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Lewis-Sigler Institute for Integrative Genomics

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Gibney PA, et al. (2013) Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome. G3 (Bethesda) 3(8):1335-40
Center participants : Botstein D, Matese JC
Links : PubMed | Full Text
Commisso C, et al. (2013) Macropinocytosis of protein is an amino acid supply route in Ras-transformed cells. Nature 497(7451):633-7
Center participants : Rabinowitz JD
Links : PubMed
Wang YC, et al. (2013) Distinct Rap1 Activity States Control the Extent of Epithelial Invagination via alpha-Catenin. Dev Cell 25(3):299-309
Center participants : Wieschaus EF
Links : PubMed
Berger B, et al. (2013) Computational solutions for omics data. Nat Rev Genet 14(5):333-46
Center participants : Singh M
Links : PubMed
Koyuncu E, et al. (2013) Saturated very long chain Fatty acids are required for the production of infectious human cytomegalovirus progeny. PLoS Pathog 9(5):e1003333
Center participants : Rabinowitz JD, Shenk T
Links : PubMed
Schneider ER, et al. (2013) Calcium-based dendritic excitability and its regulation in the deep cerebellar nuclei. J Neurophysiol 109(9):2282-92
Center participants : Wang SS
Links : PubMed
Evertts AG, et al. (2013) Quantitative Dynamics of the Link between Cellular Metabolism and Histone Acetylation. J Biol Chem 288(17):12142-51
Center participants : Coller HA, Garcia BA
Links : PubMed
Little SC and Gregor T (2013) Sorting sloppy sonic. Cell 153(3):509-10
Center participants : Gregor T
Links : PubMed
Liu F, et al. (2013) Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network. Proc Natl Acad Sci U S A 110(17):6724-9
Center participants : Gregor T
Links : PubMed
Schumer M, et al. (2013) An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences. Evolution 67(4):1155-68
Center participants : Andolfatto P
Links : PubMed
Nadell CD, et al. (2013) Cutting through the complexity of cell collectives. Proc Biol Sci 280(1755):20122770
Center participants : Bassler BL, Levin SA
Links : PubMed
Drescher K, et al. (2013) Biofilm streamers cause catastrophic disruption of flow with consequences for environmental and medical systems. Proc Natl Acad Sci U S A 110(11):4345-50
Center participants : Bassler BL
Links : PubMed
Park CY, et al. (2013) Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol 9(3):e1002957
Center participants : Troyanskaya OG
Links : PubMed
Osterfield M, et al. (2013) Three-dimensional epithelial morphogenesis in the developing Drosophila egg. Dev Cell 24(4):400-10
Center participants : Schupbach T, Shvartsman SY, Wieschaus E
Links : PubMed
Bloom JS, et al. (2013) Finding the sources of missing heritability in a yeast cross. Nature 494(7436):234-7
Center participants : Kruglyak L
Links : PubMed
Wang S and Wingreen NS (2013) Cell shape can mediate the spatial organization of the bacterial cytoskeleton. Biophys J 104(3):541-52
Center participants : Wang S, Wingreen NS
Links : PubMed
Song J and Singh M (2013) From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. PLoS Comput Biol 9(2):e1002910
Center participants : Singh M
Links : PubMed
Ghersi D and Singh M (2013) Disentangling function from topology to infer the network properties of disease genes. BMC Syst Biol 7:5
Center participants : Singh M
Links : PubMed
Dubuis JO, et al. (2013) Accurate measurements of dynamics and reproducibility in small genetic networks. Mol Syst Biol 9:639
Center participants : Gregor T
Links : PubMed
Xu YF, et al. (2013) Nucleotide degradation and ribose salvage in yeast. Mol Syst Biol 9:665
Center participants : Broach JR, Caudy AA, Rabinowitz JD
Links : PubMed
Hu TT, et al. (2013) A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence. Genome Res 23(1):89-98
Center participants : Andolfatto P
Links : PubMed
Swart EC, et al. (2013) The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 11(1):e1001473
Center participants : Matese JC, Parsons L
Links : PubMed | Full Text
Suh EJ, et al. (2012) A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts. Genome Biol 13(12):R121
Center participants : Coller HA
Links : PubMed
Pino P, et al. (2012) A tetracycline-repressible transactivator system to study essential genes in malaria parasites. Cell Host Microbe 12(6):824-34
Center participants : Llinas M
Links : PubMed
Nair VD, et al. (2012) Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells. Mol Cell Biol 32(23):4861-76
Center participants : Troyanskaya O
Links : PubMed
Babbitt SE, et al. (2012) Plasmodium falciparum responds to amino acid starvation by entering into a hibernatory state. Proc Natl Acad Sci U S A 109(47):E3278-87
Center participants : Llinas M
Links : PubMed
Gelbart MA, et al. (2012) Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis. Proc Natl Acad Sci U S A 109(47):19298-303
Center participants : Kaschube M, Wieschaus EF
Links : PubMed
Grimm O, et al. (2012) Torso RTK controls Capicua degradation by changing its subcellular localization. Development 139(21):3962-8
Center participants : Shvartsman SY, Wieschaus E
Links : PubMed
Evertts AG and Coller HA (2012) Back to the origin: reconsidering replication, transcription, epigenetics, and cell cycle control. Genes Cancer 3(11-12):678-96
Center participants : Coller HA
Links : PubMed
Murugan A, et al. (2012) Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proc Natl Acad Sci U S A 109(40):16161-6
Center participants : Callan CG Jr
Links : PubMed
Straimer J, et al. (2012) Site-specific genome editing in Plasmodium falciparum using engineered zinc-finger nucleases. Nat Methods 9(10):993-8
Center participants : Llinas M
Links : PubMed
Zhen Y, et al. (2012) Parallel molecular evolution in an herbivore community. Science 337(6102):1634-7
Center participants : Andolfatto P
Links : PubMed
Kuhlman TE and Cox EC (2012) Gene location and DNA density determine transcription factor distributions in Escherichia coli. Mol Syst Biol 8:610
Center participants : Cox EC
Links : PubMed
Legesse-Miller A, et al. (2012) Quiescent fibroblasts are protected from proteasome inhibition-mediated toxicity. Mol Biol Cell 23(18):3566-81
Center participants : Coller HA
Links : PubMed
Yakhnina AA and Gitai Z (2012) The small protein MbiA interacts with MreB and modulates cell shape in Caulobacter crescentus. Mol Microbiol 85(6):1090-104
Center participants : Gitai Z
Links : PubMed
Khan Z, et al. (2012) Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS. Mol Syst Biol 8:602
Center participants : Caudy AA, Kruglyak L, Perlman DH, Singh M
Links : PubMed
Garrigan D, et al. (2012) Genome sequencing reveals complex speciation in the Drosophila simulans clade. Genome Res 22(8):1499-511
Center participants : Andolfatto P
Links : PubMed
Wong AK, et al. (2012) IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res 40(Web Server issue):W484-90
Center participants : Troyanskaya OG
Links : PubMed
Lee SH, et al. (2012) BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection. Proc Natl Acad Sci U S A 109(24):9575-80
Center participants : Garcia BA, Shenk T
Links : PubMed
Xu YF, et al. (2012) Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase. Nat Chem Biol 8(6):562-8
Center participants : Rabinowitz JD
Links : PubMed
Slotte T, et al. (2012) GENETIC ARCHITECTURE AND ADAPTIVE SIGNIFICANCE OF THE SELFING SYNDROME IN CAPSELLA. Evolution 66(5):1360-1374
Center participants : Andolfatto P
Links : PubMed
Valcourt JR, et al. (2012) Staying alive: metabolic adaptations to quiescence. Cell Cycle 11(9):1680-96
Center participants : Coller HA
Links : PubMed
Wang YC, et al. (2012) Differential positioning of adherens junctions is associated with initiation of epithelial folding. Nature 484(7394):390-3
Center participants : Kaschube M, Wieschaus EF
Links : PubMed
Klein EY, et al. (2012) Relationship between treatment-seeking behaviour and artemisinin drug quality in Ghana. Malar J 11:110
Center participants : Levin SA, Llinas M
Links : PubMed
Morrison AH, et al. (2012) Quantifying the Bicoid morphogen gradient in living fly embryos. Cold Spring Harb Protoc 2012(4):398-406
Center participants : Gregor T
Links : PubMed
Wang S, et al. (2012) Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall. Proc Natl Acad Sci U S A 109(10):E595-604
Center participants : Shaevitz JW, Wang S
Links : PubMed
Melnikov A, et al. (2012) Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30(3):271-7
Center participants : Callan CG Jr
Links : PubMed
Ehrenreich IM, et al. (2012) Genetic architecture of highly complex chemical resistance traits across four yeast strains. PLoS Genet 8(3):e1002570
Center participants : Kruglyak L
Links : PubMed
Torabi N and Kruglyak L (2012) Genetic basis of hidden phenotypic variation revealed by increased translational readthrough in yeast. PLoS Genet 8(3):e1002546
Center participants : Kruglyak L
Links : PubMed
Andersen EC, et al. (2012) Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Nat Genet 44(3):285-90
Center participants : Kruglyak L
Links : PubMed
Chikina MD and Troyanskaya OG (2012) An effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics 28(5):607-13
Center participants : Troyanskaya OG
Links : PubMed
Kristensen VN, et al. (2012) Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling. Proc Natl Acad Sci U S A 109(8):2802-7
Center participants : Troyanskaya OG
Links : PubMed
Ghosh R, et al. (2012) Natural variation in a chloride channel subunit confers avermectin resistance in C. elegans. Science 335(6068):574-8
Center participants : Kruglyak L
Links : PubMed
Cooper RM, et al. (2012) An excitable cortex and memory model successfully predicts new pseudopod dynamics. PLoS One 7(3):e33528
Center participants : Cox EC, Wingreen NS
Links : PubMed
Chen J, et al. (2012) Accumulation of an antidepressant in vesiculogenic membranes of yeast cells triggers autophagy. PLoS One 7(4):e34024
Center participants : Perlstein EO
Links : PubMed
Zhen Y and Andolfatto P (2012) Methods to detect selection on noncoding DNA. Methods Mol Biol 856:141-59
Center participants : Andolfatto P
Links : PubMed
Taylor MP, et al. (2012) Visualization of an alphaherpesvirus membrane protein that is essential for anterograde axonal spread of infection in neurons.LID - 10.1128/mBio.00063-12 [doi]LID - e00063-12 [pii] MBio 3(2):
Center participants : Enquist LW
Links : PubMed
Leffler EM, et al. (2012) Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 10(9):e1001388
Center participants : Andolfatto P
Links : PubMed
Cande J, et al. (2012) Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS One 7(8):e43888
Center participants : Andolfatto P
Links : PubMed
Kafsack BF, et al. (2012) New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community. Malar J 11():187
Center participants : Llinas M
Links : PubMed
Guan Y, et al. (2012) Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol 8(9):e1002694
Center participants : Troyanskaya OG
Links : PubMed
Khan Z, et al. (2011) Accurate proteome-wide protein quantification from high-resolution 15N mass spectra. Genome Biol 12(12):R122
Center participants : Caudy AA, Kruglyak L, Perlman DH, Singh M, Tavazoie S
Links : PubMed
Pane A, et al. (2011) The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. EMBO J 30(22):4601-15
Center participants : Schupbach T, Singh M
Links : PubMed
Strelko CL, et al. (2011) Itaconic acid is a mammalian metabolite induced during macrophage activation. J Am Chem Soc 133(41):16386-9
Center participants : Rabinowitz JD
Links : PubMed
Szpara ML, et al. (2011) A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PLoS Pathog 7(10):e1002282
Center participants : Enquist LW, Parsons L
Links : PubMed
van Teeffelen S, et al. (2011) The bacterial actin MreB rotates, and rotation depends on cell-wall assembly. Proc Natl Acad Sci U S A 108(38):15822-7
Center participants : Gitai Z, Shaevitz JW, Wang S, Wingreen NS
Links : PubMed
Vastag L, et al. (2011) Divergent effects of human cytomegalovirus and herpes simplex virus-1 on cellular metabolism. PLoS Pathog 7(7):e1002124
Center participants : Rabinowitz JD, Shenk TE
Links : PubMed
Greene CS and Troyanskaya OG (2011) PILGRM: an interactive data-driven discovery platform for expert biologists. Nucleic Acids Res 39(Web Server issue):W368-74
Center participants : Troyanskaya OG
Links : PubMed
Clasquin MF, et al. (2011) Riboneogenesis in yeast. Cell 145(6):969-80
Center participants : Caudy AA, Rabinowitz JD
Links : PubMed
Persikov AV and Singh M (2011) An expanded binding model for Cys(2)His(2) zinc finger protein-DNA interfaces. Phys Biol 8(3):035010
Center participants : Singh M
Links : PubMed
Li L, et al. (2011) 'Dicty dynamics': Dictyostelium motility as persistent random motion. Phys Biol 8(4):046006
Center participants : Cox EC
Links : PubMed
Teng SW, et al. (2011) Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi. Mol Syst Biol 7():491
Center participants : Bassler BL, Wingreen NS
Links : PubMed
Haugo AC, et al. (2011) Herpes simplex virus type 1 pUL34 plays a critical role in cell-to-cell spread of virus in addition to its role in virus replication. J Virol ():
Center participants : Enquist LW, Parsons L
Links : PubMed
Sun M, et al. (2011) Motor-driven intracellular transport powers bacterial gliding motility. Proc Natl Acad Sci U S A 108(18):7559-64
Center participants : Shaevitz JW
Links : PubMed
Tolkunov D, et al. (2011) Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters. Mol Biol Cell ():
Center participants : Broach JR
Links : PubMed
Gordon PV, et al. (2011) Local kinetics of morphogen gradients. Proc Natl Acad Sci U S A 108(15):6157-62
Center participants : Shvartsman SY
Links : PubMed
Andolfatto P, et al. (2011) Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res 21(4):610-7
Center participants : Andolfatto P
Links : PubMed
Talbot J and Schotz EM (2011) Quantitative characterization of planarian wild-type behavior as a platform for screening locomotion phenotypes. J Exp Biol 214(Pt 7):1063-7
Center participants : Schotz EM
Links : PubMed
Ochoa A, et al. (2011) Using context to improve protein domain identification. BMC Bioinformatics 12(1):90
Center participants : Llinas M, Singh M
Links : PubMed
Bendesky A, et al. (2011) Catecholamine receptor polymorphisms affect decision-making in C. elegans. Nature ():
Center participants : Kruglyak L
Links : PubMed
Little SC, et al. (2011) The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biol 9(3):e1000596
Center participants : Gregor T, Wieschaus EF
Links : PubMed
Card JP, et al. (2011) Microdissection of neural networks by conditional reporter expression from a Brainbow herpesvirus. Proc Natl Acad Sci U S A 108(8):3377-82
Center participants : Enquist LW
Links : PubMed
Klosinska MM, et al. (2011) Yeast cells can access distinct quiescent states. Genes Dev 25(4):336-49
Center participants : Broach JR, Rabinowitz JD
Links : PubMed
Guo JY, et al. (2011) Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes Dev ():
Center participants : Coller HA, Rabinowitz JD
Links : PubMed
Chung K, et al. (2011) A microfluidic array for large-scale ordering and orientation of embryos. Nat Methods 8(2):171-6
Center participants : Shvartsman SY
Links : PubMed
Kim Y, et al. (2011) Substrate-dependent control of MAPK phosphorylation in vivo. Mol Syst Biol 7():467
Center participants : Shvartsman SY
Links : PubMed
Vastag L, et al. (2011) Remodeling of the metabolome during early frog development. PLoS One 6(2):e16881
Center participants : Rabinowitz JD
Links : PubMed
Wong LC, et al. (2011) The functioning of the Drosophila CPEB protein Orb is regulated by phosphorylation and requires casein kinase 2 activity. PLoS One 6(9):e24355
Center participants : Perlman D, Schedl P
Links : PubMed
Chikina MD and Troyanskaya OG (2011) Accurate quantification of functional analogy among close homologs. PLoS Comput Biol 7(2):e1001074
Center participants : Troyanskaya OG
Links : PubMed
Guan Y, et al. (2011) Nucleosome-coupled expression differences in closely-related species. BMC Genomics 12():466
Center participants : Dunham MJ, Troyanskaya OG
Links : PubMed
Gresham D, et al. (2011) System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae. Genetics 187(1):299-317
Center participants : Botstein D, Caudy A, Storey JD
Links : PubMed
Baryshnikova A, et al. (2010) Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nat Methods 7(12):1017-24
Center participants : Troyanskaya OG
Links : PubMed
Mehta P and Gregor T (2010) Approaching the molecular origins of collective dynamics in oscillating cell populations. Curr Opin Genet Dev 20(6):574-80
Center participants : Gregor T
Links : PubMed
Painter HJ, et al. (2010) The Apicomplexan AP2 family: Integral factors regulating Plasmodium development. Mol Biochem Parasitol ():
Center participants : Llinas M
Links : PubMed
Wellen KE, et al. (2010) The hexosamine biosynthetic pathway couples growth factor-induced glutamine uptake to glucose metabolism. Genes Dev ():
Center participants : Coller HA, Rabinowitz JD
Links : PubMed
Kaschube M, et al. (2010) Universality in the evolution of orientation columns in the visual cortex. Science 330(6007):1113-6
Center participants : Kaschube M
Links : PubMed
Park CY, et al. (2010) Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PLoS Comput Biol 6(11):e1001009
Center participants : Troyanskaya OG
Links : PubMed
Berezhkovskii AM, et al. (2010) How long does it take to establish a morphogen gradient? Biophys J 99(8):L59-61
Center participants : Shvartsman SY
Links : PubMed
Tipping M, et al. (2010) beta-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development. EMBO J 29(19):3222-35
Center participants : Shvartsman SY
Links : PubMed
Doubrovinski K, et al. (2010) A mesoscopic description of contractile cytoskeletal meshworks. Eur Phys J E Soft Matter 33(2):105-10
Center participants : Kaschube M
Links : PubMed
Plata G, et al. (2010) Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network. Mol Syst Biol 6():408
Center participants : Llinas M
Links : PubMed
Szpara ML, et al. (2010) A common neuronal response to alphaherpesvirus infection. J Neuroimmune Pharmacol 5(3):418-27
Center participants : Enquist LW
Links : PubMed
Greene CS and Troyanskaya OG (2010) Integrative systems biology for data-driven knowledge discovery. Semin Nephrol 30(5):443-54
Center participants : Troyanskaya OG
Links : PubMed
Olszewski KL, et al. (2010) Branched tricarboxylic acid metabolism in Plasmodium falciparum. Nature 466(7307):774-8
Center participants : Garcia BA, Llinas M, Rabinowitz JD
Links : PubMed
Manning ML, et al. (2010) Coaction of intercellular adhesion and cortical tension specifies tissue surface tension. Proc Natl Acad Sci U S A 107(28):12517-22
Center participants : Schoetz EM
Links : PubMed | Full Text
Keil W, et al. (2010) Reorganization of columnar architecture in the growing visual cortex. Proc Natl Acad Sci U S A ():
Center participants : Kaschube M
Links : PubMed
Kwon YK, et al. (2010) Antifolate-induced depletion of intracellular glycine and purines inhibits thymineless death in E. coli ACS Chem Biol ():
Center participants : Rabinowitz JD
Links : PubMed
Goodarzi H, et al. (2010) Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol 6():378
Center participants : Rabinowitz JD, Tavazoie S
Links : PubMed
Kuchma SL, et al. (2010) Cyclic-di-GMP-mediated repression of swarming motility by Pseudomonas aeruginosa: the pilY1 gene and its impact on surface-associated behaviors. J Bacteriol 192(12):2950-64
Center participants : Rabinowitz JD
Links : PubMed
Monds RD, et al. (2010) Di-adenosine tetraphosphate (Ap4A) metabolism impacts biofilm formation by Pseudomonas fluorescens via modulation of c-di-GMP-dependent pathways. J Bacteriol 192(12):3011-23
Center participants : Rabinowitz JD
Links : PubMed
Sample C and Shvartsman SY (2010) Multiscale modeling of diffusion in the early Drosophila embryo. Proc Natl Acad Sci U S A 107(22):10092-6
Center participants : Shvartsman SY
Links : PubMed
McKenney PT, et al. (2010) A distance-weighted interaction map reveals a previously uncharacterized layer of the Bacillus subtilis spore coat. Curr Biol 20(10):934-8
Center participants : Gitai Z
Links : PubMed
Gregor T, et al. (2010) The onset of collective behavior in social amoebae. Science 328(5981):1021-5
Center participants : Gregor T
Links : PubMed
Teng SW, et al. (2010) Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell. Biophys J 98(9):2024-31
Center participants : Bassler BL, Wingreen NS
Links : PubMed
Kinney JB, et al. (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A 107(20):9158-63
Center participants : Callan CG Jr, Cox EC
Links : PubMed
Wang S, et al. (2010) Actin-like cytoskeleton filaments contribute to cell mechanics in bacteria. Proc Natl Acad Sci U S A 107(20):9182-5
Center participants : Shaevitz JW
Links : PubMed
Szpara ML, et al. (2010) Sequence variability in clinical and laboratory isolates of herpes simplex virus 1 reveals new mutations. J Virol 84(10):5303-13
Center participants : Enquist LW, Parsons L
Links : PubMed
Landis JN and Murphy CT (2010) Integration of diverse inputs in the regulation of Caenorhabditis elegans DAF-16/FOXO. Dev Dyn 239(5):1405-12
Center participants : Murphy CT
Links : PubMed
Lu W, et al. (2010) Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal Chem 82(8):3212-21
Center participants : Caudy AA, Rabinowitz JD
Links : PubMed
Jiang P and Singh M (2010) SPICi: a fast clustering algorithm for large biological networks. Bioinformatics 26(8):1105-11
Center participants : Singh M
Links : PubMed
Ehrenreich IM, et al. (2010) Dissection of genetically complex traits with extremely large pools of yeast segregants. Nature 464(7291):1039-42
Center participants : Caudy AA, Kruglyak L
Links : PubMed
Forman JJ and Coller HA (2010) The code within the code: MicroRNAs target coding regions. Cell Cycle 9(8):
Center participants : Coller HA
Links : PubMed
Silverman SJ, et al. (2010) Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate. Proc Natl Acad Sci U S A 107(15):6946-51
Center participants : Botstein D, Parsons L
Links : PubMed
Cowles KN and Gitai Z (2010) Surface association and the MreB cytoskeleton regulate pilus production, localization and function in Pseudomonas aeruginosa. Mol Microbiol ():
Center participants : Gitai Z
Links : PubMed
Otto TD, et al. (2010) New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol 76(1):12-24
Center participants : Llinas M
Links : PubMed
Walczak AM, et al. (2010) Optimizing information flow in small genetic networks. II. Feed-forward interactions. Phys Rev E Stat Nonlin Soft Matter Phys 81(4 Pt 1):041905
Center participants : Bialek W
Links : PubMed
Kuhlman TE and Cox EC (2010) Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res 38(6):e92
Center participants : Cox EC
Links : PubMed
Kaletsky R and Murphy CT (2010) The role of insulin/IGF-like signaling in C. elegans longevity and aging. Dis Model Mech ():
Center participants : Murphy CT
Links : PubMed
Ng WL, et al. (2010) Probing bacterial transmembrane histidine kinase receptor-ligand interactions with natural and synthetic molecules. Proc Natl Acad Sci U S A 107(12):5575-80
Center participants : Bassler BL, Wingreen NS
Links : PubMed
Mora T, et al. (2010) Maximum entropy models for antibody diversity. Proc Natl Acad Sci U S A 107(12):5405-10
Center participants : Bialek W, Callan CG Jr
Links : PubMed
Ward PS, et al. (2010) The Common Feature of Leukemia-Associated IDH1 and IDH2 Mutations Is a Neomorphic Enzyme Activity Converting alpha-Ketoglutarate to 2-Hydroxyglutarate. Cancer Cell 17(3):225-234
Center participants : Coller HA, Rabinowitz JD
Links : PubMed
Kim Y, et al. (2010) MAPK substrate competition integrates patterning signals in the Drosophila embryo. Curr Biol 20(5):446-51
Center participants : Shvartsman SY
Links : PubMed
Martin AC, et al. (2010) Integration of contractile forces during tissue invagination. J Cell Biol 188(5):735-49
Center participants : Kaschube M, Wieschaus EF
Links : PubMed
Tu KC, et al. (2010) Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response. Mol Cell 37(4):567-79
Center participants : Bassler BL, Wingreen NS
Links : PubMed
Kafsack BF and Llinas M (2010) Eating at the table of another: metabolomics of host-parasite interactions. Cell Host Microbe 7(2):90-9
Center participants : Llinas M
Links : PubMed
Zee BM, et al. (2010) In vivo residue-specific histone methylation dynamics. J Biol Chem 285(5):3341-50
Center participants : Garcia BA, Levin RS, Wingreen NS
Links : PubMed
Gresham D, et al. (2010) Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proc Natl Acad Sci U S A 107(4):1482-7
Center participants : Botstein D, Kruglyak L
Links : PubMed | Full Text
Lindner SE, et al. (2010) Structural determinants of DNA binding by a P. falciparum ApiAP2 transcriptional regulator. J Mol Biol 395(3):558-67
Center participants : Llinas M
Links : PubMed
Costanzo M, et al. (2010) The genetic landscape of a cell. Science 327(5964):425-31
Center participants : Troyanskaya OG
Links : PubMed
Guan Y, et al. (2010) Systematic planning of genome-scale experiments in poorly studied species. PLoS Comput Biol 6(3):e1000698
Center participants : Caudy A, Dunham M, Troyanskaya O
Links : PubMed
Goyal S, et al. (2010) Achieving optimal growth through product feedback inhibition in metabolism. PLoS Comput Biol 6(6):e1000802
Center participants : Rabinowitz JD, Wingreen NS
Links : PubMed
Kauffman AL, et al. (2010) Insulin signaling and dietary restriction differentially influence the decline of learning and memory with age. PLoS Biol 8(5):e1000372
Center participants : Murphy CT
Links : PubMed
Lemons JM, et al. (2010) Quiescent fibroblasts exhibit high metabolic activity. PLoS Biol 8(10):e1000514
Center participants : Coller HA, Rabinowitz JD, Rabitz HA
Links : PubMed
Campbell TL, et al. (2010) Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog 6(10):e1001165
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