2ta Coordination and Integration Center

United States

2ta Coordination and Integration Center

United States

Time filter

Source Type

Rouillard A.D.,Mount Sinai School of Medicine | Rouillard A.D.,2ta Coordination and Integration Center | Rouillard A.D.,Illuminating the Druggable Genome Knowledge Management Center | Wang Z.,Mount Sinai School of Medicine | And 5 more authors.
Computational Biology and Chemistry | Year: 2015

With advances in genomics, transcriptomics, metabolomics and proteomics, and more expansive electronic clinical record monitoring, as well as advances in computation, we have entered the Big Data era in biomedical research. Data gathering is growing rapidly while only a small fraction of this data is converted to useful knowledge or reused in future studies. To improve this, an important concept that is often overlooked is data abstraction. To fuse and reuse biomedical datasets from diverse resources, data abstraction is frequently required. Here we summarize some of the major Big Data biomedical research resources for genomics, proteomics and phenotype data, collected from mammalian cells, tissues and organisms. We then suggest simple data abstraction methods for fusing this diverse but related data. Finally, we demonstrate examples of the potential utility of such data integration efforts, while warning about the inherit biases that exist within such data. © 2015 Elsevier Ltd. All rights reserved.


Rouillard A.D.,Mount Sinai School of Medicine | Rouillard A.D.,2ta Coordination and Integration Center | Rouillard A.D.,Illuminating the Druggable Genome Knowledge Management Center | Wang Z.,Mount Sinai School of Medicine | And 5 more authors.
Computational Biology and Chemistry | Year: 2015

With advances in genomics, transcriptomics, metabolomics and proteomics, and more expansive electronic clinical record monitoring, as well as advances in computation, we have entered the Big Data era in biomedical research. Data gathering is growing rapidly while only a small fraction of this data is converted to useful knowledge or reused in future studies. To improve this, an important concept that is often overlooked is data abstraction. To fuse and reuse biomedical datasets from diverse resources, data abstraction is frequently required. Here we summarize some of the major Big Data biomedical research resources for genomics, proteomics and phenotype data, collected from mammalian cells, tissues and organisms. We then suggest simple data abstraction methods for fusing this diverse but related data. Finally, we demonstrate examples of the potential utility of such data integration efforts, while warning about the inherit biases that exist within such data. © 2015 Elsevier Ltd. All rights reserved.


PubMed | Mount Sinai School of Medicine and 2ta Coordination and Integration Center
Type: | Journal: Frontiers in molecular neuroscience | Year: 2017

Adult women are twice as likely as men to suffer from affective and anxiety disorders, although the mechanisms underlying heightened female stress susceptibility are incompletely understood. Recent findings in mouse Nucleus Accumbens (NAc) suggest a role for DNA methylation-driven sex differences in genome-wide transcriptional profiles. However, the role of another epigenetic process-microRNA (miR) regulation-has yet to be explored. We exposed male and female mice to Subchronic Variable Stress (SCVS), a stress paradigm that produces depression-like behavior in female, but not male, mice, and performed next generation mRNA and miR sequencing on NAc tissue. We applied a combination of differential expression, miR-mRNA network and functional enrichment analyses to characterize the transcriptional and post-transcriptional landscape of sex differences in NAc stress response. We find that male and female mice exhibit largely non-overlapping miR and mRNA profiles following SCVS. The two sexes also show enrichment of different molecular pathways and functions. Collectively, our results suggest that males and females mount fundamentally different transcriptional and post-transcriptional responses to SCVS and engage sex-specific molecular processes following stress. These findings have implications for the pathophysiology and treatment of stress-related disorders in women.

Loading 2ta Coordination and Integration Center collaborators
Loading 2ta Coordination and Integration Center collaborators