User profiles for J. Christopher Bare
 | J. Christopher BareSenior Software Engineer Verified email at volparahealth.com Cited by 2424 |
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge …
Background Improvements to prognostic models in metastatic castration-resistant prostate
cancer have the potential to augment clinical trial design and guide treatment strategies. In …
cancer have the potential to augment clinical trial design and guide treatment strategies. In …
[HTML][HTML] A predictive model for transcriptional control of physiology in a free living cell
The environment significantly influences the dynamic expression and assembly of all
components encoded in the genome of an organism into functional biological networks. We have …
components encoded in the genome of an organism into functional biological networks. We have …
[HTML][HTML] Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
The detection of somatic mutations from cancer genome sequences is key to understanding
the genetic basis of disease progression, patient survival and response to therapy. …
the genetic basis of disease progression, patient survival and response to therapy. …
Prevalence of transcription promoters within archaeal operons and coding sequences
Despite the knowledge of complex prokaryotic‐transcription mechanisms, generalized rules,
such as the simplified organization of genes into operons with well‐defined promoters and …
such as the simplified organization of genes into operons with well‐defined promoters and …
Prediction of human population responses to toxic compounds by a collaborative competition
The ability to computationally predict the effects of toxic compounds on humans could help
address the deficiencies of current chemical safety testing. Here, we report the results from a …
address the deficiencies of current chemical safety testing. Here, we report the results from a …
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Background The phenotypes of cancer cells are driven in part by somatic structural variants.
Structural variants can initiate tumors, enhance their aggressiveness, and provide unique …
Structural variants can initiate tumors, enhance their aggressiveness, and provide unique …
Parallel evolution of transcriptome architecture during genome reorganization
…, JC Bare, D Tenenbaum, M Pan, J Slagel… - Genome …, 2011 - genome.cshlp.org
Assembly of genes into operons is generally viewed as an important process during the
continual adaptation of microbes to changing environmental challenges. However, the genome …
continual adaptation of microbes to changing environmental challenges. However, the genome …
Niche adaptation by expansion and reprogramming of general transcription factors
Numerous lineage‐specific expansions of the transcription factor B (TFB) family in archaea
suggests an important role for expanded TFBs in encoding environment‐specific gene …
suggests an important role for expanded TFBs in encoding environment‐specific gene …
Global optimization of somatic variant identification in cancer genomes with a global community challenge
Cancer is a family of diseases caused by somatic genetic mutations. Fundamental questions
remain about the causes of these mutations and their roles in shaping cellular phenotypes 1…
remain about the causes of these mutations and their roles in shaping cellular phenotypes 1…
Integration and visualization of systems biology data in context of the genome
Background High-density tiling arrays and new sequencing technologies are generating
rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization …
rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization …