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Computational methods in cell biology (2012)

Asthagiri, Anand R. [Hrsg.] ; Arkin, Adam P.

Amsterdam : Elsevier, Academic Press

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UID:

(DE-627)1617064823

Format: XVI, 410 S., [7] Bl. , Ill., graph. Darst. , 24 cm

ISBN: 9780123884039 , 0123884039

Series Statement: Methods in cell biology 110

Note: Literaturangaben , Principles of model building : an experimentation-aided approach to development of models for signaling networks , Integrated inference and analysis of regulatory networks from multi-level measurements , Swimming upstream : identifying proteomic signals that drive transciptional changes using the interactome and multiple "-Omics" datasets , A framework for modeling the relationship between cellular steady-state and stimulus-responsiveness , Stochastic modeling of cellular networks , Quantifying traction stresses in adherent cells , CellOrganizer : image-derived models of subcellular organization and protein distribution , Spatial modeling of cell signaling networks , Stochastic models of cell protrusion arising from spatiotemporal signaling and adhesion dynamics , Nonparametric variable selection and modeling for spatial and temporal regulatory networks , Quantitative models of the mechanisms that control genome-wide patterns of animal transcription factor binding , Computational analysis of live cell images of the arabidopsis thaliana plant , Multi-scale modeling of tissues using CompuCell3D , Multiscale model of fibrin accumulation on the blood clot surface and platelet dynamincs

Additional Edition: Erscheint auch als Online-Ausgabe Computational methods in cell biology Amsterdam : Elsevier/Academic Press, 2012 9780123884213

Additional Edition: 0123884217

Additional Edition: 9780123884039

Additional Edition: 0123884039

Language: English

Subjects: Biology

RVK:

WC 7700

RVK:

WC 5100

Keywords: Cytologie ; Bioinformatik ; Cytologie ; Mathematisches Modell

URL: Inhaltsverzeichnis

URL: Verlagsangaben

URL: http://www.sciencedirect.com/science/bookseries/0091679X/110

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Fast, cheap and somewhat in control (2006)

Arkin, Adam P. [Verfasser] ; Fletcher, Daniel A. [Mitwirkender] ; SpringerLink (Online service)

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UID:

(DE-101)1098922743

Format: Online-Ressource , online resource.

ISSN: 1474-760X , 1474-760X

In: volume:7

In: number:8

In: day:30

In: month:8

In: year:2006

In: pages:1-6

In: date:8.2006

In: Genome biology, London : BioMed Central, 2000-, 7, Heft 8 (30.8.2006), 1-6, 8.2006, 1474-760X

Language: English

DOI: 10.1186/gb-2006-7-8-114

URN: urn:nbn:de:1111-2016050140059

URL: https://doi.org/10.1186/gb-2006-7-8-114

URL: https://nbn-resolving.org/urn:nbn:de:1111-2016050140059

URL: https://d-nb.info/1098922743/34

URL: http://dx.doi.org/10.1186/gb-2006-7-8-114

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Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data (2023)

Bernstein, David B. [Verfasser] ; Akkas, Batu [Verfasser] ; Price, Morgan N. [Verfasser] ; [et al.]

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UID:

(DE-101)1307613535

Format: Online-Ressource

ISSN: 1744-4292

Content: Abstract: The Escherichia coli genome‐scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision–recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene‐protein‐reaction mapping as a key source of inaccurate predictions. A machine learning approach further identified metabolic fluxes through hydrogen ion exchange and specific central metabolism branch points as important determinants of model accuracy. This work outlines improved practices for the assessment of GEM accuracy with high‐throughput mutant fitness data and highlights promising areas for future model refinement in E. coli and beyond.

In: day:27

In: month:10

In: year:2023

In: extent:14

In: Molecular systems biology, Heidelberg : EMBO Press, [2005]-, (27.10.2023) (gesamt 14), 1744-4292

Language: English

DOI: 10.15252/msb.202311566

URN: urn:nbn:de:101:1-2023102715204192254975

URL: https://doi.org/10.15252/msb.202311566

URL: https://nbn-resolving.org/urn:nbn:de:101:1-2023102715204192254975

URL: https://d-nb.info/1307613535/34

URL: https://doi.org/10.15252/msb.202311566

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Evolution, ecology and the engineered organism: lessons for synthetic biology (2009)

Skerker, Jeffrey M. [Verfasser] ; Lucks, Julius B. [Mitwirkender] ; Arkin, Adam P. [Mitwirkender] ; [et al.]

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UID:

(DE-101)1098937171

Format: Online-Ressource , online resource.

ISSN: 1474-760X , 1474-760X

In: volume:10

In: number:11

In: day:30

In: month:11

In: year:2009

In: pages:1-7

In: date:11.2009

In: Genome biology, London : BioMed Central, 2000-, 10, Heft 11 (30.11.2009), 1-7, 11.2009, 1474-760X

Language: English

DOI: 10.1186/gb-2009-10-11-114

URN: urn:nbn:de:1111-2016050147719

URL: https://doi.org/10.1186/gb-2009-10-11-114

URL: https://nbn-resolving.org/urn:nbn:de:1111-2016050147719

URL: https://d-nb.info/1098937171/34

URL: http://dx.doi.org/10.1186/gb-2009-10-11-114

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OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments (2006)

Price, Morgan N. [Verfasser] ; Arkin, Adam P. [Mitwirkender] ; Alm, Eric J. [Mitwirkender] ; [et al.]

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UID:

(DE-101)108260416X

Format: Online-Ressource , online resource.

ISSN: 1471-2105 , 1471-2105

In: volume:7

In: number:1

In: day:13

In: month:1

In: year:2006

In: pages:1-16

In: date:12.2006

In: BMC bioinformatics, London : BioMed Central, 2000-, 7, Heft 1 (13.1.2006), 1-16, 12.2006, 1471-2105

Language: English

DOI: 10.1186/1471-2105-7-19

URN: urn:nbn:de:1111-2016021626501

URL: https://doi.org/10.1186/1471-2105-7-19

URL: https://nbn-resolving.org/urn:nbn:de:1111-2016021626501

URL: https://d-nb.info/108260416X/34

URL: http://dx.doi.org/10.1186/1471-2105-7-19

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Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli (2008)

Price, Morgan N. [Verfasser] ; Dehal, Paramvir S. [Mitwirkender] ; Arkin, Adam P. [Mitwirkender] ; [et al.]

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UID:

(DE-101)1098930487

Format: Online-Ressource , online resource.

ISSN: 1474-760X , 1474-760X

In: volume:9

In: number:1

In: day:07

In: month:01

In: year:2008

In: pages:1-20

In: date:9.2008

In: Genome biology, London : BioMed Central, 2000-, 9, Heft 1 (07.01.2008), 1-20, 9.2008, 1474-760X

Language: English

DOI: 10.1186/gb-2008-9-1-r4

URN: urn:nbn:de:1111-2016050144243

URL: https://doi.org/10.1186/gb-2008-9-1-r4

URL: https://nbn-resolving.org/urn:nbn:de:1111-2016050144243

URL: https://d-nb.info/1098930487/34

URL: http://dx.doi.org/10.1186/gb-2008-9-1-r4

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Global analysis of host response to induction of a latent bacteriophage (2007)

Osterhout, Robin E. [Verfasser] ; Figueroa, Israel A. [Mitwirkender] ; Keasling, Jay D. [Mitwirkender] ; [et al.]

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UID:

(DE-101)108477738X

Format: Online-Ressource , online resource.

ISSN: 1471-2180 , 1471-2180

In: volume:7

In: number:1

In: day:31

In: month:8

In: year:2007

In: pages:1-12

In: date:12.2007

In: BMC microbiology, London : BioMed Central, 2001-, 7, Heft 1 (31.8.2007), 1-12, 12.2007, 1471-2180

Language: English

DOI: 10.1186/1471-2180-7-82

URN: urn:nbn:de:1111-2016030219281

URL: https://doi.org/10.1186/1471-2180-7-82

URL: https://nbn-resolving.org/urn:nbn:de:1111-2016030219281

URL: https://d-nb.info/108477738X/34

URL: http://dx.doi.org/10.1186/1471-2180-7-82

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Erratum to: Global analysis of host response to induction of a latent bacteriophage (2013)

Osterhout, Robin E. [Verfasser] ; Figueroa, Israel A. [Mitwirkender] ; Keasling, Jay D. [Mitwirkender] ; [et al.]

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UID:

(DE-101)108481711X

Format: Online-Ressource , online resource.

ISSN: 1471-2180 , 1471-2180

In: volume:13

In: number:1

In: day:6

In: month:8

In: year:2013

In: pages:1

In: date:12.2013

In: BMC microbiology, London : BioMed Central, 2001-, 13, Heft 1 (6.8.2013), 1, 12.2013, 1471-2180

Language: English

DOI: 10.1186/1471-2180-13-183

URN: urn:nbn:de:1111-2016030238754

URL: https://doi.org/10.1186/1471-2180-13-183

URL: https://nbn-resolving.org/urn:nbn:de:1111-2016030238754

URL: https://d-nb.info/108481711X/34

URL: http://dx.doi.org/10.1186/1471-2180-13-183

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Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products (2023)

Adams, Jeremy David [Verfasser] ; Sander, Kyle B. [Verfasser] ; Criddle, Craig S. [Verfasser] ; [et al.]

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UID:

(DE-101)1300188391

Format: Online-Ressource, 1 online resource.

ISSN: 1475-2859

In: volume:22

In: number:1

In: day:12

In: month:4

In: year:2023

In: pages:1-16

In: date:12.2023

In: Microbial cell factories, London : Biomed Central, 2002-, 22, Heft 1 (12.4.2023), 1-16, 12.2023, 1475-2859

Language: English

DOI: 10.1186/s12934-023-02064-8

URN: urn:nbn:de:101:1-2023082609141441771349

URL: https://doi.org/10.1186/s12934-023-02064-8

URL: https://nbn-resolving.org/urn:nbn:de:101:1-2023082609141441771349

URL: https://d-nb.info/1300188391/34

URL: https://doi.org/10.1186/s12934-023-02064-8

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Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation (2016)

Zhang, Shuyan [Verfasser] ; Ito, Masakazu [Sonstige] ; Skerker, Jeffrey M. [Sonstige] ; [et al.]

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UID:

(DE-101)1118727223

Format: Online-Ressource , online resource.

ISSN: 1432-0614 , 1432-0614

In: volume:100

In: number:21

In: day:27

In: month:9

In: year:2016

In: pages:9393-9405

In: date:11.2016

In: Applied microbiology and biotechnology, Berlin ; Heidelberg ; New York : Springer, 1975-, 100, Heft 21 (27.9.2016), 9393-9405, 11.2016, 1432-0614

Language: English

DOI: 10.1007/s00253-016-7815-y

URN: urn:nbn:de:1111-201611109942

URL: https://doi.org/10.1007/s00253-016-7815-y

URL: https://nbn-resolving.org/urn:nbn:de:1111-201611109942

URL: https://d-nb.info/1118727223/34

URL: http://dx.doi.org/10.1007/s00253-016-7815-y

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