Markus W Covert: search on Z-Library

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1

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Jonathan R. Karr, Jayodita C. Sanghvi, Derek N. Macklin, Miriam V. Gutschow, Jared M. Jacobs, Benjamin Bolival Jr., Nacyra Assad-Garcia, John I. Glass, Markus W. Covert

Journal:

Year:

2012

Language:

english

File:

PDF, 1.13 MB

english, 2012

2

High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells

Regot, Sergi, Hughey, Jacob J., Bajar, Bryce T., Carrasco, Silvia, Covert, Markus W.

Journal:

Year:

2014

Language:

english

File:

PDF, 3.87 MB

english, 2014

3

Metabolic modelling of microbes: the flux-balance approach

Jeremy S. Edwards, Markus Covert, Bernhard Palsson

Journal:

Environmental Microbiology

Year:

2002

Language:

english

File:

PDF, 278 KB

english, 2002

4

In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans

Kaleta, Christoph, de Figueiredo, Luís F., Werner, Sarah, Guthke, Reinhard, Ristow, Michael, Schuster, Stefan, Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 604 KB

english, 2011

5

Live-cell measurements of kinase activity in single cells using translocation reporters

Kudo, Takamasa, Jeknić, Stevan, Macklin, Derek N, Akhter, Sajia, Hughey, Jacob J, Regot, Sergi, Covert, Markus W

Journal:

Nature Protocols

Year:

2017

Language:

english

File:

PDF, 2.50 MB

english, 2017

6

Deep learning for cellular image analysis

Moen, Erick, Bannon, Dylan, Kudo, Takamasa, Graf, William, Covert, Markus, Van Valen, David

Journal:

Year:

2019

Language:

english

File:

PDF, 11.08 MB

english, 2019

7

Accelerated discovery via a whole-cell model

Sanghvi, Jayodita C, Regot, Sergi, Carrasco, Silvia, Karr, Jonathan R, Gutschow, Miriam V, Bolival, Benjamin, Covert, Markus W

Journal:

Year:

2013

Language:

english

File:

PDF, 639 KB

english, 2013

8

Functional Modules, Structural Topology, and Optimal Activity in Metabolic Networks

Resendis-Antonio, Osbaldo, Hernández, Magdalena, Mora, Yolanda, Encarnación, Sergio, Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 729 KB

english, 2012

9

High-resolution imaging and computational analysis of haematopoietic cell dynamics in vivo

Koechlein, Claire S., Harris, Jeffrey R., Lee, Timothy K., Weeks, Joi, Fox, Raymond G., Zimdahl, Bryan, Ito, Takahiro, Blevins, Allen, Jung, Seung-Hye, Chute, John P., Chourasia, Amit, Covert, Markus

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 2.45 MB

english, 2016

10

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

Tay, Savaş, Hughey, Jacob J., Lee, Timothy K., Lipniacki, Tomasz, Quake, Stephen R., Covert, Markus W.

Journal:

Year:

2010

Language:

english

File:

PDF, 883 KB

english, 2010

11

A Whole Cell Model of Mycoplasma Genitalium Elucidates Mechanisms of Bacterial Replication

Karr, Jonathan R., Sanghvi, Jayodita C., Jacobs, Jared M., Macklin, Derek N., Covert, Markus W.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 75 KB

english, 2012

12

Toward a Whole Cell Model of Mycoplasma Genitalium

Karr, Jonathan R., Sanghvi, Jayodita C., Jacobs, Jared M., Covert, Markus W.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 33 KB

english, 2011

13

The future of whole-cell modeling

Macklin, Derek N, Ruggero, Nicholas A, Covert, Markus W

Journal:

Current Opinion in Biotechnology

Year:

2014

Language:

english

File:

PDF, 286 KB

english, 2014

14

Integrating high-throughput and computational data elucidates bacterial networks

Palsson, Bernhard O., Covert, Markus W., Knight, Eric M., Reed, Jennifer L., Herrgard, Markus J.

Journal:

Year:

2004

Language:

english

File:

PDF, 885 KB

english, 2004

15

Computational Systems Biology || Integrated Regulatory and Metabolic Models

Covert, Markus W.

Year:

2006

Language:

english

File:

PDF, 164 KB

english, 2006

16

WholeCellViz: data visualization for whole-cell models

Lee, Ruby, Karr, Jonathan R, Covert, Markus W

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1017 KB

english, 2013

17

NF-κB signaling dynamics is controlled by a dose-sensing autoregulatory loop

DeFelice, Mialy M., Clark, Helen R., Hughey, Jacob J., Maayan, Inbal, Kudo, Takamasa, Gutschow, Miriam V., Covert, Markus W., Regot, Sergi

Journal:

Science Signaling

Year:

2019

Language:

english

File:

PDF, 1.54 MB

english, 2019

18

Techniques for Studying Decoding of Single Cell Dynamics

Jeknić, Stevan, Kudo, Takamasa, Covert, Markus W.

Journal:

Frontiers in Immunology

Year:

2019

Language:

english

File:

PDF, 2.30 MB

english, 2019

19

Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation

Lane, Keara, Van Valen, David, DeFelice, Mialy M., Macklin, Derek N., Kudo, Takamasa, Jaimovich, Ariel, Carr, Ambrose, Meyer, Tobias, Pe'er, Dana, Boutet, Stéphane C., Covert, Markus W.

Journal:

Year:

2017

Language:

english

File:

PDF, 3.20 MB

english, 2017

20

The Enemy of My Enemy: New Insights Regarding BacteriophageâMammalian Cell Interactions

Bodner, Katie, Melkonian, Arin L., Covert, Markus W.

Journal:

Trends in Microbiology

Year:

2020

File:

PDF, 509 KB

2020

21

A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli

Gelens, Lendert, Hill, Lydia, Vandervelde, Alexandra, Danckaert, Jan, Loris, Remy, Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.15 MB

english, 2013

22

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

Van Valen, David A., Kudo, Takamasa, Lane, Keara M., Macklin, Derek N., Quach, Nicolas T., DeFelice, Mialy M., Maayan, Inbal, Tanouchi, Yu, Ashley, Euan A., Covert, Markus W., Meier-Schellersheim, Mar

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 2.47 MB

english, 2016

23

Cells Respond Digitally to Variation in Signal Intensity via Stochastic Activation of NF-κB

Tay, Savas, Hughey, Jake, Lee, Tim K., Covert, Markus, Quake, Stephen R.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 55 KB

english, 2010

24

Computational modeling of mammalian signaling networks

Jacob J. Hughey, Timothy K. Lee, Markus W. Covert

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2010

Language:

english

File:

PDF, 313 KB

english, 2010

25

Metabolic modeling of microbial strains in silico

Markus W. Covert, Christophe H. Schilling, Iman Famili, Jeremy S. Edwards, Igor I. Goryanin, Evgeni Selkov, Bernhard O. Palsson

Journal:

Trends in Biochemical Sciences

Year:

2001

Language:

english

File:

PDF, 137 KB

english, 2001

26

A dynamic network of transcription in LPS-treated human subjects

Junhee Seok, Wenzhong Xiao, Lyle L Moldawer, Ronald W Davis, Markus W Covert

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 5.73 MB

english, 2009

27

Incorporation of flexible objectives and time-linked simulation with flux balance analysis

Birch, Elsa W., Udell, Madeleine, Covert, Markus W.

Journal:

Journal of Theoretical Biology

Year:

2014

Language:

english

File:

PDF, 1.30 MB

english, 2014

28

The international society for the study of individual differences (ISSID)

Birch, Elsa W., Udell, Madeleine, Covert, Markus W.

Journal:

Personality and Individual Differences

Year:

1991

Language:

english

File:

PDF, 107 KB

english, 1991

29

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation

Lequieu, Joshua, Chakrabarti, Anirikh, Nayak, Satyaprakash, Varner, Jeffrey D., Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.39 MB

english, 2011

30

Simultaneous Cross-Evaluation of Heterogeneous E. coli Datasets via Mechanistic Simulation

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 44 KB

english, 2019

31

Engineered Fluorescent E.Â coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages

Bodner, Katie, Melkonian, Arin L., Barth, Angela I.M., Kudo, Takamasa, Tanouchi, Yu, Covert, Markus W.

Journal:

Year:

2020

Language:

english

File:

PDF, 1.57 MB

english, 2020

32

Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression

Miller-Jensen, Kathryn, Skupsky, Ron, Shah, Priya S., Arkin, Adam P., Schaffer, David V., Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

33

NetworkPainter: dynamic intracellular pathway animation in Cytobank

Karr, Jonathan R, Guturu, Harendra, Chen, Edward Y, Blair, Stuart L, Irish, Jonathan M, Kotecha, Nikesh, Covert, Markus W

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1.76 MB

english, 2015

34

Regulation of Gene Expression in Flux Balance Models of Metabolism

MARKUS W. COVERT, CHRISTOPHE H. SCHILLING, BERNHARD PALSSON

Journal:

Journal of Theoretical Biology

Year:

2001

Language:

english

File:

PDF, 806 KB

english, 2001

35

The virus as metabolic engineer

Nathaniel D. Maynard, Miriam V. Gutschow, Elsa W. Birch, Markus W. Covert

Journal:

Biotechnology Journal

Year:

2010

Language:

english

File:

PDF, 407 KB

english, 2010

36

Simulating a Living Cell

Covert, Markus W.

Journal:

Scientific American

Year:

2013

Language:

english

File:

PDF, 1.15 MB

english, 2013

37

Reconstruction of microbial transcriptional regulatory networks

Markus J Herrgård, Markus W Covert, Bernhard Ø Palsson

Journal:

Current Opinion in Biotechnology

Year:

2004

Language:

english

File:

PDF, 267 KB

english, 2004

38

High-throughput, single-cell NF-κB dynamics

Timothy K Lee, Markus W Covert

Journal:

Current Opinion in Genetics & Development

Year:

2010

Language:

english

File:

PDF, 373 KB

english, 2010

39

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

Kim, Yoo-Ah, Wuchty, Stefan, Przytycka, Teresa M., Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 794 KB

english, 2011

40

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology

Tanouchi, Yu, Covert, Markus W., Lee, Sang Yup

Journal:

Year:

2017

Language:

english

File:

PDF, 1.63 MB

english, 2017

41

Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level

Gutschow, Miriam V., Mason, John C., Lane, Keara M., Maayan, Inbal, Hughey, Jacob J., Bajar, Bryce T., Amatya, Debha N., Valle, Sean D., Covert, Markus W., Edelstein-Keshet, Leah

Journal:

Molecular Biology of the Cell

Year:

2019

Language:

english

File:

PDF, 2.27 MB

english, 2019

42

Competing pathways control host resistance to virus via tRNA modification and programmed ribosomal frameshifting

Maynard, Nathaniel D, Macklin, Derek N, Kirkegaard, Karla, Covert, Markus W

Journal:

Molecular Systems Biology

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

43

The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation

Vaggi, Federico, Disanza, Andrea, Milanesi, Francesca, Di Fiore, Pier Paolo, Menna, Elisabetta, Matteoli, Michela, Gov, Nir S., Scita, Giorgio, Ciliberto, Andrea, Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.84 MB

english, 2011

44

Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis

Lee, Yun, Chen, Fang, Gallego-Giraldo, Lina, Dixon, Richard A., Voit, Eberhard O., Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1008 KB

english, 2011

45

Deep learning for cellular image analysis

Moen, Erick, Bannon, Dylan, Kudo, Takamasa, Graf, William, Covert, Markus, Van Valen, David

Journal:

Year:

2019

File:

PDF, 11.08 MB

2019

46

Multiscale models of infection

Talman, Lee, Agmon, Eran, Peirce, Shayn M., Covert, Markus W.

Journal:

Current Opinion in Biomedical Engineering

Year:

2019

Language:

english

File:

PDF, 654 KB

english, 2019

47

Constraints-based models: Regulation of Gene Expression Reduces the Steady-state Solution Space

MARKUS W. COVERT, BERNHARD O. PALSSON

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 1.47 MB

english, 2003

48

Neuron-to-neuron transmission of α-synuclein fibrils through axonal transport

Freundt, Eric C., Maynard, Nate, Clancy, Eileen K., Roy, Shyamali, Bousset, Luc, Sourigues, Yannick, Covert, Markus, Melki, Ronald, Kirkegaard, Karla, Brahic, Michel

Journal:

Annals of Neurology

Year:

2012

Language:

english

File:

PDF, 401 KB

english, 2012

49

Towards a whole-cell modeling approach for synthetic biology

Purcell, Oliver, Jain, Bonny, Karr, Jonathan R., Covert, Markus W., Lu, Timothy K.

Journal:

Chaos An Interdisciplinary Journal of Nonlinear Science

Year:

2013

Language:

english

File:

PDF, 2.94 MB

english, 2013

50

Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics

Peng, Jyh-Ying, Lin, Chung-Chih, Chen, Yen-Jen, Kao, Lung-Sen, Liu, Young-Chau, Chou, Chung-Chien, Huang, Yi-Hung, Chang, Fang-Rong, Wu, Yang-Chang, Tsai, Yuh-Show, Hsu, Chun-Nan, Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.84 MB

english, 2011

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