Mih, Nathan: search on Z-Library

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1

iML1515, a knowledgebase that computes Escherichia coli traits

Monk, Jonathan M, Lloyd, Colton J, Brunk, Elizabeth, Mih, Nathan, Sastry, Anand, King, Zachary, Takeuchi, Rikiya, Nomura, Wataru, Zhang, Zhen, Mori, Hirotada, Feist, Adam M, Palsson, Bernhard O

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 1.77 MB

english, 2017

2

Systems biology of the structural proteome

Brunk, Elizabeth, Mih, Nathan, Monk, Jonathan, Zhang, Zhen, O’Brien, Edward J., Bliven, Spencer E., Chen, Ke, Chang, Roger L., Bourne, Philip E., Palsson, Bernhard O.

Journal:

BMC Systems Biology

Year:

2016

Language:

english

File:

PDF, 3.27 MB

english, 2016

3

Recon3D enables a three-dimensional view of gene variation in human metabolism

Brunk, Elizabeth, Sahoo, Swagatika, Zielinski, Daniel C, Altunkaya, Ali, Dräger, Andreas, Mih, Nathan, Gatto, Francesco, Nilsson, Avlant, Preciat Gonzalez, German Andres, Aurich, Maike Kathrin, Prlić,

Journal:

Nature Biotechnology

Year:

2018

Language:

english

File:

PDF, 6.22 MB

english, 2018

4

Probing the Selectivity and Protein⋅Protein Interactions of a Nonreducing Fungal Polyketide Synthase Using Mechanism-Based Crosslinkers

Bruegger, Joel, Haushalter, Robert W., Vagstad, Anna L., Beld, Joris, Shakya, Gaurav, Mih, Nathan, Townsend, Craig A., Burkart, Michael D., Tsai, Shiou-Chuan

Journal:

Chemistry & Biology

Year:

2014

Language:

english

File:

PDF, 97 KB

english, 2014

5

ssbio: A Python Framework for Structural Systems Biology

Mih, Nathan, Brunk, Elizabeth, Chen, Ke, Catoiu, Edward, Sastry, Anand, Kavvas, Erol, Monk, Jonathan M, Zhang, Zhen, Palsson, Bernhard O, Valencia, Alfonso

Journal:

Year:

2018

Language:

english

File:

PDF, 585 KB

english, 2018

6

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Seif, Yara, Monk, Jonathan M., Mih, Nathan, Tsunemoto, Hannah, Poudel, Saugat, Zuniga, Cristal, Broddrick, Jared, Zengler, Karsten, Palsson, Bernhard O., Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 3.21 MB

2019

7

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Yang, Laurence, Mih, Nathan, Anand, Amitesh, Park, Joon Ho, Tan, Justin, Yurkovich, James T., Monk, Jonathan M., Lloyd, Colton J., Sandberg, Troy E., Seo, Sang Woo, Kim, Donghyuk, Sastry, Anand V., Ph

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 1.63 MB

english, 2019

8

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

Kavvas, Erol S., Catoiu, Edward, Mih, Nathan, Yurkovich, James T., Seif, Yara, Dillon, Nicholas, Heckmann, David, Anand, Amitesh, Yang, Laurence, Nizet, Victor, Monk, Jonathan M., Palsson, Bernhard O.

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.66 MB

english, 2018

9

A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism

Mih, Nathan, Brunk, Elizabeth, Bordbar, Aarash, Palsson, Bernhard O., Punta, Marco

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 5.53 MB

english, 2016

10

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

Broddrick, Jared T., Rubin, Benjamin E., Welkie, David G., Du, Niu, Mih, Nathan, Diamond, Spencer, Lee, Jenny J., Golden, Susan S., Palsson, Bernhard O.

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.07 MB

english, 2016

11

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

Chen, Ke, Gao, Ye, Mih, Nathan, O’Brien, Edward J., Yang, Laurence, Palsson, Bernhard O.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 973 KB

english, 2017

12

Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Fang, Xin, Monk, Jonathan M., Mih, Nathan, Du, Bin, Sastry, Anand V., Kavvas, Erol, Seif, Yara, Smarr, Larry, Palsson, Bernhard O.

Journal:

BMC Systems Biology

Year:

2018

Language:

english

File:

PDF, 1.21 MB

english, 2018

13

Probing the Selectivity and Protein⋅Protein Interactions of a Nonreducing Fungal Polyketide Synthase Using Mechanism-Based Crosslinkers

Bruegger, Joel, Haushalter, Bob, Vagstad, Anna, Shakya, Gaurav, Mih, Nathan, Townsend, Craig A., Burkart, Michael D., Tsai, Shiou-Chuan

Journal:

Chemistry & Biology

Year:

2013

Language:

english

File:

PDF, 2.75 MB

english, 2013

14

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types

Seif, Yara, Monk, Jonathan M., Mih, Nathan, Tsunemoto, Hannah, Poudel, Saugat, Zuniga, Cristal, Broddrick, Jared, Zengler, Karsten, Palsson, Bernhard O., Wallqvist, Anders

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 3.21 MB

english, 2019

15

Expanding the uses of genome‐scale models with protein structures

Mih, Nathan, Palsson, Bernhard O

Journal:

Molecular Systems Biology

Year:

2019

Language:

english

File:

PDF, 3.31 MB

english, 2019

16

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Gao, Ye, Yurkovich, James T, Seo, Sang Woo, Kabimoldayev, Ilyas, Dräger, Andreas, Chen, Ke, Sastry, Anand V, Fang, Xin, Mih, Nathan, Yang, Laurence, Eichner, Johannes, Cho, Byung-Kwan, Kim, Donghyuk,

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 1.82 MB

english, 2018

17

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

Mih, Nathan, Monk, Jonathan M., Fang, Xin, Catoiu, Edward, Heckmann, David, Yang, Laurence, Palsson, Bernhard O.

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 2.00 MB

2020

18

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

Fang, Xin, Sastry, Anand, Mih, Nathan, Kim, Donghyuk, Tan, Justin, Yurkovich, James T., Lloyd, Colton J., Gao, Ye, Yang, Laurence, Palsson, Bernhard O.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 895 KB

english, 2017

19

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

Choudhary, Kumari S., Mih, Nathan, Monk, Jonathan, Kavvas, Erol, Yurkovich, James T., Sakoulas, George, Palsson, Bernhard O.

Journal:

Frontiers in Microbiology

Year:

2018

Language:

english

File:

PDF, 2.84 MB

english, 2018

20

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 793 KB

english, 2018

21

Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment

Rosas‐Lemus, Monica, Minasov, George, Shuvalova, Ludmilla, Wawrzak, Zdzislaw, Kiryukhina, Olga, Mih, Nathan, Jaroszewski, Lukasz, Palsson, Bernhard, Godzik, Adam, Satchell, Karla J. F.

Journal:

Protein Science

Year:

2019

File:

PDF, 4.13 MB

2019

22

Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant

Feher, Victoria A., Schiffer, Jamie M., Mermelstein, Daniel J., Mih, Nathan, Pierce, Levi C.T., McCammon, J. Andrew, Amaro, Rommie E.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 1.91 MB

english, 2018

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