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1

Mathematical modeling of gene expression: a guide for the perplexed biologist

Ay, Ahmet, Arnosti, David N.

Journal:

Critical Reviews in Biochemistry and Molecular Biology

Year:

2011

Language:

english

File:

PDF, 974 KB

english, 2011

2

Two-Layer Mathematical Modeling of Gene Expression: Incorporating DNA-Level Information and System Dynamics

Dresch, Jacqueline M., Thompson, Marc A., Arnosti, David N., Chiu, Chichia

Journal:

SIAM Journal on Applied Mathematics

Year:

2013

Language:

english

File:

PDF, 1.77 MB

english, 2013

3

Transcriptional Regulation of INSR, the Insulin Receptor Gene

Payankaulam, Sandhya, Raicu, Ana-Maria, Arnosti, David N.

Journal:

Year:

2019

File:

PDF, 1.40 MB

2019

4

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

David N. Arnosti, Meghana M. Kulkarni

Journal:

Journal of Cellular Biochemistry

Year:

2005

Language:

english

File:

PDF, 133 KB

english, 2005

5

Developmental expression and phylogenetic conservation of alternatively spliced forms of the C-terminal binding protein corepressor

Priya Mani-Telang, David N. Arnosti

Journal:

Development Genes and Evolution

Year:

2007

Language:

english

File:

PDF, 503 KB

english, 2007

6

ANALYSIS AND FUNCTION OF TRANSCRIPTIONAL REGULATORY ELEMENTS: Insights from Drosophila

Arnosti, David N.

Journal:

Annual Review of Entomology

Year:

2003

Language:

english

File:

PDF, 268 KB

english, 2003

7

Conserved cysteine residues of Oct-2 POU domain confer sensitivity to oxidation but are dispensable for sequence-specific DNA binding

Patrick Rigoni, Licen Xu, Keith Harshman, Walter Schaffner, David N. Arnosti

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression

Year:

1993

Language:

english

File:

PDF, 473 KB

english, 1993

8

Gene Regulation: Boundaries within Limits

Sandhya Payankaulam, David N. Arnosti

Journal:

Current Biology

Year:

2008

Language:

english

File:

PDF, 110 KB

english, 2008

9

Nucleosome Positioning: An Essential Component of the Enhancer Regulatory Code?

Ahmet Ay, David N. Arnosti

Journal:

Current Biology

Year:

2010

Language:

english

File:

PDF, 298 KB

english, 2010

10

Transcriptional Repression: Conserved and Evolved Features

Sandhya Payankaulam, Li M. Li, David N. Arnosti

Journal:

Current Biology

Year:

2010

Language:

english

File:

PDF, 655 KB

english, 2010

11

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

Li M. Li, David N. Arnosti

Journal:

Current Biology

Year:

2011

Language:

english

File:

PDF, 876 KB

english, 2011

12

Transcriptional Repressors: Shutting Off Gene Expression at the Source Affects Developmental Dynamics

David N. Arnosti

Journal:

Current Biology

Year:

2011

Language:

english

File:

PDF, 44 KB

english, 2011

13

Distinct developmental expression of Drosophila retinoblastoma factors

Scott A. Keller, Zakir Ullah, Martin S. Buckley, R. William Henry, David N. Arnosti

Journal:

Gene Expression Patterns

Year:

2005

Language:

english

File:

PDF, 569 KB

english, 2005

14

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects

Jacqueline M Dresch, Xiaozhou Liu, David N Arnosti, Ahmet Ay

Journal:

BMC Systems Biology

Year:

2010

Language:

english

File:

PDF, 736 KB

english, 2010

15

Role of CtBP in Transcriptional Repression by the Drosophila giant Protein

Bethany Strunk, Paolo Struffi, Kevin Wright, Brandon Pabst, Jelani Thomas, Ling Qin, David N. Arnosti

Journal:

Developmental Biology

Year:

2001

Language:

english

File:

PDF, 471 KB

english, 2001

16

POU-specific domain of Oct-2 factor confers ‘octamer’ motif DNA binding specificity on heterologous Antennapedia homeodomain

Enrico Brugnera, Licen Xu, Walter Schaffner, David N. Arnosti

Journal:

Year:

1992

Language:

english

File:

PDF, 491 KB

english, 1992

17

A two-scale mathematical model for DNA transcription

Chichia Chiu, Walid Fakhouri, Nianzheng Liu, Evan Dayringer, Jacqueline Dresch, David Arnosti

Journal:

Mathematical Biosciences

Year:

2012

Language:

english

File:

PDF, 1.27 MB

english, 2012

18

Regulation of retinoblastoma protein stability and function by the COP signalosome

Martin S. Buckley, Zakir Ullah, Geoffrey L. Williams, David N. Arnosti, R. William Henry

Journal:

Developmental Biology

Year:

2006

Language:

english

File:

PDF, 54 KB

english, 2006

19

Phylogenetic conservation and characterization of CtBP corepressor activity in Drosophila

Priya Mani, Montserrat Sutrias-Grau, David N. Arnosti

Journal:

Developmental Biology

Year:

2006

Language:

english

File:

PDF, 64 KB

english, 2006

20

Identification and characterization of Groucho as a component of the Drosophila Knirps repressor complex

Sandhya Payankaulam, Paolo Struffi, David Arnosti

Journal:

Developmental Biology

Year:

2006

Language:

english

File:

PDF, 56 KB

english, 2006

21

Role of NAD binding and catalytic residues in the C-terminal binding protein corepressor

Priya Mani-Telang, Montserrat Sutrias-Grau, Geoffrey Williams, David N. Arnosti

Journal:

Year:

2007

Language:

english

File:

PDF, 820 KB

english, 2007

22

Rbf1 degron dysfunction enhances cellular DNA replication

Raj, Nitin, Zhang, Liang, Wei, Yiliang, Arnosti, David N., Henry, R. William

Journal:

Year:

2012

Language:

english

File:

PDF, 1.99 MB

english, 2012

23

Modeling gene expression

Journal:

Year:

2013

Language:

english

File:

PDF, 181 KB

english, 2013

24

Secondary σ Factor Controls Transcription of Flagellar and Chemotaxis Genes in Escherichia coli

David N. Arnosti and Michael J. Chamberlin

Journal:

Proceedings of the National Academy of Sciences

Year:

1989

Language:

english

File:

PDF, 1.10 MB

english, 1989

25

An apaH Mutation Causes AppppA to Accumulate and Affects Motility and Catabolite Repression in Escherichia coli

Spencer B. Farr, David N. Arnosti, Michael J. Chamberlin and Bruce N. Ames

Journal:

Proceedings of the National Academy of Sciences

Year:

1989

Language:

english

File:

PDF, 1.41 MB

english, 1989

26

Long-Range Repression in the Drosophila Embryo

Haini N. Cai, David N. Arnosti and Michael Levine

Journal:

Proceedings of the National Academy of Sciences

Year:

1996

Language:

english

File:

PDF, 1.51 MB

english, 1996

27

Global parameter estimation for thermodynamic models of transcriptional regulation

Suleimenov, Yerzhan, Ay, Ahmet, Samee, Md. Abul Hassan, Dresch, Jacqueline M., Sinha, Saurabh, Arnosti, David N.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.66 MB

english, 2013

28

Image Processing and Analysis for Quantifying Gene Expression from Early Drosophila Embryos

Ay, Ahmet, Fakhouri, Walid D., Chiu, Chichia, Arnosti, David N.

Journal:

Tissue Engineering Part A

Year:

2008

Language:

english

File:

PDF, 338 KB

english, 2008

29

Enhancer Trafficking: Free Throws and Three-Pointers

Wei, Yiliang, Arnosti, David N.

Journal:

Developmental Cell

Year:

2015

Language:

english

File:

PDF, 248 KB

english, 2015

30

Role of Drosophila retinoblastoma protein instability element in cell growth and proliferation

Elenbaas, Jared S, Mouawad, Rima, Henry, R William, Arnosti, David N, Payankaulam, Sandhya

Journal:

Year:

2015

Language:

english

File:

PDF, 4.81 MB

english, 2015

31

New Tools, Resources for Gene Regulatory Analysis in Drosophila

Halfon, Marc S., Arnosti, David N.

Journal:

Year:

2007

Language:

english

File:

PDF, 214 KB

english, 2007

32

Dynamic reprogramming of chromatin: paradigmatic palimpsests and HES factors

Kok, Kurtulus, Arnosti, David N.

Journal:

Frontiers in Genetics

Year:

2015

Language:

english

File:

PDF, 585 KB

english, 2015

33

Specific transcriptional activation in vitro by the herpes simplex virus protein VP16

Arnosti, David N., Preston, Chris M., Hagmann, Michael, Schaffner, Walter, Hope, R.Graham, Laughlan, Gerard, Luisi, Ben F.

Journal:

Nucleic Acids Research

Year:

1993

Language:

english

File:

PDF, 4.73 MB

english, 1993

34

The Evolutionarily Conserved C-terminal Domains in the Mammalian Retinoblastoma Tumor Suppressor Family Serve as Dual Regulators of Protein Stability and Transcriptional Potency

Sengupta, Satyaki, Lingnurkar, Raj, Carey, Timothy S., Pomaville, Monica, Kar, Parimal, Feig, Michael, Wilson, Catherine A., Knott, Jason G., Arnosti, David N., Henry, R. William

Journal:

Journal of Biological Chemistry

Year:

2015

Language:

english

File:

PDF, 1.77 MB

english, 2015

35

Fine mapping of chromatin structure in Drosophila melanogaster embryos using micrococcal nuclease

Li, Li M., Arnosti, David N.

Journal:

Year:

2010

Language:

english

File:

PDF, 527 KB

english, 2010

36

Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis

Wei, Yiliang, Mondal, Shamba S., Mouawad, Rima, Wilczyński, Bartek, Henry, R. William, Arnosti, David N.

Journal:

G3 Genes|Genome|Genetics

Year:

2015

Language:

english

File:

PDF, 2.77 MB

english, 2015

37

Transcriptional Perspectives from San Diego

Arnosti, David N.

Journal:

Year:

2008

Language:

english

File:

PDF, 246 KB

english, 2008

38

Optimization of reporter gene architecture for quantitative measurements of gene expression in the Drosophila embryo

Sayal, Rupinder, Ryu, Seuk-Min, Arnosti, David N.

Journal:

Year:

2011

File:

PDF, 719 KB

2011

39

Optimization of reporter gene architecture for quantitative measurements of gene expression in the Drosophila embryo

Sayal, Rupinder, Ryu, Seuk-Min, Arnosti, David N.

Journal:

Year:

2011

Language:

english

File:

PDF, 719 KB

english, 2011

40

The Wisdom of Crowds: Can Mathematical Models Crack the cis Regulatory Code?

Dresch, Jacqueline M., Arnosti, David N.

Journal:

Year:

2015

Language:

english

File:

PDF, 321 KB

english, 2015

41

Cori meets Dobzhansky: Evolution and Gene Expression in St. Louis

Arnosti, David N., Fay, Justin C., Zeitlinger, Julia

Journal:

Year:

2015

Language:

english

File:

PDF, 120 KB

english, 2015

42

Complex cis -regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator

Wei, Yiliang, Gokhale, Rewatee H., Sonnenschein, Anne, Montgomery, Kelly Mone't, Ingersoll, Andrew, Arnosti, David N.

Journal:

Development (The Company of Biologists)

Year:

2016

Language:

english

File:

PDF, 871 KB

english, 2016

43

Regulation of cell polarity determinants by the Retinoblastoma tumor suppressor protein

Payankaulam, Sandhya, Yeung, Kelvin, McNeill, Helen, Henry, R. William, Arnosti, David N.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.73 MB

english, 2016

44

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

Martinez-Garcia, Manuel, Brazel, David M., Swan, Brandon K., Arnosti, Carol, Chain, Patrick S. G., Reitenga, Krista G., Xie, Gary, Poulton, Nicole J., Gomez, Monica Lluesma, Masland, Dashiell E. D., T

Journal:

Year:

2012

Language:

english

File:

PDF, 1.87 MB

english, 2012

45

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

Fakhouri, Walid D, Ay, Ahmet, Sayal, Rupinder, Dresch, Jacqueline, Dayringer, Evan, Arnosti, David N

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.60 MB

english, 2010

46

Diversification of retinoblastoma protein function associated with cis and trans adaptations

Mouawad, Rima, Prasad, Jaideep, Thorley, Dominic, Himadewi, Pamela, Kadiyala, Dhruva, Wilson, Nathan, Kapranov, Philipp, Arnosti, David N, Wittkopp, Patricia

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 12.00 MB

english, 2019

47

Selective repression of the Drosophila cyclin B promoter by retinoblastoma and E2F proteins

Mouawad, Rima, Himadewi, Pamela, Kadiyala, Dhruva, Arnosti, David N.

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Year:

2020

File:

PDF, 1.49 MB

2020

48

Transcriptional Enhancers in Drosophila

Small, Stephen, Arnosti, David N.

Journal:

Year:

2020

File:

PDF, 1.63 MB

2020