Joshua A Lerman
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Explore the profile of Joshua A Lerman including associated specialties, affiliations and a list of published articles.
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15
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2594
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Recent Articles
1.
Ebrahim A, Brunk E, Tan J, OBrien E, Kim D, Szubin R, et al.
Nat Commun
. 2016 Oct;
7:13091.
PMID: 27782110
Rapid growth in size and complexity of biological data sets has led to the 'Big Data to Knowledge' challenge. We develop advanced data integration methods for multi-level analysis of genomic,...
2.
King Z, Lu J, Drager A, Miller P, Federowicz S, Lerman J, et al.
Nucleic Acids Res
. 2015 Oct;
44(D1):D515-22.
PMID: 26476456
Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental...
3.
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard A, Chang R, et al.
Mol Syst Biol
. 2015 Oct;
11(10):831.
PMID: 26467284
No abstract available.
4.
Liu J, OBrien E, Lerman J, Zengler K, Palsson B, Feist A
BMC Syst Biol
. 2014 Sep;
8:110.
PMID: 25227965
Background: Membranes play a crucial role in cellular functions. Membranes provide a physical barrier, control the trafficking of substances entering and leaving the cell, and are a major determinant of...
5.
Monk J, Charusanti P, Aziz R, Lerman J, Premyodhin N, Orth J, et al.
Proc Natl Acad Sci U S A
. 2013 Nov;
110(50):20338-43.
PMID: 24277855
Genome-scale models (GEMs) of metabolism were constructed for 55 fully sequenced Escherichia coli and Shigella strains. The GEMs enable a systems approach to characterizing the pan and core metabolic capabilities...
6.
OBrien E, Lerman J, Chang R, Hyduke D, Palsson B
Mol Syst Biol
. 2013 Oct;
9:693.
PMID: 24084808
Growth is a fundamental process of life. Growth requirements are well-characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive...
7.
Ebrahim A, Lerman J, Palsson B, Hyduke D
BMC Syst Biol
. 2013 Aug;
7:74.
PMID: 23927696
Background: COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an...
8.
Latif H, Lerman J, Portnoy V, Tarasova Y, Nagarajan H, Schrimpe-Rutledge A, et al.
PLoS Genet
. 2013 May;
9(4):e1003485.
PMID: 23637642
The generation of genome-scale data is becoming more routine, yet the subsequent analysis of omics data remains a significant challenge. Here, an approach that integrates multiple omics datasets with bioinformatics...
9.
Fong N, Lerman J, Lam I, Palsson B, Charusanti P
FEMS Microbiol Lett
. 2013 Feb;
342(1):62-9.
PMID: 23432746
The in silico reconstruction of metabolic networks has become an effective and useful systems biology approach to predict and explain many different cellular phenotypes. When simulation outputs do not match...
10.
Nam H, Lewis N, Lerman J, Lee D, Chang R, Kim D, et al.
Science
. 2012 Sep;
337(6098):1101-4.
PMID: 22936779
Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% of its enzymes...