genome Res· November 2011

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Niche adaptation by expansion and reprogramming of general transcription factors.
Serdar Turkarslan, David J Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J Christopher Bare

Mol Syst Biol· November 2011

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miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling.
Christopher L Plaisier, J Christopher Bare, Nitin S Baliga

Nucleic Acids Res· July 2011

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GTC: A web server for integrating systems biology data with web tools and desktop applications.
Dan Tenenbaum, J Christopher Bare, Nitin S Baliga

Source Code Biol Med· July 2010

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Integration and visualization of systems biology data in context of the genome.
J Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, Nitin S Baliga

BMC Bioinformatics· July 2010

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Prevalence of transcription promoters within archaeal operons and coding sequences.
Tie Koide, David J Reiss, J Christopher Bare, Wyming Lee Pang, Marc T Facciotti

Mol Syst Biol· September 2009

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A predictive model for transcriptional control of physiology in a free living cell.
Richard Bonneau, Marc T Facciotti, David J Reiss, Amy K Schmid, Min Pan, J Christopher Bare

Cell· December 2007

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The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.
J Christopher Bare, Paul T Shannon, Amy K Schmid, Nitin S Baliga

BMC Bioinformatics· November 2007

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Osteoblast-like cell attachment to and calcification of novel phosphonate-containing polymeric substrates.
Richard A Gemeinhart, Christopher M Bare, Richard T Haasch, Ernest J Gemeinhart

J Biomed Mater Res A· September 2006

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