Publications

2010

Lott SE, Ludwig MZ, Kreitman M. Evolution and Inheritance of Early Embyonic Patterning in D. Sechellia Evolution. 2010 Dec 1. doi: 10.1111/j.1558-5646.2010.01206.x. [Epub ahead of print] PMID: 21121913 [PubMed - as supplied by publisher] Related citations

Maienschein-Cline M, Warmflash A, Dinner AR. Defining cooperativity in gene regulation locally through intrinsic noise. IET Syst Biol. 2010 Nov;4(6):379. PubMed PMID: 21073237.

Park H, Pontius W, Guet CC, Marko JF, Emonet T, Cluzel P. Interdependence of behavioural variability and response to small stimuli in bacteria. Nature. 2010 Nov 14. [Epub ahead of print] PubMed PMID: 21076396.

Hua, S, Kittler R & White KP. (2009). Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 137(7): 1259-71. "PMC Journal- In Process"

Miles CM, Lott SE, Luengo Hendriks CL, Ludwig MZ, Manu, Williams CL, Kreitman M. (2010). Artificial Selection on egg size perturbs early pattern formation in D. melanogaster. Evolution. Jul 16. [Epub ahead of print]. "PMC Journal- In Process"

Feng Shen, Wenbin Du, Jason E. Kreutz, Alice Fok, and Ismagilov R. (2010) Digital PCR on a SlipChip. Lab Chip. July 1 [Epub ahead of print]. PMCID: PMC2948063.

Gao Z, Huang, Z, Olivey, HE, Gurbuxani, S, Crispino, JD, Svensson, E. (2010) FOG-1 mediated recruitment of NuRD is required for cell lineage re-enforcement during hematopoiesis. EMBO J. 29:457-468. PMCID: PMC2824465

Zhang J., Graham T.G., Vivekanand P., Cote L., Cetera M. and Rebay I. (2010). Sterile Alpha Motif Domain-Mediated Self-Association Plays an Essential Role in Modulating the Activity of the Drosophila ETS Family Transcriptional Repressor Yan. Mol Cell Biol. 30, 1158-1170. PMCID: PMC2820895

Graham, T.G.W, Tabei, S.M.A., Dinner, A., Rebay, I. (2010). "Modeling bistable cell fate choices in the Drosophila eye: qualitative and quantitative perspectives" Development. 137(14):2265-78. PMCID: PMC2889600

Heinz, S, Benner, C, Bertolino, E, Lin, YC, Laslo, P, Cheng, JX, Murre C, Singh, H, and Glass, CK (2010) Simple combinations of lineage determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell. 38:576-589. PMCID: PMC2898526

Marques JT, Kim K, Wu PH, Alleyne TM, Jafari N, Carthew RW (2010). Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat Struct Mol Biol. 17(1):24-30. PMCID: PMC2919300

McMullen PD, Morimoto RI, Amaral LA (2010). Physically grounded approach for estimating gene expression from microarray data. Proc Natl Acad Sci U S A. 107(31):13690-5. "PMC Journal- In Process"

Qi B, Muff S, Caflisch A, Dinner AR (2010). Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein. J Phys Chem B. 114(20):6979-89. "PMC Journal- In Process"

Wang PP, Ruvinsky I. (2010). Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes. RNA. 16(2):290- 8. PMCID: PMC2811658

Evans J, Rzhetsky A. (2010). Philosophy of science. Machine science. Science. 329(5990): 399-400. "PMC Journal- In Process"

Yao L, Evans JA, Rzhetsky A. (2010). Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol. 28(4):161-70. Review "PMC Journal- In Process"

Li L, Karymov MA, Nichols KP, Ismagilov RF.(2010). Dead-end filling of SlipChip evaluated theoretically and experimentally as a function of the surface chemistry and the gap size between the plates for lubricated and dry SlipChips. Langmuir. 26(14):12465-71. PMCID: PMC2923639

Chen, H.; Yi, C.; Zhang, J.; Zhang, W.; Ge, Z.; Yang, C.-G.; He, C. (2010). "Structural insight into the oxidation-sensing mechanism of the antibiotic resistance regulator MexR" EMBO Rep. [Epub ahead of print] "PMC Journal- In Process"

Chen, P.R.; Brugarolas, P.; He, C. (2010). "Redox Signaling in Human Pathogens" Antioxid. Redox Signal. [Epub ahead of print] June 25, 2010. "PMC Journal- In Process"

Chun-Xiao Song, Keith E Szulwach, Ye Fu, Qing Dai, Chengqi Yi, Xuekun Li, Yujing Li, Chih-Hsin Chen, Wen Zhang, Xing Jian, Jing Wang, Li Zhang, Timothy J Looney, Baichen Zhang, Lucy A Godley, Leslie M Hicks, Bruce T Lahn, Peng Jin & Chuan He (2010) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine Nature Biotechnology, November 15, 2010

2009

Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A & White KP. (2009). Analysis of Drosophila segmentation network identifies a JNK pathway factor over expressed in kidney cancer. Science. 27;323(5918):1218-22. PMCID: PMC2756524

Tian F, Shah PK, Liu X, Negre N, Chen J, Karpenko O, White KP & Grossman RL (2009). Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. Bioinformatics. 15;25(22):3001-4 PMCID: PMC2773252

Li X, Cassidy JJ, Reinke CA, Fischboeck S, Carthew RW. (2009). A microRNA imparts robustness against environmental fluctuation during development. Cell. 137:273-82. PMCID: PMC2674871

Lucchetta EM, Carthew RW, Ismagilov RF. (2009). The endo-siRNA pathway is essential for robust development of the Drosophila embryo. PLoS One. 23; 4(10). PMCID: PMC2761733

Iossifov I, Rodriguez-Esteban R, Mayzus I, Millen KJ, Rzhetsky A. (2009). Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol. Nov;5(11):e1000559. PMCID: PMC2767227

Westerheide, S.D., J. Anckar, S. Stevens, L. Sistonen, Morimoto RI. (2009). Stress-Inducible Regulation of Heat Shock Factor 1 by the Deacetylase SIRT1. Science. 323: 1063-1066. "PMC Journal- In Process"

Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, A. R. Kim, O. Radulescu, C. E. Vanario-Alonso, D. H. Sharp, M. Samsonova, and Reinitz J. (2009). Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biology. 7:e1000049. PMCID: PMC2653557

K. N. Kozlov, E. Myasnikova, A. A. Samsonova, S. Surkova, J. Reinitz, and M. Samsonova. (2009). GCPReg package for registration of the segmentation gene expression data in Drosophila. Fly. 2:151-156. "PMC Journal- In Process"

Huang, Z, Dore, LC, Li, Z, Orkin, SH, Feng, G, Lin, S, and Crispino JD. (2009) GATA-2 reinforces megakaryocyte development in the absence of GATA-1. Mol Cell Bio. 29:5168-5180. PMCID: PMC2738300

S. Vakulenko, Manu, J. Reinitz, and O. Radelescu (2009). Morphogenetic Field Theory of Size Regulation in Drosophila by Interacting Local Modes. Physical Review Letters. 103:168102. NIHMSID:242204

Barrière A, Yang SP, Pekarek E, Thomas CG, Haag ES, Ruvinsky I. (2009). Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res. 2009 Mar;19(3):470-80. PMCID: PMC2661809

Liu J, Ghanim M, Xue L, Brown CD, Iossifov I, Angeletti C, Hua S, Nègre N, Ludwig M, Stricker T, Al-Ahmadie HA, Tretiakova M, Camp RL, Perera-Alberto M, Rimm DL, Xu T, Rzhetsky A, White KP. Analysis of Drosophila Segmentation Network Identifies a JNK Pathway Factor Overexpressed in Kidney Cancer (2009) Science, Jan 22, 2009 [Epub ahead of print]

2008

Veena Prahlad, Tyler Cornelius, Richard I. Morimoto Regulation of the cellular heat shock response in Caenorhabditis elegans by thermosensory neurons Science, May 9, 2008; 320(5877):811-4