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1

DNA microarray technologies for measuring protein–DNA interactions

Journal:

Current Opinion in Biotechnology

Year:

2006

Language:

english

File:

PDF, 422 KB

english, 2006

2

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

3

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

4

10.1038/9878

Church, George M., Bulyk, Martha L., Gentalen, Erik, Lockhart, David J.

Journal:

Nature Biotechnology

Year:

1999

Language:

english

File:

PDF, 405 KB

english, 1999

5

Discovering DNA regulatory elements with bacteria

Bulyk, Martha L

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 150 KB

english, 2005

6

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

7

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

8

Systematic identification of mammalian regulatory motifs' target genes and functions

Warner, Jason B, Philippakis, Anthony A, Jaeger, Savina A, He, Fangxue Sherry, Lin, Jolinta, Bulyk, Martha L

Journal:

Year:

2008

Language:

english

File:

PDF, 551 KB

english, 2008

9

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

10

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

11

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

12

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

13

LUX ARRHYTHMO Encodes a Nighttime Repressor of Circadian Gene Expression in the Arabidopsis Core Clock

Anne Helfer, Dmitri A. Nusinow, Brenda Y. Chow, Andrew R. Gehrke, Martha L. Bulyk, Steve A. Kay

Journal:

Current Biology

Year:

2011

Language:

english

File:

PDF, 642 KB

english, 2011

14

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

15

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

16

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

17

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

18

A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors

Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, Albertha J.M. Walhout

Journal:

Year:

2009

Language:

english

File:

PDF, 2.43 MB

english, 2009

19

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

20

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

21

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

22

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

23

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

24

DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes

Varodom Charoensawan, Sarath Chandra Janga, Martha L. Bulyk, M. Madan Babu, Sarah A. Teichmann

Journal:

Year:

2012

Language:

english

File:

PDF, 1.23 MB

english, 2012

25

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

26

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

27

Prep1 regulates lens induction via direct regulation of the Pax6 ectodermal enhancer

Sheldon Rowan, Trevor Siggers, Salil Lachke, Martha L. Bulyk, Richard L. Maas

Journal:

Developmental Biology

Year:

2009

Language:

english

File:

PDF, 69 KB

english, 2009

28

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

29

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

30

Handbook of Systems Biology || Gene Regulatory Networks

Bulyk, Martha L.

Year:

2013

Language:

english

File:

PDF, 914 KB

english, 2013

31

Linking Yeast Transcription Factor Structural Class and Detailed Binding Preferences with in vivo Regulatory Functions

McCord, Rachel Patton, Zhu, Cong, Siggers, Trevor W., Bulyk, Martha L.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 45 KB

english, 2009

32

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

33

Integrative functional genomics

Journal:

Year:

2004

Language:

english

File:

PDF, 52 KB

english, 2004

34

Computational prediction of transcription-factor binding site locations

Journal:

Year:

2003

Language:

english

File:

PDF, 148 KB

english, 2003

35

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

36

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

37

71 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:

Journal of Biomolecular Structure and Dynamics

Year:

2013

Language:

english

File:

PDF, 140 KB

english, 2013

38

Diversification of Transcription Factor Paralogs via Noncanonical Modularity in C2H2 Zinc Finger DNA Binding

Siggers, Trevor, Reddy, Jessica, Barron, Brian, Bulyk, Martha L.

Journal:

Year:

2014

Language:

english

File:

PDF, 2.33 MB

english, 2014

39

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments

Philippakis, Anthony A., Qureshi, Aaron M., Berger, Michael F., Bulyk, Martha L.

Journal:

Journal of Computational Biology

Year:

2008

Language:

english

File:

PDF, 268 KB

english, 2008

40

Jury remains out on simple models of transcription factor specificity

Morris, Quaid, Bulyk, Martha L, Hughes, Timothy R

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 133 KB

english, 2011

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

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

43

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

44

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

45

Context influences on TALE–DNA binding revealed by quantitative profiling

Rogers, Julia M., Barrera, Luis A., Reyon, Deepak, Sander, Jeffry D., Kellis, Manolis, Keith Joung, J, Bulyk, Martha L.

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 580 KB

english, 2015

46

[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

47

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

48

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

49

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

50

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

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