David J Reiss
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Explore the profile of David J Reiss including associated specialties, affiliations and a list of published articles.
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45
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2051
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Recent Articles
11.
Plaisier C, OBrien S, Bernard B, Reynolds S, Simon Z, Toledo C, et al.
Cell Syst
. 2016 Jul;
3(2):172-186.
PMID: 27426982
We developed the transcription factor (TF)-target gene database and the Systems Genetics Network Analysis (SYGNAL) pipeline to decipher transcriptional regulatory networks from multi-omic and clinical patient data, and we applied...
12.
de Lomana A, Schauble S, Valenzuela J, Imam S, Carter W, Bilgin D, et al.
Biotechnol Biofuels
. 2015 Dec;
8:207.
PMID: 26633994
Background: Algae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding of the transcriptional regulatory network...
13.
Turkarslan S, Peterson E, Rustad T, Minch K, Reiss D, Morrison R, et al.
Sci Data
. 2015 May;
2:150010.
PMID: 25977815
Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of tuberculosis (TB) worldwide. The complexity and critical regulatory components of MTB pathogenicity are still poorly understood...
14.
Danziger S, Reiss D, Ratushny A, Smith J, Plaisier C, Aitchison J, et al.
BMC Syst Biol
. 2015 Apr;
9 Suppl 2:S1.
PMID: 25881257
Background: Biclustering is a popular method for identifying under which experimental conditions biological signatures are co-expressed. However, the general biclustering problem is NP-hard, offering room to focus algorithms on specific...
15.
Reiss D, Plaisier C, Wu W, Baliga N
Nucleic Acids Res
. 2015 Apr;
43(13):e87.
PMID: 25873626
The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be...
16.
Minch K, Rustad T, Peterson E, Winkler J, Reiss D, Ma S, et al.
Nat Commun
. 2015 Jan;
6:5829.
PMID: 25581030
Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20-30 s. Here we report genome-wide binding for ~80% of all predicted MTB transcription factors (TFs), and assayed...
17.
Plaisier C, Lo F, Ashworth J, Brooks A, Beer K, Kaur A, et al.
BMC Syst Biol
. 2014 Nov;
8:122.
PMID: 25394904
Background: Expansion of transcription factors is believed to have played a crucial role in evolution of all organisms by enabling them to deal with dynamic environments and colonize new environments....
18.
Ashworth J, Plaisier C, Lo F, Reiss D, Baliga N
PLoS One
. 2014 Sep;
9(9):e107863.
PMID: 25255272
Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are...
19.
Peterson E, Reiss D, Turkarslan S, Minch K, Rustad T, Plaisier C, et al.
Nucleic Acids Res
. 2014 Sep;
42(18):11291-303.
PMID: 25232098
The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability to effectively counteract and even take advantage of the hostile environments of a host. In order to accelerate...
20.
Brooks A, Reiss D, Allard A, Wu W, Salvanha D, Plaisier C, et al.
Mol Syst Biol
. 2014 Jul;
10:740.
PMID: 25028489
Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data-driven models that capture the dynamic interplay of...