Princeton University
Lewis-Sigler Institute for Integrative Genomics

Princeton
Center for Quantitative Biology Publications

Faculty , Fellows

Publications

Bioinformatics tools and resources
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Lewis-Sigler Institute Microarray Facility
Lewis-Sigler Institute Imaging Facility
Princeton Mass Spectrometry Facility

Undergraduate Curriculum
Princeton Molecular Biology Outreach

Harvard-Princeton NIGMS Centers Seminars
Tuesday, May 13, 2008
From nuclear pores to mucus - a study of hydrogel-based biofilters
Katharina Ribbeck , Harvard University FAS Center for Systems Biology
Home and Away: Harvard-Princeton NIGMS Centers Seminars (101 Carl Icahn Laboratory, 4:30PM)

Goodpaster T, et al. (2008) An Immunohistochemical Method for Identifying Fibroblasts in Formalin-fixed, Paraffin-embedded Tissue. J Histochem Cytochem 56(4):347-58
Center participants : Coller HA
Links : PubMed
Kryazhimskiy S, et al. (2008) Natural selection for nucleotide usage at synonymous and non-synonymous sites in the influenza A genes. J Virol ():
Links : PubMed
Eva-Maria Schoetz, Rebecca D. Burdine, Frank Julicher, Malcom S. Steinberg, Carl.-Philipp Heisenberg, and Ramsey A. Foty. Quantitative differences in tissue surface tension influence zebrafish germlayer positioning. HFSP Journal -- February 2008. Volume 2, Issue 1, pp. 1-56
Center participants : Eva-Maria Schoetz
Links : HFSP Journal
Seidel HS, et al. (2008) Widespread Genetic Incompatibility in C. Elegans Maintained by Balancing Selection. Science ():
Center participants : Kruglyak L
Links : PubMed
Toward a statistical mechanics of four letter words. GJ Stephens & W Bialek, arXiv.org:0801.0253 [q-bio.NC] (2008).
Center participants : W Bialek
Links : arXiv.org
Brauer MJ, et al. (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell 19(1):352-67
Center participants : Botstein D , Matese JC , Troyanskaya OG
Links : PubMed | Full Text | Web Supplement
Coppey M, et al. (2007) Modeling the bicoid gradient: diffusion and reversible nuclear trapping of a stable protein. Dev Biol 312(2):623-30
Center participants : Shvartsman SY
Links : PubMed
Yakoby N, et al. (2007) Drosophila eggshell is patterned by sequential action of feedforward and feedback loops. Development ():
Center participants : Schupbach T , Shvartsman SY
Links : PubMed
Foss EJ, et al. (2007) Genetic basis of proteome variation in yeast. Nat Genet ():
Center participants : Kruglyak L
Links : PubMed
Shaw WM, et al. (2007) The C. elegans TGF-beta Dauer pathway regulates longevity via insulin signaling. Curr Biol 17(19):1635-45
Center participants : Murphy CT
Links : PubMed
Desai MM, et al. (2007) Evolution can favor antagonistic epistasis. Genetics 177(2):1001-10
Center participants : Desai MM
Links : PubMed
Qiao L, et al. (2007) Bistability and oscillations in the Huang-Ferrell model of MAPK signaling. PLoS Comput Biol 3(9):1819-26
Center participants : Shvartsman SY
Links : PubMed
Hibbs MA, et al. (2007) Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics ():
Center participants : Li K , Troyanskaya OG
Links : PubMed
Girgis HS, et al. (2007) A comprehensive genetic characterization of bacterial motility. PLoS Genet 3(9):e154
Center participants : Ryu WS , Tavazoie S
Links : PubMed | Full Text
Coller HA, et al. (2007) "Myc'ed messages": myc induces transcription of E2F1 while inhibiting its translation via a microRNA polycistron. PLoS Genet 3(8):e146
Center participants : Coller HA
Links : PubMed
Torres EM, et al. (2007) Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science 317(5840):916-24
Center participants : Dunham MJ
Links : PubMed
Yorimitsu T, et al. (2007) Protein Kinase A and Sch9 Cooperatively Regulate Induction of Autophagy in Saccharomyces cerevisiae. Mol Biol Cell ():
Center participants : Broach JR
Links : PubMed
Kruglyak L and Stern DL (2007) Evolution. An embarrassment of switches. Science 317(5839):758-9
Center participants : Kruglyak L
Links : PubMed
Coller HA (2007) What's taking so long? S-phase entry from quiescence versus proliferation. Nat Rev Mol Cell Biol 8(8):667-70
Center participants : Coller HA
Links : PubMed
Simonsen L, et al. (2007) The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Mol Biol Evol 24(8):1811-20
Links : PubMed
Sawai S, et al. (2007) High-throughput analysis of spatio-temporal dynamics in Dictyostelium. Genome Biol 8(7):R144
Center participants : Cox EC
Links : PubMed
Gregor T, et al. (2007) Stability and nuclear dynamics of the bicoid morphogen gradient. Cell 130(1):141-52
Center participants : Bialek W , Tank DW , Wieschaus EF
Links : PubMed
Gregor T, et al. (2007) Probing the limits to positional information. Cell 130(1):153-64
Center participants : Bialek W , Tank DW , Wieschaus EF
Links : PubMed
Markowetz F and Troyanskaya OG (2007) Computational identification of cellular networks and pathways. Mol Biosyst 3(7):478-82
Center participants : Troyanskaya OG
Links : PubMed | Full Text
Markowetz F, et al. (2007) Nested effects models for high-dimensional phenotyping screens. Bioinformatics 23(13):i305-12
Center participants : Troyanskaya OG
Links : PubMed
Desai MM and Fisher DS (2007) Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics 176(3):1759-98
Center participants : Desai MM
Links : PubMed
Urban J, et al. (2007) Sch9 is a major target of TORC1 in Saccharomyces cerevisiae. Mol Cell 26(5):663-74
Center participants : Broach JR
Links : PubMed
Feierbach B, et al. (2007) In vitro analysis of trans-neuronal spread of an alpha-herpesvirus infection in peripheral nervous system neurons. J Virol ():
Center participants : Enquist LW
Links : PubMed
Perlstein EO, et al. (2007) Genetic basis of individual differences in the response to small-molecule drugs in yeast. Nat Genet 39(4):496-502
Center participants : Kruglyak L
Links : PubMed
De Renzis S, et al. (2007) Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol 5(5):e117
Center participants : Tavazoie S , Wieschaus EF
Links : PubMed
Desai MM, et al. (2007) The speed of evolution and maintenance of variation in asexual populations. Curr Biol 17(5):385-94
Center participants : Desai MM
Links : PubMed
McClean MN, et al. (2007) Cross-talk and decision making in MAP kinase pathways. Nat Genet 39(3):409-14
Center participants : Broach JR
Links : PubMed
Xavier KB, et al. (2007) Phosphorylation and processing of the quorum-sensing molecule autoinducer-2 in enteric bacteria. ACS Chem Biol 2(2):128-36
Center participants : Bassler BL , Rabinowitz J
Links : PubMed
Guan Y, et al. (2007) Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 175(2):933-43
Center participants : Dunham MJ , Troyanskaya OG
Links : PubMed
Bao Q, et al. (2007) Calcium blocks formation of apoptosome by preventing nucleotide exchange in Apaf-1. Mol Cell 25(2):181-92
Center participants : Rabinowitz JD
Links : PubMed
Tu KC and Bassler BL (2007) Multiple small RNAs act additively to integrate sensory information and control quorum sensing in Vibrio harveyi. Genes Dev 21(2):221-33
Center participants : Bassler BL
Links : PubMed
Schacherer J, et al. (2007) Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains. PLoS ONE 2():e322
Center participants : Botstein D , Dolinski K , Kruglyak L
Links : PubMed | Full Text | Web Supplement
Demeter J, et al. (2007) The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 35(Database issue):D766-70
Center participants : Matese JC
Links : PubMed
Elemento O, Slomin M, Tavazoie S (2007) A universal framework for regulatory element discovery across all genomes and data-types Molecular Cell (accepted)
Center participants : Tavazoie S
Huttenhower C, et al. (2007) Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. BMC Bioinformatics 8():250
Center participants : Coller HA , Troyanskaya OG
Links : PubMed
Güldal, C.G., Koblish, H.K., Schneper, L., Wang, Y., Davis, C., Breitkreutz, A., Tyers M., Broach J.R. (2007) Ras Affects Filamentous Growth in Saccharomyces cerevisiae Solely Through Regulation of Protein Kinase A. Proc. Natl. Acad. Sci., USA, Submitted.
Center participants : Broach J.R.
Miller DL, et al. (2007) Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival. Genome Biol 8(4):R58
Center participants : Coller HA
Links : PubMed
Bongo LA, Wallace G, Larsen T, Li K, Troyanskaya OG. Systems Support for Remote Visualization of Genomics Applications over Wide Area Networks. Proceedings of the International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology. In: Lecture Notes in Computer Science. Springer Berlin/Heidelberg, 2007. (in press)
Center participants : Li K , Troyanskaya OG.
Rediscovering the power of pairwise interactions. W Bialek & R Ranganathan, arXiv.org:0712.4397 [q-bio.QM] (2007).
Center participants : W Bialek
Links : arXiv.org
Information flow and optimization in transcriptional regulation. G Tkacik, CG Callan Jr & W Bialek, arXiv:0705.0313 [q–bio.MN] (2007).
Center participants : W Bialek , WS Ryu
Links : arXiv.org
The role of input noise in transcriptional regulation. G Tkacik, T Gregor & W Bialek, q–bio.MN/0701002 (2007).
Center participants : W Bialek
Links : arXiv.org
Elemento, O., Tavazoie, S. Fastcompare: A non-alignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation. Methods in Molecular Biology (in press)
Center participants : Tavazoie
Svenningsen, S.L., C.M. Waters and B.L. Bassler. 2007. A positive feedback loop involving small RNAs accelerates Vibrio cholerae’s transition out of quorum sensing mode. Genes & Development(in press)
Center participants : Bassler B.L.
Hibbs M, Wallace G, Dunham M, Li K, Troyanskaya OG. Viewing the Larger Context of Genomic Data through Horizontal Integration. Proceedings of the 11th Int. Conf. on Information Visualization (IV07), 2007.
Center participants : Dunham M , Li K , Troyanskaya OG.
Heinicke S, et al. (2007) The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS ONE 2:e766
Center participants : Botstein D , Dolinski K
Links : PubMed
Tan, M.P., Broach, J.R.,Floudas, C.A (2007) A novel clusting approach and prediction of optimum number of clusters: II. Evaluation of normalization and pre-clustering issues. J. Bioinformatics Computational Biology, 5: 895-913
Center participants : Broach , Floudas
Cell biology: Networks, regulation, pathways. G Tkacik & W Bialek, to be published in Encyclopedia of Complexity and Systems Science, RA Meyers, ed (Springer-Verlag, Berlin, 2008); arXiv.org:0712.4385 [q-bio.MN].
Center participants : & W Bialek
Links : arXiv.org
Information and fitness. SF Taylor, N Tishby & W Bialek, arXiv.org:0712.4382 [q-bio.PE] (2007).
Center participants : & W Bialek
Links : arXiv.org
Faster solutions of the inverse pairwise Ising problem. T Broderick, M Dudik, G Tkacik, RE Schapire & W Bialek, arXiv:0712.2437 [q–bio.QM] (2007).
Center participants : & W Bialek
Links : arXiv.org
Diffusion, dimensionality and noise in transcriptional regulation. G Tkacik & W Bialek, arXiv:0712.1852 [q–bio.MN] (2007).
Center participants : & W Bialek
Links : arXiv.org
Information capacity of genetic regulatory elements. G Tkacik, CG Callan Jr & W Bialek, arXiv:0709.4209 [q–bio.MN] (2007).
Center participants : & W Bialek , CG Callan Jr
Links : arXiv.org
Dimensionality and dynamics in the behavior of C. elegans. GJ Stephens, B Johnson-Kerner, W Bialek & WS Ryu, arXiv:0705:1548 [q–bio.OT] (2007)
Center participants : Ryu WS
Links : arXiv.org
Pelham RJ, et al. (2006) Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A 103(52):19848-53
Center participants : Botstein D
Links : PubMed
Brauer MJ, et al. (2006) Conservation of the metabolomic response to starvation across two divergent microbes. Proc Natl Acad Sci U S A 103(51):19302-7
Center participants : Botstein D , Rabinowitz JD
Links : PubMed
Bazykin GA, et al. (2006) Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites. Proc Natl Acad Sci U S A 103(51):19396-401
Center participants : Levin SA
Links : PubMed
Munger J, et al. (2006) Dynamics of the Cellular Metabolome during Human Cytomegalovirus Infection. PLoS Pathog 2(12):e132
Center participants : Coller HA , Rabinowitz JD , Shenk T
Links : PubMed | Full Text
Gabriel A, et al. (2006) Global mapping of transposon location. PLoS Genet 2(12):e212
Center participants : Dunham MJ
Links : PubMed
Huang KC, et al. (2006) A curvature-mediated mechanism for localization of lipids to bacterial poles. PLoS Comput Biol 2(11):e151
Center participants : Wingreen NS
Links : PubMed
Rockman MV and Kruglyak L (2006) Genetics of global gene expression. Nat Rev Genet 7(11):862-72
Center participants : Kruglyak L
Links : PubMed
Plotkin JB, et al. (2006) Codon usage and selection on proteins. J Mol Evol 63(5):635-53
Center participants : Desai MM
Links : PubMed
Hess DC, et al. (2006) Ammonium toxicity and potassium limitation in yeast. PLoS Biol 4(11):e351
Center participants : Botstein D , Rabinowitz JD
Links : PubMed
Waters CM and Bassler BL (2006) The Vibrio harveyi quorum-sensing system uses shared regulatory components to discriminate between multiple autoinducers. Genes Dev 20(19):2754-67
Center participants : Bassler BL
Links : PubMed
Huttenhower C, et al. (2006) A scalable method for integration and functional analysis of multiple microarray data sets. Bioinformatics ():
Center participants : Troyanskaya OG
Links : PubMed
Wingreen N and Botstein D (2006) Back to the future: education for systems-level biologists. Nat Rev Mol Cell Biol ():
Center participants : Botstein D , Wingreen N
Links : PubMed
Eberle MA, et al. (2006) Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. PLoS Genet 2(9):e142
Center participants : Kruglyak L
Links : PubMed
Wingreen NS and Levin SA (2006) Cooperation among microorganisms. PLoS Biol 4(9):e299
Center participants : Levin SA , Wingreen NS
Links : PubMed
Reeves GT, et al. (2006) Quantitative models of developmental pattern formation. Dev Cell 11(3):289-300
Center participants : Schupbach T , Shvartsman SY
Links : PubMed
Ruderfer DM, et al. (2006) Population genomic analysis of outcrossing and recombination in yeast. Nat Genet ():
Center participants : Kruglyak L
Links : PubMed
Feierbach B, et al. (2006) Alpha-herpesvirus infection induces the formation of nuclear actin filaments. PLoS Pathog 2(8):e85
Center participants : Enquist LW
Links : PubMed
Goentoro LA, et al. (2006) Quantifying the Gurken morphogen gradient in Drosophila oogenesis. Dev Cell 11(2):263-72
Center participants : Schupbach T , Shvartsman SY
Links : PubMed
Ivanova N, et al. (2006) Dissecting self-renewal in stem cells with RNA interference. Nature ():
Links : PubMed
Thomason PA, et al. (2006) A series of Dictyostelium expression vectors for recombination cloning. Plasmid ():
Center participants : Cox EC
Links : PubMed
Reguly T, et al. (2006) Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol 5(4):11
Center participants : Botstein D , Troyanskya OG , Dolinski K
Links : PubMed | Web Supplement | Full Text
Plotkin JB, et al. (2006) Estimating Selection Pressures from Limited Comparative Data. Mol Biol Evol ():
Center participants : Dushoff J
Links : PubMed
Bajad SU, et al. (2006) Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J Chromatogr A ():
Center participants : Rabinowitz JD
Links : PubMed
Golding I and Cox EC (2006) Eukaryotic transcription: what does it mean for a gene to be 'on'? Curr Biol 16(10):R371-3
Center participants : Cox EC
Links : PubMed
Riehle MM, et al. (2006) Natural malaria infection in Anopheles gambiae is regulated by a single genomic control region. Science 312(5773):577-9
Center participants : Kruglyak L
Links : PubMed
Schneidman E, et al. (2006) Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 440(7087):1007-12
Center participants : Bialek W
Links : PubMed
Brauer MJ, et al. (2006) Mapping Novel Traits by Array-assisted Bulk Segregant Analysis in Saccharomyces cerevisiae. Genetics ():
Center participants : Dunham MJ
Links : PubMed | Full Text
Barutcuoglu Z, et al. (2006) Hierarchical multi-label prediction of gene function. Bioinformatics 22(7):830-6
Center participants : Troyanskaya OG
Links : PubMed
Gatbonton T, et al. (2006) Telomere Length as a Quantitative Trait: Genome-Wide Survey and Genetic Mapping of Telomere Length-Control Genes in Yeast. PLoS Genet 2(3):e35
Center participants : Kruglyak L
Links : PubMed
Golding I and Cox EC (2006) Physical nature of bacterial cytoplasm. Phys Rev Lett 96(9):098102
Center participants : Cox EC
Links : PubMed
Parker HG, et al. (2006) Molecular genetics: DNA analysis of a putative dog clone. Nature 440(7081):E1-2
Center participants : Kruglyak L
Links : PubMed
Gresham D, et al. (2006) Genome-wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA Microarray. Science ():
Center participants : Botstein D , Dunham M , Kruglyak L
Links : Web Supplement | PubMed
Perlstein EO, et al. (2006) Revealing complex traits with small molecules and naturally recombinant yeast strains. Chem Biol 13(3):319-27
Center participants : Kruglyak L
Links : PubMed
Coller HA, et al. (2006) A new description of cellular quiescence. PLoS Biol 4(3):e83
Center participants : Coller HA
Links : PubMed
Keymer JE, et al. (2006) Chemosensing in Escherichia coli: two regimes of two-state receptors. Proc Natl Acad Sci U S A 103(6):1786-91
Center participants : Wingreen NS
Links : PubMed
Paulus C, et al. (2006) Transcriptome signature of virulent and attenuated pseudorabies virus-infected rodent brain. J Virol 80(4):1773-86
Center participants : Enquist LW
Links : PubMed
Goentoro LA, et al. (2006) Quantitative analysis of the GAL4/UAS system in Drosophila oogenesis. Genesis 44(2):66-74
Center participants : Schupbach T , Shvartsman SY
Links : PubMed
Lim SF, et al. (2006) In vivo and scanning electron microscopy imaging of up-converting nanophosphors in Caenorhabditis elegans. Nano Lett 6(2):169-74
Center participants : Ryu WS , Tank D
Links : PubMed
Slonim N, et al. (2006) Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Molecular Systems Biology 10.1038/msb4100047
Center participants : Tavazoie S
Links : Full Text
Lu W, et al. (2006) A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites. J Am Soc Mass Spectrom 17(1):37-50
Center participants : Rabinowitz JD
Links : PubMed
Slonim N, et al. (2006) Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol 2():2006.0005
Center participants : Tavazoie S
Links : PubMed
Brown JA, et al. (2006) Global analysis of gene function in yeast by quantitative phenotypic profiling. Mol Syst Biol 2():2006.0001
Center participants : Troyanskaya OG
Links : PubMed
Ault AD and Broach JR (2006) Creation of GPCR-based chemical sensors by directed evolution in yeast. Protein Eng Des Sel 19(1):1-8
Center participants : Broach JR
Links : PubMed
Niida A, et al. (2006) Design and synthesis of downsized metastin (45-54) analogs with maintenance of high GPR54 agonistic activity. Bioorg Med Chem Lett 16(1):134-7
Center participants : Broach JR
Links : PubMed
Myers CL, et al. (2006) Finding function: evaluation methods for functional genomic data. BMC Genomics 7():187
Center participants : Troyanskaya OG
Links : PubMed
Bayesian Data Integration: A Functional Perspective. Series on Advances in Bioinformatics and ComputationalBiology: Computational Systems Bioinformatics. 4: 341
Center participants : Troyanskaya OG
Sealfon RS, et al. (2006) GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics 7():443
Center participants : Troyanskaya OG
Links : PubMed
Cooperativity, sensitivity and noise in biochemical signaling. W Bialek & S Setayeshgar, q–bio.MN/0601001 (2006).
Center participants : W Bialek
Links : arXiv.org
Ising models for networks of real neurons. G Tkacik, E Schneidman, MJ Berry II & W Bialek, q–bio.NC/0611072 (2006).
Center participants : W Bialek
Links : arXiv.org
Myers CL, et al. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol 6:R114
Center participants : Dolinski K , Troyanskaya OG
Links : Full Text | Web Supplement
Golding I, et al. (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123(6):1025-36
Center participants : Cox EC
Links : PubMed | Full Text
Gregor T, et al. (2005) Diffusion and scaling during early embryonic pattern formation. Proc Natl Acad Sci U S A [Epub ahead of print]
Center participants : Bialek W , Tank DW , Wieschaus EF
Links : PubMed | Full Text
Slonim N, et al. (2005) Information-based clustering. Proc Natl Acad Sci U S A [Epub ahead of print]
Center participants : Bialek W
Links : PubMed | Full Text
Wang D and Shenk T (2005) Human cytomegalovirus virion protein complex required for epithelial and endothelial cell tropism. Proc Natl Acad Sci U S A 102(50):18153-8
Center participants : Shenk T
Links : PubMed
Dolinski K and Botstein D (2005) Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res 15(12):1611-9
Center participants : Botstein D , Dolinski K
Links : PubMed | Full Text
Kruglyak L (2005) Power tools for human genetics. Nat Genet 37(12):1299-300
Center participants : Kruglyak L
Links : PubMed
Chan CS, et al. (2005) Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol 1(7):e69
Center participants : Tavazoie S
Links : PubMed
Tavazoie SF, et al. (2005) Regulation of neuronal morphology and function by the tumor suppressors Tsc1 and Tsc2. Nat Neurosci 8(12):1727-34
Center participants : Tavazoie SF
Links : PubMed
Dolinski K and Troyanskaya OG (2005) Functional genomics in Saccharomcyes cerevisiae, in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Michael J. Dunn (Editor), Lynn B. Jorde (Editor), Peter F. R. Little (Editor), Shankar Subramaniam (Editor), John Wiley & Sons
Center participants : Dolinski K , Troyanskaya O
Owen JP, Ryu WS. The effects of linear and quadratic drag on falling spheres: an undergraduate laboratory. Eur. J. Phys. 2005; 26: 1085-1091.
Center participants : Ryu WS
Ronald J, et al. (2005) Local Regulatory Variation in Saccharomyces cerevisiae. PLoS Genet 1(2):e25
Center participants : Kruglyak L
Links : PubMed
Brem RB, et al. (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436(7051):701-3
Center participants : Kruglyak L
Links : PubMed
Llinas M and del Portillo HA (2005) Mining the malaria transcriptome. Trends Parasitol 21(8):350-2
Center participants : Llinas M
Links : PubMed | Full Text
Storey JD, et al. (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biol 3(8):e267
Center participants : Kruglyak L
Links : PubMed
O'Connor DH, et al. (2005) Dissection of bidirectional synaptic plasticity into saturable unidirectional processes. J Neurophysiol 94(2):1565-73
Center participants : Wang SS
Links : PubMed
Wang D and Shenk T (2005) Human cytomegalovirus UL131 open reading frame is required for epithelial cell tropism. J Virol 79(16):10330-8
Center participants : Shenk T
Links : PubMed
Bialek W and Setayeshgar S (2005) Physical limits to biochemical signaling. Proc Natl Acad Sci U S A 102(29):10040-5
Center participants : Bialek W
Links : PubMed
O'Connor DH, et al. (2005) Graded bidirectional synaptic plasticity is composed of switch-like unitary events. Proc Natl Acad Sci U S A 102(27):9679-84
Center participants : Wang SS
Links : PubMed
Chen Y, et al. (2005) Population fitness and the regulation of Escherichia coli genes by bacterial viruses. PLoS Biol 3(7):e229
Center participants : Cox EC
Links : PubMed
Myers CL, et al. (2005) Visualization-based discovery and analysis of genomic aberrations in microarray data. BMC Bioinformatics 6(1):146
Center participants : Troyanskaya OG
Links : PubMed
Nabieva E, et al. (2005) Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21 Suppl 1():i302-i310
Center participants : Singh M
Links : PubMed
Neiditch MB, et al. (2005) Regulation of LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. Mol Cell 18(5):507-18
Center participants : Bassler BL
Links : PubMed
Hibbs MA, et al. (2005) Visualization methods for statistical analysis of microarray clusters. BMC Bioinformatics 6(1):115
Center participants : Li K , Troyanskaya OG
Links : PubMed | Full Text | Web Supplement
Eichinger L, et al. (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435(7038):43-57
Center participants : Cox EC
Links : PubMed
Brauer MJ, et al. (2005) Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell 16(5):2503-17
Center participants : Botstein D , Dolinski K
Links : PubMed | Full Text | Web Supplement
Kingsford CL, et al. (2005) Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinformatics 21(7):1028-36
Center participants : Singh M
Links : PubMed
Ulrich DL, et al. (2005) Solution structure and dynamics of LuxU from Vibrio harveyi, a phosphotransferase protein involved in bacterial quorum sensing. J Mol Biol 347(2):297-307
Center participants : Bassler BL
Links : PubMed
Troyanskaya OG (2005) Putting microarrays in a context: integrated analysis of diverse biological data. Brief Bioinform 6(1):34-43
Center participants : Troyanskaya OG
Links : PubMed | Full Text
Sawai S, et al. (2005) An autoregulatory circuit for long-range self-organization in Dictyostelium cell populations. Nature 433(7023):323-6
Center participants : Cox EC
Links : PubMed | Full Text
Troyanskaya OG (2005) Putting the 'bio' into bioinformatics. Genome Biol 6(10):351
Center participants : Troyanskaya OG
Links : PubMed | Full Text
Wallace G, et al. (2005) Tools and applications for large-scale display walls. IEEE Comput Graph Appl 25(4):24-33
Center participants : Li K , Troyanskaya O
Links : PubMed
Elemento O and Tavazoie S (2005) Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 6(2):R18
Center participants : Tavazoie S
Links : PubMed
Xavier KB and Bassler BL (2005) Regulation of uptake and processing of the quorum-sensing autoinducer AI-2 in Escherichia coli. J Bacteriol 187(1):238-48
Center participants : Bassler BL
Links : PubMed
Estimating mutual information and multi–information in large networks. N Slonim, GS Atwal, G Tkacik & W Bialek, cs.IT/0502017 (2005).
Center participants : W Bialek
Links : arXiv.org
Myers CL, et al. (2004) Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 20(18):3533-43
Center participants : Dunham MJ , Troyanskaya OG
Links : PubMed | Full Text | Web Supplement
Jorgensen P, et al. (2004) A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev 18(20):2491-505
Center participants : Broach JR
Links : PubMed
Rees CA, et al. (2004) GeneXplorer: an interactive web application for microarray data visualization and analysis. BMC Bioinformatics 5():141
Center participants : Botstein D , Matese JC
Links : PubMed | Full Text | Software Download
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