Martha L Bulyk: search on Z-Library

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1

MEDEA: analysis of transcription factor binding motifs in accessible chromatin

Mariani, Luca, Weinand, Kathryn, Gisselbrecht, Stephen S., Bulyk, Martha L.

Journal:

Genome Research

Year:

2020

File:

PDF, 2.98 MB

2020

2

A Transcriptional Signature and Common Gene Networks Link Cancer with Lipid Metabolism and Diverse Human Diseases

Heather A. Hirsch, Dimitrios Iliopoulos, Amita Joshi, Yong Zhang, Savina A. Jaeger, Martha Bulyk, Philip N. Tsichlis, X. Shirley Liu, Kevin Struhl

Journal:

Year:

2010

Language:

english

File:

PDF, 1.90 MB

english, 2010

3

Non-Cooperative Interactions Between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses To Environmental Inputs

Giorgetti, Luca, Siggers, Trevor, Tiana, Guido, Caprara, Greta, Notarbartolo, Samuele, Corona, Teresa, Pasparakis, Manolis, Milani, Paolo, Bulyk, Martha L., Natoli, Gioacchino

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 34 KB

english, 2010

4

[Methods in Enzymology] DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols Volume 410 || [13] Analysis of Sequence Specificities of DNA‐Binding Proteins with Protein Binding Microarrays

Bulyk, Martha L.

Year:

2006

Language:

english

File:

PDF, 424 KB

english, 2006

5

DNA microarray technologies for measuring protein–DNA interactions

Journal:

Current Opinion in Biotechnology

Year:

2006

Language:

english

File:

PDF, 422 KB

english, 2006

6

The Vibrio harveyi master quorum-sensing regulator, LuxR, a TetR-type protein is both an activator and a repressor: DNA recognition and binding specificity at target promoters

Audra J. Pompeani, Joseph J. Irgon, Michael F. Berger, Martha L. Bulyk, Ned S. Wingreen, Bonnie L. Bassler

Journal:

Molecular Microbiology

Year:

2008

Language:

english

File:

PDF, 4.53 MB

english, 2008

7

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

Luca Giorgetti, Trevor Siggers, Guido Tiana, Greta Caprara, Samuele Notarbartolo, Teresa Corona, Manolis Pasparakis, Paolo Milani, Martha L. Bulyk, Gioacchino Natoli

Journal:

Year:

2010

Language:

english

File:

PDF, 807 KB

english, 2010

8

Distant cis-regulatory elements in human skeletal muscle differentiation

Rachel Patton McCord, Vicky W. Zhou, Tiffany Yuh, Martha L. Bulyk

Journal:

Year:

2011

Language:

english

File:

PDF, 1.40 MB

english, 2011

9

Integrative functional genomics

Journal:

Year:

2004

Language:

english

File:

PDF, 52 KB

english, 2004

10

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

Gordân, Raluca, Shen, Ning, Dror, Iris, Zhou, Tianyin, Horton, John, Rohs, Remo, Bulyk, Martha L.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.45 MB

english, 2013

11

A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites

Datta, Rhea R., Ling, Jia, Kurland, Jesse, Ren, Xiaotong, Xu, Zhe, Yucel, Gozde, Moore, Jackie, Shokri, Leila, Baker, Isabel, Bishop, Timothy, Struffi, Paolo, Levina, Rimma, Bulyk, Martha L., Johnston

Journal:

Genes & Development

Year:

2018

Language:

english

File:

PDF, 8.71 MB

english, 2018

12

Computational comparison of two draft sequences of the human genome

Aach, John, Bulyk, Martha L., Church, George M., Comander, Jason, Derti, Adnan, Shendure, Jay

Journal:

Year:

2001

Language:

english

File:

PDF, 193 KB

english, 2001

13

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

Siggers, Trevor, Chang, Abraham B, Teixeira, Ana, Wong, Daniel, Williams, Kevin J, Ahmed, Bilal, Ragoussis, Jiannis, Udalova, Irina A, Smale, Stephen T, Bulyk, Martha L

Journal:

Nature Immunology

Year:

2011

Language:

english

File:

PDF, 1.33 MB

english, 2011

14

Handbook of Systems Biology || Gene Regulatory Networks

Bulyk, Martha L.

Year:

2013

Language:

english

File:

PDF, 914 KB

english, 2013

15

Computational prediction of transcription-factor binding site locations

Journal:

Year:

2003

Language:

english

File:

PDF, 148 KB

english, 2003

16

A Statistical Model for Investigating Binding Probabilities of DNA Nucleotide Sequences Using Microarrays

Mei-Ling Ting Lee, Martha L. Bulyk, G. A. Whitmore and George M. Church

Journal:

Year:

2002

Language:

english

File:

PDF, 1.66 MB

english, 2002

17

Notch and MAML-1 Complexation Do Not Detectably Alter the DNA Binding Specificity of the Transcription Factor CSL

Del Bianco, Cristina, Vedenko, Anastasia, Choi, Sung Hee, Berger, Michael F., Shokri, Leila, Bulyk, Martha L., Blacklow, Stephen C., Bergmann, Andreas

Journal:

Year:

2010

Language:

english

File:

PDF, 405 KB

english, 2010

18

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data

Bertrand R Huber, Martha L Bulyk

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 3.30 MB

english, 2006

19

A Graded Response of a Transcription Factor to Increasing Doses of External Stimuli: A Thermodynamic Framework Describing the Behavior of NF-kB

Giorgetti, Luca, Siggers, Trevor, Yaeger, Savina, Tiana, Guido, Caprara, Greta, Milani, Paolo, Bulyk, Martha L., Natoli, Gioacchino

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 50 KB

english, 2009

20

Differential Occupancy of Two GA-Binding Proteins Promotes Targeting of the Drosophila Dosage Compensation Complex to the Male X Chromosome

Kaye, Emily G., Booker, Matthew, Kurland, Jesse V., Conicella, Alexander E., Fawzi, Nicolas L., Bulyk, Martha L., Tolstorukov, Michael Y., Larschan, Erica

Journal:

Year:

2018

Language:

english

File:

PDF, 8.86 MB

english, 2018

21

Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex

Siggers, Trevor, Duyzend, Michael H, Reddy, Jessica, Khan, Sidra, Bulyk, Martha L

Journal:

Molecular Systems Biology

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

22

Bioinformatic and molecular investigation of Sirt3 expression

Satterstrom, F, Swindell, William R, Bulyk, Martha L, Haigis, Marcia C

Journal:

BMC Proceedings

Year:

2012

Language:

english

File:

PDF, 172 KB

english, 2012

23

Polycomb-like proteins link the PRC2 complex to CpG islands

Li, Haojie, Liefke, Robert, Jiang, Junyi, Kurland, Jesse Vigoda, Tian, Wei, Deng, Pujuan, Zhang, Weidi, He, Qian, Patel, Dinshaw J., Bulyk, Martha L., Shi, Yang, Wang, Zhanxin

Journal:

Year:

2017

Language:

english

File:

PDF, 14.02 MB

english, 2017

24

Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks

Rogers, Julia M., Bulyk, Martha L.

Journal:

Wiley Interdisciplinary Reviews: Systems Biology and Medicine

Year:

2018

Language:

english

File:

PDF, 2.17 MB

english, 2018

25

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts

Gisselbrecht, Stephen S., Palagi, Alexandre, Kurland, Jesse V., Rogers, Julia M., Ozadam, Hakan, Zhan, Ye, Dekker, Job, Bulyk, Martha L.

Journal:

Year:

2019

Language:

english

File:

PDF, 3.66 MB

english, 2019

26

Abstract not submitted for online publication: Metabolism, diet and disease

Satterstrom, F, Swindell, William R, Bulyk, Martha L, Haigis, Marcia C

Journal:

BMC Proceedings

Year:

2012

File:

PDF, 152 KB

2012

27

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays

Mukherjee, Sonali, Berger, Michael F, Jona, Ghil, Wang, Xun S, Muzzey, Dale, Snyder, Michael, Young, Richard A, Bulyk, Martha L

Journal:

Nature Genetics

Year:

2004

Language:

english

File:

PDF, 556 KB

english, 2004

28

Abstract not submitted for online publication: Metabolism, diet and disease

Satterstrom, F, Swindell, William R, Bulyk, Martha L, Haigis, Marcia C

Journal:

BMC Proceedings

Year:

2012

File:

PDF, 152 KB

2012

29

Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development

Menke, Chelsea, Cionni, Megan, Siggers, Trevor, Bulyk, Martha L., Beier, David R., Stottmann, Rolf W.

Journal:

Year:

2015

Language:

english

File:

PDF, 521 KB

english, 2015

30

[WORLD SCIENTIFIC Proceedings of the Pacific Symposium - Kohala Coast, Hawaii, USA (3 – 7 January 2012)] Biocomputing 2012 - IDENTIFICATION OF CELL CYCLE-REGULATED, PUTATIVE HYPHAL GENES IN CANDIDA ALBICANS

GORDÂN, RALUCA, PYNE, SAUMYADIPTA, BULYK, MARTHA L.

Language:

english

File:

PDF, 1.03 MB

english

31

Toward a systems-level understanding of developmental regulatory networks

Brian W Busser, Martha L Bulyk, Alan M Michelson

Journal:

Current Opinion in Genetics & Development

Year:

2008

Language:

english

File:

PDF, 565 KB

english, 2008

32

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

Daniel Wong, Ana Teixeira, Spyros Oikonomopoulos, Peter Humburg, Imtiaz Nisar Lone, David Saliba, Trevor Siggers, Martha Bulyk, Dimitar Angelov, Stefan Dimitrov, Irina A Udalova, Jiannis Ragoussis

Journal:

Year:

2011

Language:

english

File:

PDF, 956 KB

english, 2011

33

Discovering DNA regulatory elements with bacteria

Bulyk, Martha L

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 150 KB

english, 2005

34

DNA binding site analysis of Burkholderia thailandensis response regulators

Kristy L. Nowak-Lovato, Alexana J. Hickmott, Tuhin S. Maity, Martha L. Bulyk, John Dunbar, Elizabeth Hong-Geller

Journal:

Journal of Microbiological Methods

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

35

Biological code breaking in the 21st century

Michelson, Alan M, Bulyk, Martha L

Journal:

Molecular Systems Biology

Year:

2006

Language:

english

File:

PDF, 255 KB

english, 2006

36

Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds

Mariani, Luca, Weinand, Kathryn, Vedenko, Anastasia, Barrera, Luis A., Bulyk, Martha L.

Journal:

Year:

2017

Language:

english

File:

PDF, 4.38 MB

english, 2017

37

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

Berger, Michael F, Philippakis, Anthony A, Qureshi, Aaron M, He, Fangxue S, Estep, Preston W, Bulyk, Martha L

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 2.00 MB

english, 2006

38

Nuclear respiratory factor 2 induces SIRT3 expression

Satterstrom, F. Kyle, Swindell, William R., Laurent, Gaëlle, Vyas, Sejal, Bulyk, Martha L., Haigis, Marcia C.

Journal:

Year:

2015

Language:

english

File:

PDF, 349 KB

english, 2015

39

Genomes and evolution: advances in deciphering the genomics of gene regulation in evolution

Martha L Bulyk, Michael Levine

Journal:

Current Opinion in Genetics & Development

Year:

2009

Language:

english

File:

PDF, 89 KB

english, 2009

40

A Statistical Model for Investigating Binding Probabilities of DNA Nucleotide Sequences Using Microarrays

Mei-Ling Ting Lee, Martha L. Bulyk, G. A. Whitmore, George M. Church

Journal:

Year:

2002

Language:

english

File:

PDF, 843 KB

english, 2002

41

Inferring condition-specific transcription factor function from DNA binding and gene expression data

McCord, Rachel Patton, Berger, Michael F, Philippakis, Anthony A, Bulyk, Martha L

Journal:

Molecular Systems Biology

Year:

2007

Language:

english

File:

PDF, 357 KB

english, 2007

42

A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis

Casanovas, Guillem, Banerji, Anashua, d'Alessio, Flavia, Muckenthaler, Martina U., Legewie, Stefan, Bulyk, Martha L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 684 KB

english, 2014

43

ye Gene Discovery

Lachke, Salil A., Ho, Joshua W. K., Kryukov, Gregory V., O'Connell, Daniel J., Aboukhalil, Anton, Bulyk, Martha L., Park, Peter J., Maas, Richard L.

Journal:

Investigative Ophthalmology & Visual Science

Year:

2012

Language:

english

File:

PDF, 2.91 MB

english, 2012

44

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

Savina A. Jaeger, Esther T. Chan, Michael F. Berger, Rolf Stottmann, Timothy R. Hughes, Martha L. Bulyk

Journal:

Year:

2010

Language:

english

File:

PDF, 1.60 MB

english, 2010

45

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

Philippakis, Anthony A., Busser, Brian W., Gisselbrecht, Stephen S., He, Fangxue Sherry, Estrada, Beatriz, Michelson, Alan M., Bulyk, Martha L.

Journal:

PLoS Computational Biology

Year:

2006

Language:

english

File:

PDF, 655 KB

english, 2006

46

Inferring condition-specific transcription factor function from DNA binding and gene expression data

McCord, Rachel Patton, Berger, Michael F, Philippakis, Anthony A, Bulyk, Martha L

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 730 KB

english, 2010

47

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

Berger, Michael F, Bulyk, Martha L

Journal:

Nature Protocols

Year:

2009

Language:

english

File:

PDF, 1.17 MB

english, 2009

48

STAT3 Activation of miR-21 and miR-181b-1 via PTEN and CYLD Are Part of the Epigenetic Switch Linking Inflammation to Cancer

Dimitrios Iliopoulos, Savina A. Jaeger, Heather A. Hirsch, Martha L. Bulyk, Kevin Struhl

Journal:

Year:

2010

Language:

english

File:

PDF, 856 KB

english, 2010

49

Transcription factor–DNA binding: beyond binding site motifs

Inukai, Sachi, Kock, Kian Hong, Bulyk, Martha L

Journal:

Current Opinion in Genetics & Development

Year:

2017

Language:

english

File:

PDF, 607 KB

english, 2017

50

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts

Gisselbrecht, Stephen S., Palagi, Alexandre, Kurland, Jesse V., Rogers, Julia M., Ozadam, Hakan, Zhan, Ye, Dekker, Job, Bulyk, Martha L.

Journal:

Year:

2019

File:

PDF, 3.66 MB

2019

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