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Using Genome-scale Models to Predict Biological Capabilities

Cell, 2015-05, Vol.161 (5), p.971-987

2015

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COBRAme: A computational framework for genome-scale models of metabolism and gene expression

PLoS computational biology, 2018-07, Vol.14 (7), p.e1006302-e1006302

2018

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Computing the functional proteome: recent progress and future prospects for genome-scale models

Current opinion in biotechnology, 2015-08, Vol.34, p.125-134

2015

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Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium

Applied and Environmental Microbiology, 2015-01, Vol.81 (1), p.17-30

2015

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Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Molecular systems biology, 2013, Vol.9 (1), p.693-n/a

2013

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Multi-omic data integration enables discovery of hidden biological regularities

Nature communications, 2016-10, Vol.7 (1), p.13091-13091, Article 13091

2016

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Text-Based Manipulation of the Coherence Threshold

Discourse processes, 2021-07, Vol.58 (5-6), p.549-568

2021

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Processing real-world violations embedded within a fantasy-world narrative

Quarterly journal of experimental psychology (2006), 2018-11, Vol.71 (11), p.2282-2294

2018

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Exploring the spatial gradient effect in narratives

Discourse processes, 2023-08, Vol.60 (7), p.522-533

2023

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Can readers fully adopt the perspective of the protagonist?

Quarterly journal of experimental psychology (2006), 2020-05, Vol.73 (5), p.664-675

2020

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Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

PLoS computational biology, 2019-06, Vol.15 (6), p.e1007066-e1007066

2019

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The genetic basis for adaptation of model-designed syntrophic co-cultures

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006213-e1006213

2019

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Systems biology of the structural proteome

BMC systems biology, 2016-03, Vol.10 (1), p.26-26, Article 26

2016

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Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

Proceedings of the National Academy of Sciences - PNAS, 2015-08, Vol.112 (34), p.10810-10815

2015

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Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

PLoS computational biology, 2016-06, Vol.12 (6), p.e1004998-e1004998

2016

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Processing the Outcomes of Characters' Actions: The Impacts of Character Goals and Situational Context

Discourse processes, 2018-08, Vol.55 (5-6), p.497-509

2018

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Competing Activation during Fantasy Text Comprehension

Scientific studies of reading, 2018-07, Vol.22 (4), p.308-320

2018

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Enhancing Memory Access for Less Skilled Readers

Scientific studies of reading, 2016-11, Vol.20 (6), p.421-435

2016

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Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

Proceedings of the National Academy of Sciences - PNAS, 2017-10, Vol.114 (43), p.11548-11553

2017

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Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

Nature communications, 2014-09, Vol.5 (1), p.4910-4910, Article 4910

2014

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Updating during Reading Comprehension: Why Causality Matters

Journal of experimental psychology. Learning, memory, and cognition, 2013-05, Vol.39 (3), p.854-865

2013

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SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial

Clinical infectious diseases, 2021-06, Vol.72 (12), p.2132-2140

2021

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When prospective information conflicts with current information

Discourse processes, 2024-07, p.1-18

2024

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Coherence Threshold and the Continuity of Processing: The RI-Val Model of Comprehension

Discourse processes, 2016-07, Vol.53 (5-6), p.326-338

2016

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Knowledge Revision Processes in Refutation Texts

Discourse processes, 2014-01, Vol.51 (5-6), p.374-397

2014

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Using Genome-scale Models to Predict Biological Capabilities

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Computing the functional proteome: recent progress and future prospects for genome-scale models

Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium

Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction

Multi-omic data integration enables discovery of hidden biological regularities

Text-Based Manipulation of the Coherence Threshold

Processing real-world violations embedded within a fantasy-world narrative

Exploring the spatial gradient effect in narratives

Can readers fully adopt the perspective of the protagonist?

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

The genetic basis for adaptation of model-designed syntrophic co-cultures

Systems biology of the structural proteome

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

Processing the Outcomes of Characters' Actions: The Impacts of Character Goals and Situational Context

Competing Activation during Fantasy Text Comprehension

Enhancing Memory Access for Less Skilled Readers

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

Updating during Reading Comprehension: Why Causality Matters

SER-109, an Investigational Microbiome Drug to Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial

When prospective information conflicts with current information

Coherence Threshold and the Continuity of Processing: The RI-Val Model of Comprehension

Knowledge Revision Processes in Refutation Texts

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