Research

Papers Archive

Research Papers

Genome-wide Association of Yorkie with Chromatin and Chromatin-Remodeling Complexes

by Matt Slattery, Lijia Ma, Alex Crofts, Kevin White, Hyangyee Oh, Richard S. Mann, Kenneth D. Irvine

CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia

by Christopher Brown, Chaitanya Bandlamudi, John Cunningham, Michelle Le Beau, Megan McNerney, Shi Yu, Subhradip Karmakar, Xiaoyue Wang, Robert Grossman, Kevin White, Thomas Stricker, Bartom ET, Ko J, Sandall BP, Anastasi J,

Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

by Barbara Stranger, Qiyuan Li, Ji-Heui Seo, Aaron McKenna, Itsik Pe’er, Thomas LaFramboise, Myles Brown, Svitlana Tyekucheva, Matthew L. Freedman

Robust and tunable circadian rhythms from differentially sensitive catalytic domains

by Connie Phong, Crystal Wilhoite, Michael Rust, Markson JS

A cis-regulatory map of the Drosophila genome

by Christopher Brown, Alec Victorsen, Lijia Ma, Rebecca Spokony, Jason Grundstad, David Hanley, Robert Grossman, Kevin White, Nicolas Nègre, Christopher Aaron Bristow, Steven W. Miller, Ulrich Wagner, Pouya Kheradpour, Matthew L. Eaton, Paul Loriaux, Rachel Sealfon, Zirong Li, Haruhiko Ishii, Jia Chen, Lindsay Hwang, Chao Cheng, Richard P. Auburn,11 Melissa B. Davis, Marc Domanus, Parantu K. Shah, Carolyn A. Morrison, Jennifer Zieba, Sarah Suchy, Lionel Senderowicz, David M. MacAlpine, Mattias Mannervik, Koen Venken, Hugo Bellen, Robert White,Mark Gerstein, Steven Russell, Bing Ren, James W. Posakony, Manolis Kellis

Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis

by Kevin White, John Crispino, Christopher Brown, Louis C. Doré, Timothy M. Chlon

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome

by Xiaochun Ni, Manyuan Long, Siquan Chen, Kevin White, Zhang YE, Negre N,

A conserved eEF2 coding variant in SCA26 leads to loss of translational fidelity and increased susceptibility to proteostatic insult

by Christopher Brown, April Peterson, Kevin White, Hekman KE, Yu GY, Zhu H, Du X, Gervin K, Undlien DE, Stevanin G, Pulst SM, Bird TD, Gomez CM

Orderly wheels of the cyanobacterial clock

by Michael Rust

Caffeic acid phenethyl ester suppresses the proliferation of human prostate cancer cells through inhibition of p70S6K and Akt signaling networks

by Chih-Pin Chuu (Max), Mark Ciaccio, Ronald Hause, Richard Jones, Lin HP, Kokontis JM, Hiipakka RA, Liao S

Relating human genetic variation to variation in drug responses.

by Richard Jones, Madian, A.G., Wheeler, H.E., Jones, R.B. and Dolan, M.E.,

Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel

by Ronald Hause, Kin Leung, John Barkinge, Mark Ciaccio, Chih-Pin Chuu (Max), Richard Jones

Light-Driven Changes in Energy Metabolism Directly Entrain the Cyanobacterial Circadian Oscillator

by Michael Rust, Susan S. Golden, Erin K. O'Shea

A Vision for a Biomedical Cloud

by Robert Grossman, Kevin White

Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness

by Martin Kreitman, Kevin White, Ludwig MZ, Manu, Kittler R

Single-virus tracking in live cells

by Michael Rust, Rust MJ, Lakadamyali M, Brandenburg B, Zhuang X.

Single-particle virus tracking

by Michael Rust, Rust MJ, Lakadamyali M, Brandenburg B, Zhuang X.

Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations.

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data

Integrated genomic analyses of ovarian carcinoma Nature 474, 609–615 (30 June 2011) doi:10.1038/nature10166

by Kevin White, The Cancer Genome Atlas Research Network, et al.

A user's guide to the encyclopedia of DNA elements (ENCODE). (PLoS Biol. 2011 Apr;9(4):e1001046. Epub 2011 Apr 19)

Determinants of Antigenicity and Specificity in immune response for Protein Sequences (BMC Bioinformatics. 2011 Jun 21;12(1):251)

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis (BMC Genomics. 2011 Feb 28;12:134)

Large-scale genetic epistasis networks using RNAi (Nat Methods. 2011 Apr;8(4):341-6)

Beta-Blocker Use Is Associated With Improved Relapse-Free Survival in Patients With Triple-Negative Breast Cancer (J Clin Oncol. 2011 May 31)

Genetic pathways leading to therapy-related myeloid neoplasms (Mediterr J Hematol Infect Dis. 2011;3(1):e2011019. Epub 2011 May 16.)

Genome-wide tissue-specific occupancy of the hox protein ultrabithorax and hox cofactor homothorax in Drosophila (PLoS One, 2011 Apr 5)

Large-scale genetic epistasis networks using RNAi. (Nat Methods, 2011 Apr 8)

A cis-regulatory map of the Drosophila genome (Nature, 2011 March 24)

Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator (Science, 2011 Jan 14)

Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator

by Michael Rust, Rust MJ, Golden SS, O'Shea EK.

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE (Science, 2010 Dec 22)

Evolution and inheritance of early embryonic patterning in D. Simulans and D. Sechellia (Evolution, Dec 1 2010)

Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase (Nature. 2010 Nov 11)

Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives (Development July 15, 2010)

Sterile alpha motif domain-mediated self-association plays an essential role in modulating the activity of the Drosophila ETS family transcriptional repressor Yan (Molecular and Cellular Biology, March 2010)

Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila (Nat Struct Mol Biol. Jan 2010)

Novel opportunities for computational biology and sociology in drug discovery (Trends Biotechnol. April 2010)

Mutational bias shaping fly copy number variation: implications for genome evolution

Cleavable C-terminal His-tag vectors for structure determination.

Geometric cues for directing the differentiation of mesenchymal stem cells.

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Chaperone networks: Tipping the balance in protein folding diseases

A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain

A comprehensive map of insulator elements for the Drosophila genome

Systems analysis of EGF receptor signaling dynamics with microwestern arrays

Innate immune and chemically triggered oxidative stress modifies translational fidelity.

Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer

Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks

Structures of SPOP-substrate complexes: insights into molecular architectures of BTB-Cul3 ubiquitin ligases

Genomic antagonism between retinoic acid and estrogen signaling in breast cancer

Dissecting the cell entry pathway of dengue virus by single-particle tracking in living cells

by Michael Rust, van der Schaar HM, Rust MJ, Chen C, van der Ende-Metselaar H, Wilschut J, Zhuang X, Smit JM.

Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer

Ordered phosphorylation governs oscillation of a three-protein circadian clock

by Michael Rust, Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK.

Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM).

by Michael Rust, Rust MJ, Bates M, Zhuang X.

Ligands for clathrin-mediated endocytosis are differentially sorted into distinct populations of early endosomes

by Michael Rust, Lakadamyali M, Rust MJ, Zhuang X.

Assembly of endocytic machinery around individual influenza viruses during viral entry

by Michael Rust, Rust MJ, Lakadamyali M, Zhang F, Zhuang X.

Visualizing infection of individual influenza viruses

by Michael Rust, Lakadamyali M, Rust MJ, Babcock HP, Zhuang X.

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