Publications by Students
Students in the Graduate Bioinformatics & Systems Biology Program have been (co)authors on numerous publications; their names are highlighted in red on the list below.
Students, please keep the Graduate Program Coordinator (Laura Gracia) appraised of your new publications and any inaccuracies or omissions on this list. Most articles are indexed in PubMed; please provide the PubMed ID numbers (PMID) for your articles if available, to expedite the maintenance of this list.
2009 2008 2007 2006 2005 2004 2003 2002 2001
2009
| Date | Publications | Links | ||
|---|---|---|---|---|
| 24 Apr 2009 | R. E. Valas, S. Yang, and P. E. Bourne. Nothing about protein structure classification makes sense except in the light of evolution. Curr Opin Struct Biol, Apr 2009. | PubMed | Journal | |
| 16 Mar 2009 | S. Yang, R. Valas, and P. E. Bourne. Evolution Studied Using Protein Structure. In Jenny Gu and Philip Bourne, Eds., Structural Bioinformatics (Methods of Biochemical Analysis), pages 559– 571. Wiley & Sons, Inc., Hoboken, N.J., 2nd edition, 2009. | Amazon | Publisher | |
| 13 Mar 2009 | S. Veretnik, C. Wills, P. Youkharibache, R. E. Valas, and P. E. Bourne. Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome. PLoS Comput Biol, 5(3), Mar 2009. | PubMed
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| 20 Feb 2009 | F. Li, I. Thiele, N. Jamshidi, and B. Ø. Palsson. Identification of potential pathway mediation targets in Toll-like receptor signaling. PLoS Comput Biol, 5(2), Feb 2009. | PubMed
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| 15 Feb 2009 | T. Hawkins, M. Chitale, S. Luban, and D. Kihara. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins, 74(3):566– 582, Feb 2009. | PubMed | Journal | |
| 27 Jan 2009 | H. Wang, B. Kakaradov, S. R. Collins, L. Karotki, D. Fiedler, M. Shales, K. M. Shokat, T. Walther, N. J. Krogan, and D. Koller. A complex-based reconstruction of the S. cerevisiae interactome. Mol Cell Proteomics, Jan 2009. | PubMed | Journal | |
| 14 Jan 2009 | D. M. Smith, S. J. May, S. Tweeten, L. Drumright, M. E. Pacold, S. L. Kosakovsky Pond, R. L. Pesano, Y. S. Lie, D. D. Richman, S. D. Frost, C. H. Woelk, and S. J. Little. A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS, 23(2):225– 232, Jan 2009. | PubMed | Journal | |
| Epub 31 Dec 2008 | A. M. Feist, M. J. Herrgård, I. Thiele, J. L. Reed, and B. Ø. Palsson. Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol, 7(2):129– 143, Feb 2009. | PubMed | Journal | |
| Epub 3 Dec 2008 | M. J. Chaisson, D. Brinza, and P. A. Pevzner. De novo fragment assembly with short mate-paired reads: Does the read length matter?. Genome Res, 19(2):336– 346, Feb 2009. | PubMed | Journal | |
| Epub 14 Aug 2008 | S. Kim, N. Gupta, N. Bandeira, and P. A. Pevzner. Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics, 8(1):53– 69, Jan 2009. | PubMed | Journal |
2008
| Date | Publications | Links | ||
|---|---|---|---|---|
| Epub 19 Dec 2008 | N. E. Castellana, S. H. Payne, Z. Shen, M. Stanke, V. Bafna, and S. P. Briggs. Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A, 105(52):21034– 21038, Dec 2008. | PubMed | Journal | |
| 5 Dec 2008 | G. M. Wilmes, M. Bergkessel, S. Bandyopadhyay, M. Shales, H. Braberg, G. Cagney, S. R. Collins, G. B. Whitworth, T. L. Kress, J. S. Weissman, T. Ideker, C. Guthrie, and N. J. Krogan. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell, 32(5):735– 746, Dec 2008. | PubMed | Journal | |
| 7 Nov 2008 | E. Lee, H. Y. Chuang, J. W. Kim, T. Ideker, and D. Lee. Inferring pathway activity toward precise disease classification. PLoS Comput Biol, 4(11), Nov 2008. | PubMed
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| 17 Oct 2008 | G. Hon, B. Ren, and W. Wang. ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol, 4(10), Oct 2008. | PubMed
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| Epub 4 Oct 2008 | K. Lee, H. Y. Chuang, A. Beyer, M. K. Sung, W. K. Huh, B. Lee, and T. Ideker. Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res, 36(20), Nov 2008. | PubMed
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| 3 Oct 2008 | R. König, Y. Zhou, D. Elleder, T. L. Diamond, G. M. Bonamy, J. T. Irelan, C. Y. Chiang, B. P. Tu, P. D. De Jesus, C. E. Lilley, S. Seidel, A. M. Opaluch, J. S. Caldwell, M. D. Weitzman, K. L. Kuhen, S. Bandyopadhyay, T. Ideker, A. P. Orth, L. J. Miraglia, F. D. Bushman, J. A. Young, and S. K. Chanda. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell, 135(1):49– 60, Oct 2008. | PubMed | Journal | |
| Epub 25 Sep 2008 | A. Roguev, S. Bandyopadhyay, M. Zofall, K. Zhang, T. Fischer, S. R. Collins, H. Qu, M. Shales, H. O. Park, J. Hayles, K. L. Hoe, D. U. Kim, T. Ideker, S. I. Grewal, J. S. Weissman, and N. J. Krogan. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science, 322(5900):405– 410, Oct 2008. | PubMed | Journal | |
| Sep 2008 | B. Dost, T. Shlomi, N. Gupta, E. Ruppin, V. Bafna, and R. Sharan. QNet: a tool for querying protein interaction networks. J Comput Biol, 15(7):913– 925, Sep 2008. | PubMed | Journal | |
| Aug 2008 | M. W. Chang, R. K. Belew, K. S. Carroll, A. J. Olson, and D. S. Goodsell. Empirical entropic contributions in computational docking: evaluation in APS reductase complexes. J Comput Chem, 29(11):1753– 1761, Aug 2008. | PubMed | Journal | |
| Epub 3 Jul 2008 | S. Kim, N. Gupta, and P. A. Pevzner. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res, 7(8):3354– 3363, Aug 2008. | PubMed | Journal | |
| Epub 19 Jun 2008 | S. H. Payne, M. Yau, M. B. Smolka, S. Tanner, H. Zhou, and V. Bafna. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res, 7(8):3373– 3381, Aug 2008. | PubMed | Journal | |
| 12 Jun 2008 | J. M. Bechtel, T. Wittenschlaeger, T. Dwyer, J. Song, S. Arunachalam, S. K. Ramakrishnan, S. Shepard, and A. Fedorov. Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures. BMC Genomics, 9:284– 284, 2008. | PubMed
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| Epub 16 May 2008 | M. K. Applebee, M. J. Herrgård, and B. Ø. Palsson. Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. J Bacteriol, 190(14):5087– 5094, Jul 2008. | PubMed
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| 1 May 2008 | C. S. Cheng, T. L. Johnson, and A. Hoffmann. Epigenetic control: slow and global, nimble and local. Genes Dev, 22(9):1110– 1114, May 2008. | PubMed | Journal | |
| 25 Apr 2008 | A. Bashir, S. Volik, C. Collins, V. Bafna, and B. J. Raphael. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol, 4(4), Apr 2008. | PubMed
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| Epub 23 Apr 2008 | Y. Chen, F. Rao, J. L. Rodriguez-Flores, N. R. Mahapatra, M. Mahata, G. Wen, R. M. Salem, P. A. Shih, M. Das, N. J. Schork, M. G. Ziegler, B. A. Hamilton, S. K. Mahata, and D. T. O'Connor. Common genetic variants in the chromogranin A promoter alter autonomic activity and blood pressure. Kidney Int, 74(1):115– 125, Jul 2008. | PubMed
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| Epub 21 Apr 2008 | N. Gupta, J. Benhamida, V. Bhargava, D. Goodman, E. Kain, I. Kerman, N. Nguyen, N. Ollikainen, J. Rodriguez, J. Wang, M. S. Lipton, M. Romine, V. Bafna, R. D. Smith, and P. A. Pevzner. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res, 18(7):1133– 1142, Jul 2008. | PubMed
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| 18 Apr 2008 | S. Bandyopadhyay, R. Kelley, N. J. Krogan, and T. Ideker. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol, 4(4), Apr 2008. | PubMed
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| 15 Apr 2008 | E. R. Cachay, S. D. Frost, A. F. Poon, D. Looney, S. M. Rostami, M. E. Pacold, D. D. Richman, S. J. Little, and D. M. Smith. Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels. J Acquir Immune Defic Syndr, 47(5):592– 596, Apr 2008. | PubMed
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| Epub 11 Apr 2008 | C. P. Albuquerque, M. B. Smolka, S. H. Payne, V. Bafna, J. Eng, and H. Zhou. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics, 7(7):1389– 1396, Jul 2008. | PubMed | Journal | |
| 9 Apr 2008 | A. R. Joyce and B. Ø. Palsson. Predicting gene essentiality using genome-scale in silico models. Methods Mol Biol, 416:433– 457, 2008. | PubMed | Journal | |
| Epub 4 Apr 2008 | R. E. Valas and P. E. Bourne. Rethinking proteasome evolution: two novel bacterial proteasomes. J Mol Evol, 66(5):494– 504, May 2008. | PubMed | Journal | |
| Apr 2008 | M. Pacold and P. Soto. Retroviruses and opportunistic infections - 15th annual conference. IDrugs, 11(4):233– 235, Apr 2008. | PubMed | ||
| 25 Mar 2008 | B. J. Raphael, S. Volik, P. Yu, C. Wu, G. Huang, E. V. Linardopoulou, B. J. Trask, F. Waldman, J. Costello, K. J. Pienta, G. B. Mills, K. Bajsarowicz, Y. Kobayashi, S. Sridharan, P. L. Paris, Q. Tao, S. J. Aerni, R. P. Brown, A. Bashir, J. W. Gray, J. F. Cheng, P. de Jong, M. Nefedov, T. Ried, H. M. Padilla-Nash, and C. C. Collins. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol, 9(3), 2008. | PubMed
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| 4 Mar 2008 | S. Suthram, A. Beyer, R. M. Karp, Y. Eldar, and T. Ideker. eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol, 4:162– 162, 2008. | PubMed
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| Mar 2008 | H. M. Kang, N. A. Zaitlen, C. M. Wade, A. Kirby, D. Heckerman, M. J. Daly, and E. Eskin. Efficient control of population structure in model organism association mapping. Genetics, 178(3):1709– 1723, Mar 2008. | PubMed
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| 26 Feb 2008 | J. M. Bechtel, P. Rajesh, I. Ilikchyan, Y. Deng, P. K. Mishra, Q. Wang, X. Wu, K. A. Afonin, W. E. Grose, Y. Wang, S. Khuder, and A. Fedorov. Calculation of splicing potential from the alternative splicing mutation database. BMC Res Notes, 1:4– 4, 2008. | PubMed
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| 26 Feb 2008 | J. M. Bechtel, P. Rajesh, I. Ilikchyan, Y. Deng, P. K. Mishra, Q. Wang, X. Wu, K. A. Afonin, W. E. Grose, Y. Wang, S. Khuder, and A. Fedorov. The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence. BMC Res Notes, 1:3– 3, 2008. | PubMed
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| 13 Feb 2008 | K. M. Briedis, A. Starr, and P. E. Bourne. Analysis of the human kinome using methods including fold recognition reveals two novel kinases. PLoS ONE, 3(2), 2008. | PubMed
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| 7 Feb 2008 | J. A. Young, J. R. Johnson, C. Benner, S. F. Yan, K. Chen, K. G. Le Roch, Y. Zhou, and E. A. Winzeler. In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics, 9:70– 70, 2008. | PubMed
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| Jan 2008 | J. Ng and P. A. Pevzner. Algorithm for identification of fusion proteins via mass spectrometry. J Proteome Res, 7(1):89– 95, Jan 2008. | PubMed | Journal | |
| Epub 14 Dec 2007 | M. J. Chaisson and P. A. Pevzner. Short read fragment assembly of bacterial genomes. Genome Res, 18(2):324– 330, Feb 2008. | PubMed
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| Epub 8 Dec 2007 | J. Rodriguez, N. Gupta, R. D. Smith, and P. A. Pevzner. Does trypsin cut before proline?. J Proteome Res, 7(1):300– 305, Jan 2008. | PubMed | Journal | |
| Epub 8 Dec 2007 | A. M. Frank, N. Bandeira, Z. Shen, S. Tanner, S. P. Briggs, R. D. Smith, and P. A. Pevzner. Clustering millions of tandem mass spectra. J Proteome Res, 7(1):113– 122, Jan 2008. | PubMed
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| Epub 27 Nov 2007 | L. O. Barrera, Z. Li, A. D. Smith, K. C. Arden, W. K. Cavenee, M. Q. Zhang, R. D. Green, and B. Ren. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res, 18(1):46– 59, Jan 2008. | PubMed
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| Epub 23 Nov 2007 | S. Tanner, S. H. Payne, S. Dasari, Z. Shen, P. A. Wilmarth, L. L. David, W. F. Loomis, S. P. Briggs, and V. Bafna. Accurate annotation of peptide modifications through unrestrictive database search. J Proteome Res, 7(1):170– 181, Jan 2008. | PubMed | Journal | |
| Epub 10 Jul 2007 | R. Kelley, H. Feizi, and T. Ideker. Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood. Bioinformatics, 24(1):71– 77, Jan 2008. | PubMed | Journal |
2007
| Date | Publications | Links | ||
|---|---|---|---|---|
| 20 Oct 2007 | M. S. Cline, M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, I. Avila-Campilo, M. Creech, B. Gross, K. Hanspers, R. Isserlin, R. Kelley, S. Killcoyne, S. Lotia, S. Maere, J. Morris, K. Ono, V. Pavlovic, A. R. Pico, A. Vailaya, P. L. Wang, A. Adler, B. R. Conklin, L. Hood, M. Kuiper, C. Sander, I. Schmulevich, B. Schwikowski, G. J. Warner, T. Ideker, and G. D. Bader. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc, 2(10):2366– 2382, 2007. | PubMed | Journal | |
| 16 Oct 2007 | H. Y. Chuang, E. Lee, Y. T. Liu, D. Lee, and T. Ideker. Network-based classification of breast cancer metastasis. Mol Syst Biol, 3:140– 140, 2007. | PubMed
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| 27 Sep 2007 | M. Yeung, I. Thiele, and B. O. Palsson. Estimation of the number of extreme pathways for metabolic networks. BMC Bioinformatics, 8(1):363– 363, 2007. | PubMed | Journal | |
| 26 Sep 2007 | M. R. Maurya, C. Benner, S. Pradervand, C. Glass, and S. Subramaniam. Systems biology of macrophages. Adv Exp Med Biol, 598:62– 79, 2007. | PubMed | ||
| Epub 26 Sep 2007 | L. Xie, J. Wang, and P. E. Bourne. In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comput Biol, 3(11), Nov 2007. | PubMed
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| Sep 2007 | M. Zheng, L. O. Barrera, B. Ren, and Y. N. Wu. ChIP-chip: data, model, and analysis. Biometrics, 63(3):787– 796, Sep 2007. | PubMed | Journal | |
| Sep 2007 | L. Zhang, F. Rao, K. Zhang, S. Khandrika, M. Das, S. M. Vaingankar, X. Bao, B. K. Rana, D. W. Smith, J. Wessel, R. M. Salem, J. L. Rodriguez-Flores, S. K. Mahata, N. J. Schork, M. G. Ziegler, and D. T. O'Connor. Discovery of common human genetic variants of GTP cyclohydrolase 1 (GCH1) governing nitric oxide, autonomic activity, and cardiovascular risk. J Clin Invest, 117(9):2658– 2671, Sep 2007. | PubMed
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| Sep 2007 | A. Beyer, S. Bandyopadhyay, and T. Ideker. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet, 8(9):699– 710, Sep 2007. | PubMed | Journal | |
| Epub 30 Aug 2007 | A. Bashir, Y. T. Liu, B. J. Raphael, D. Carson, and V. Bafna. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics, 23(21):2807– 2815, Nov 2007. | PubMed | Journal | |
| Epub 13 Aug 2007 | F. Rao, L. Zhang, J. Wessel, K. Zhang, G. Wen, B. P. Kennedy, B. K. Rana, M. Das, J. L. Rodriguez-Flores, D. W. Smith, P. E. Cadman, R. M. Salem, S. K. Mahata, N. J. Schork, L. Taupenot, M. G. Ziegler, and D. T. O'Connor. Tyrosine hydroxylase, the rate-limiting enzyme in catecholamine biosynthesis: discovery of common human genetic variants governing transcription, autonomic activity, and blood pressure in vivo. Circulation, 116(9):993– 1006, Aug 2007. | PubMed | Journal | |
| Epub 9 Aug 2007 | N. Gupta, S. Tanner, N. Jaitly, J. N. Adkins, M. Lipton, R. Edwards, M. Romine, A. Osterman, V. Bafna, R. D. Smith, and P. A. Pevzner. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res, 17(9):1362– 1377, Sep 2007. | PubMed
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| 13 Jul 2007 | V. V. Lunyak, G. G. Prefontaine, E. Núñez, T. Cramer, B. G. Ju, K. A. Ohgi, K. Hutt, R. Roy, A. García-Díaz, X. Zhu, Y. Yung, L. Montoliu, C. K. Glass, and M. G. Rosenfeld. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science, 317(5835):248– 251, Jul 2007. | PubMed | Journal | |
| 5 Jul 2007 | J. R. Parrish, J. Yu, G. Liu, J. A. Hines, J. E. Chan, B. A. Mangiola, H. Zhang, S. Pacifico, F. Fotouhi, V. J. DiRita, T. Ideker, P. Andrews, and R. L. Finley. A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol, 8(7), 2007. | PubMed
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| Jul 2007 | T. H. Kim, L. O. Barrera, and B. Ren. ChIP-chip for genome-wide analysis of protein binding in mammalian cells. Curr Protoc Mol Biol, Chapter 21, Jul 2007. | PubMed | Journal | |
| 26 Jun 2007 | A. M. Feist, C. S. Henry, J. L. Reed, M. Krummenacker, A. R. Joyce, P. D. Karp, L. J. Broadbelt, V. Hatzimanikatis, and B. Ø. Palsson. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol, 3:121– 121, 2007. | PubMed
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| 14 Jun 2007 | ENCODE Project Consortium, E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigó, T. R. Gingeras, E. H. Margulies, Z. Weng, M. Snyder, E. T. Dermitzakis, R. E. Thurman, M. S. Kuehn, C. M. Taylor, S. Neph, C. M. Koch, S. Asthana, A. Malhotra, I. Adzhubei, J. A. Greenbaum, R. M. Andrews, P. Flicek, P. J. Boyle, H. Cao, N. P. Carter, G. K. Clelland, S. Davis, N. Day, P. Dhami, S. C. Dillon, M. O. Dorschner, H. Fiegler, P. G. Giresi, J. Goldy, M. Hawrylycz, A. Haydock, R. Humbert, K. D. James, B. E. Johnson, E. M. Johnson, T. T. Frum, E. R. Rosenzweig, N. Karnani, K. Lee, G. C. Lefebvre, P. A. Navas, F. Neri, S. C. Parker, P. J. Sabo, R. Sandstrom, A. Shafer, D. Vetrie, M. Weaver, S. Wilcox, M. Yu, F. S. Collins, J. Dekker, J. D. Lieb, T. D. Tullius, G. E. Crawford, S. Sunyaev, W. S. Noble, I. Dunham, F. Denoeud, A. Reymond, P. Kapranov, J. Rozowsky, D. Zheng, R. Castelo, A. Frankish, J. Harrow, S. Ghosh, A. Sandelin, I. L. Hofacker, R. Baertsch, D. Keefe, S. Dike, J. Cheng, H. A. Hirsch, E. A. Sekinger, J. Lagarde, J. F. Abril, A. Shahab, C. Flamm, C. Fried, J. Hackermüller, J. Hertel, M. Lindemeyer, K. Missal, A. Tanzer, S. Washietl, J. Korbel, O. Emanuelsson, J. S. Pedersen, N. Holroyd, R. Taylor, D. Swarbreck, N. Matthews, M. C. Dickson, D. J. Thomas, M. T. Weirauch, J. Gilbert, J. Drenkow, I. Bell, X. Zhao, K. G. Srinivasan, W. K. Sung, H. S. Ooi, K. P. Chiu, S. Foissac, T. Alioto, M. Brent, L. Pachter, M. L. Tress, A. Valencia, S. W. Choo, C. Y. Choo, C. Ucla, C. Manzano, C. Wyss, E. Cheung, T. G. Clark, J. B. Brown, M. Ganesh, S. Patel, H. Tammana, J. Chrast, C. N. Henrichsen, C. Kai, J. Kawai, U. Nagalakshmi, J. Wu, Z. Lian, J. Lian, P. Newburger, X. Zhang, P. Bickel, J. S. Mattick, P. Carninci, Y. Hayashizaki, S. Weissman, T. Hubbard, R. M. Myers, J. Rogers, P. F. Stadler, T. M. Lowe, C. L. Wei, Y. Ruan, K. Struhl, M. Gerstein, S. E. Antonarakis, Y. Fu, E. D. Green, U. Karaöz, A. Siepel, J. Taylor, L. A. Liefer, K. A. Wetterstrand, P. J. Good, E. A. Feingold, M. S. Guyer, G. M. Cooper, G. Asimenos, C. N. Dewey, M. Hou, S. Nikolaev, J. I. Montoya-Burgos, A. Löytynoja, S. Whelan, F. Pardi, T. Massingham, H. Huang, N. R. Zhang, I. Holmes, J. C. Mullikin, A. Ureta-Vidal, B. Paten, M. Seringhaus, D. Church, K. Rosenbloom, W. J. Kent, E. A. Stone, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, S. Batzoglou, N. Goldman, R. C. Hardison, D. Haussler, W. Miller, A. Sidow, N. D. Trinklein, Z. D. Zhang, L. Barrera, R. Stuart, D. C. King, A. Ameur, S. Enroth, M. C. Bieda, J. Kim, A. A. Bhinge, N. Jiang, J. Liu, F. Yao, V. B. Vega, C. W. Lee, P. Ng, A. Shahab, A. Yang, Z. Moqtaderi, Z. Zhu, X. Xu, S. Squazzo, M. J. Oberley, D. Inman, M. A. Singer, T. A. Richmond, K. J. Munn, and A. Rada-Iglesias, O. Wallerman, J. Komorowski, J. C. Fowler, P. Couttet, A. W. Bruce, O. M. Dovey, P. D. Ellis, C. F. Langford, D. A. Nix, G. Euskirchen, S. Hartman, A. E. Urban, P. Kraus, S. Van. Calcar, N. Heintzman, T. H. Kim, K. Wang, C. Qu, G. Hon, R. Luna, C. K. Glass, M. G. Rosenfeld, S. F. Aldred, S. J. Cooper, A. Halees, J. M. Lin, H. P. Shulha, X. Zhang, M. Xu, J. N. Haidar, Y. Yu, Y. Ruan, V. R. Iyer, R. D. Green, C. Wadelius, P. J. Farnham, B. Ren, R. A. Harte, A. S. Hinrichs, H. Trumbower, H. Clawson, J. Hillman-Jackson, A. S. Zweig, K. Smith, A. Thakkapallayil, G. Barber, R. M. Kuhn, D. Karolchik, L. Armengol, C. P. Bird, P. I. de. Bakker, A. D. Kern, N. Lopez-Bigas, J. D. Martin, B. E. Stranger, A. Woodroffe, E. Davydov, A. Dimas, E. Eyras, I. B. Hallgrímsdóttir, J. Huppert, M. C. Zody, G. R. Abecasis, X. Estivill, G. G. Bouffard, X. Guan, N. F. Hansen, J. R. Idol, V. V. Maduro, B. Maskeri, J. C. McDowell, M. Park, P. J. Thomas, A. C. Young, R. W. Blakesley, D. M. Muzny, E. Sodergren, D. A. Wheeler, K. C. Worley, H. Jiang, G. M. Weinstock, R. A. Gibbs, T. Graves, R. Fulton, E. R. Mardis, R. K. Wilson, M. Clamp, J. Cuff, S. Gnerre, D. B. Jaffe, J. L. Chang, K. Lindblad-Toh, E. S. Lander, M. Koriabine, M. Nefedov, K. Osoegawa, Y. Yoshinaga, B. Zhu, and P. J. de. Jong. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146):799– 816, Jun 2007. | PubMed
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| Epub 24 May 2007 | A. L. Hevener, J. M. Olefsky, D. Reichart, M. T. Nguyen, G. Bandyopadyhay, H. Y. Leung, M. J. Watt, C. Benner, M. A. Febbraio, A. K. Nguyen, B. Folian, S. Subramaniam, F. J. Gonzalez, C. K. Glass, and M. Ricote. Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones. J Clin Invest, 117(6):1658– 1669, Jun 2007. | PubMed
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| Epub 18 May 2007 | Q. Hua, A. R. Joyce, B. Ø. Palsson, and S. S. Fong. Metabolic characterization of Escherichia coli strains adapted to growth on lactate. Appl Environ Microbiol, 73(14):4639– 4647, Jul 2007. | PubMed
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| 8 May 2007 | E. L. O'Dea, D. Barken, R. Q. Peralta, K. T. Tran, S. L. Werner, J. D. Kearns, A. Levchenko, and A. Hoffmann. A homeostatic model of IkappaB metabolism to control constitutive NF-kappaB activity. Mol Syst Biol, 3:111– 111, 2007. | PubMed | Journal | |
| Epub 21 Apr 2007 | M. W. Chang, W. Lindstrom, A. J. Olson, and R. K. Belew. Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries. J Chem Inf Model, 47(3):1258– 1262, May-Jun 2007. | PubMed | Journal | |
| 7 Apr 2007 | S. Luban and D. Kihara. Comparative genomics of small RNAs in bacterial genomes. OMICS, 11(1):58– 73, 2007. | PubMed | Journal | |
| Epub 14 Mar 2007 | Y. S. Kwon, I. Garcia-Bassets, K. R. Hutt, C. S. Cheng, M. Jin, D. Liu, C. Benner, D. Wang, Z. Ye, M. Bibikova, J. B. Fan, L. Duan, C. K. Glass, M. G. Rosenfeld, and X. D. Fu. Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A, 104(12):4852– 4857, Mar 2007. | PubMed
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| Epub 2 Mar 2007 | N. Zaitlen, H. M. Kang, E. Eskin, and E. Halperin. Leveraging the HapMap correlation structure in association studies. Am J Hum Genet, 80(4):683– 691, Apr 2007. | PubMed
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| 9 Feb 2007 | I. Garcia-Bassets, Y. S. Kwon, F. Telese, G. G. Prefontaine, K. R. Hutt, C. S. Cheng, B. G. Ju, K. A. Ohgi, J. Wang, L. Escoubet-Lozach, D. W. Rose, C. K. Glass, X. D. Fu, and M. G. Rosenfeld. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell, 128(3):505– 518, Feb 2007. | PubMed
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| Epub 4 Feb 2007 | N. D. Heintzman, R. K. Stuart, G. Hon, Y. Fu, C. W. Ching, R. D. Hawkins, L. O. Barrera, S. Van Calcar, C. Qu, K. A. Ching, W. Wang, Z. Weng, R. D. Green, G. E. Crawford, and B. Ren. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet, 39(3):311– 318, Mar 2007. | PubMed | Journal | |
| Epub 31 Jan 2007 | N. C. Duarte, S. A. Becker, N. Jamshidi, I. Thiele, M. L. Mo, T. D. Vo, R. Srivas, and B. Ø. Palsson. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A, 104(6):1777– 1782, Feb 2007. | PubMed
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| 15 Jan 2007 | C. Ye and E. Eskin. Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. Bioinformatics, 23(2):84– 90, Jan 2007. | PubMed | Journal | |
| 2 Jan 2007 | A. R. Joyce and B. O. Palsson. Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach. Prog Drug Res, 64:267– 309, 2007. | PubMed | ||
| Epub 22 Dec 2006 | S. Tanner, Z. Shen, J. Ng, L. Florea, R. Guigó, S. P. Briggs, and V. Bafna. Improving gene annotation using peptide mass spectrometry. Genome Res, 17(2):231– 239, Feb 2007. | PubMed
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| Epub 21 Dec 2006 | V. Bansal, A. Bashir, and V. Bafna. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res, 17(2):219– 230, Feb 2007. | PubMed
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| Epub 11 Dec 2006 | B. K. Rana, P. A. Insel, S. H. Payne, K. Abel, E. Beutler, M. G. Ziegler, N. J. Schork, and D. T. O'Connor. Population-based sample reveals gene-gender interactions in blood pressure in White Americans. Hypertension, 49(1):96– 106, Jan 2007. | PubMed | Journal |
2006
| Date | Publications | Links | ||
|---|---|---|---|---|
| 5 Apr 2007 | S. Tanner, P. A. Pevzner, and V. Bafna. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc, 1(1):67– 72, 2006. | PubMed | Journal | |
| Epub 22 Dec 2006 | M. J. Chaisson, B. J. Raphael, and P. A. Pevzner. Microinversions in mammalian evolution. Proc Natl Acad Sci U S A, 103(52):19824– 19829, Dec 2006. | PubMed
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| 5 Dec 2006 | Q. Hua, A. R. Joyce, S. S. Fong, and B. Ø. Palsson. Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains. Biotechnol Bioeng, 95(5):992– 1002, Dec 2006. | PubMed | Journal | |
| 11 Nov 2006 | S. Bandyopadhyay, R. Kelley, and T. Ideker. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput, pages 354– 366, 2006. | PubMed | ||
| Epub 6 Nov 2006 | J. L. Reed, T. R. Patel, K. H. Chen, A. R. Joyce, M. K. Applebee, C. D. Herring, O. T. Bui, E. M. Knight, S. S. Fong, and B. O. Palsson. Systems approach to refining genome annotation. Proc Natl Acad Sci U S A, 103(46):17480– 17484, Nov 2006. | PubMed
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| Epub 5 Nov 2006 | C. D. Herring, A. Raghunathan, C. Honisch, T. Patel, M. K. Applebee, A. R. Joyce, T. J. Albert, F. R. Blattner, D. van den Boom, C. R. Cantor, and B. Ø. Palsson. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet, 38(12):1406– 1412, Dec 2006. | PubMed | Journal | |
| Oct 2006 | P. A. Wilmarth, S. Tanner, S. Dasari, S. R. Nagalla, M. A. Riviere, V. Bafna, P. A. Pevzner, and L. L. David. Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?. J Proteome Res, 5(10):2554– 2566, Oct 2006. | PubMed
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| Epub 29 Sep 2006 | A. R. Joyce, J. L. Reed, A. White, R. Edwards, A. Osterman, T. Baba, H. Mori, S. A. Lesely, B. Ø. Palsson, and S. Agarwalla. Experimental and computational assessment of conditionally essential genes in Escherichia coli. J Bacteriol, 188(23):8259– 8271, Dec 2006. | PubMed
PMC | Journal | |
| 11 Aug 2006 | E. P. Gianchandani, J. A. Papin, N. D. Price, A. R. Joyce, and B. O. Palsson. Matrix formalism to describe functional states of transcriptional regulatory systems. PLoS Comput Biol, 2(8), Aug 2006. | PubMed
PMC | Journal | |
| 26 Jul 2006 | S. Suthram, T. Shlomi, E. Ruppin, R. Sharan, and T. Ideker. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics, 7:360– 360, 2006. | PubMed
PMC | Journal | |
| 1 Jul 2006 | N. Harish, R. Gupta, P. Agarwal, V. Scaria, and B. Pillai. DyNAVacS: an integrative tool for optimized DNA vaccine design. Nucleic Acids Res, 34(Web Server issue):264– 266, Jul 2006. | PubMed
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| Jul 2006 | S. Hirose, S. H. Payne, and W. F. Loomis. cis-Acting site controlling bidirectional transcription at the growth-differentiation transition in Dictyostelium discoideum. Eukaryot Cell, 5(7):1104– 1110, Jul 2006. | PubMed
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| 8 Jun 2006 | T. Reguly, A. Breitkreutz, L. Boucher, B. J. Breitkreutz, G. C. Hon, C. L. Myers, A. Parsons, H. Friesen, R. Oughtred, A. Tong, C. Stark, Y. Ho, D. Botstein, B. Andrews, C. Boone, O. G. Troyanskya, T. Ideker, K. Dolinski, N. N. Batada, and M. Tyers. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol, 5(4):11– 11, 2006. | PubMed
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| Epub 2 May 2006 | T. Hawkins, S. Luban, and D. Kihara. Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci, 15(6):1550– 1556, Jun 2006. | PubMed
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| Epub 2 May 2006 | L. O. Barrera and B. Ren. The transcriptional regulatory code of eukaryotic cells– insights from genome-wide analysis of chromatin organization and transcription factor binding. Curr Opin Cell Biol, 18(3):291– 298, Jun 2006. | PubMed | Journal | |
| Epub 17 Apr 2006 | E. P. Gianchandani, D. L. Brautigan, and J. A. Papin. Systems analyses characterize integrated functions of biochemical networks. Trends Biochem Sci, 31(5):284– 291, May 2006. | PubMed | Journal | |
| Epub 13 Mar 2006 | N. D. Price, I. Thiele, and B. Ø. Palsson. Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys J, 90(11):3919– 3928, Jun 2006. | PubMed
PMC | Journal | |
| Mar 2006 | S. Bandyopadhyay, R. Sharan, and T. Ideker. Systematic identification of functional orthologs based on protein network comparison. Genome Res, 16(3):428– 435, Mar 2006. | PubMed
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| Mar 2006 | A. R. Joyce and B. Ø. Palsson. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol, 7(3):198– 210, Mar 2006. | PubMed | Journal | |
| Epub 14 Feb 2006 | C. R. Raetz, T. A. Garrett, C. M. Reynolds, W. A. Shaw, J. D. Moore, D. C. Smith, A. A. Ribeiro, R. C. Murphy, R. J. Ulevitch, C. Fearns, D. Reichart, C. K. Glass, C. Benner, S. Subramaniam, R. Harkewicz, R. C. Bowers-Gentry, M. W. Buczynski, J. A. Cooper, R. A. Deems, and E. A. Dennis. Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4. J Lipid Res, 47(5):1097– 1111, May 2006. | PubMed | Journal | |
| Feb 2006 | S. H. Payne and W. F. Loomis. Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. Eukaryot Cell, 5(2):272– 276, Feb 2006. | PubMed
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| Feb 2006 | J. L. Reed, I. Famili, I. Thiele, and B. O. Palsson. Towards multidimensional genome annotation. Nat Rev Genet, 7(2):130– 141, Feb 2006. | PubMed | Journal | |
| 13 Jan 2006 | T. E. Allen, N. D. Price, A. R. Joyce, and B. Ø. Palsson. Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization. PLoS Comput Biol, 2(1), Jan 2006. | PubMed
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2005
| Date | Publications | Links | ||
|---|---|---|---|---|
| 2 Feb 2006 | D. Tsur, S. Tanner, E. Zandi, V. Bafna, and P. A. Pevzner. Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf, pages 157– 166, 2005. | PubMed | ||
| Epub 27 Nov 2005 | D. Tsur, S. Tanner, E. Zandi, V. Bafna, and P. A. Pevzner. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol, 23(12):1562– 1567, Dec 2005. | PubMed | Journal | |
| 3 Nov 2005 | S. Suthram, T. Sittler, and T. Ideker. The Plasmodium protein network diverges from those of other eukaryotes. Nature, 438(7064):108– 112, Nov 2005. | PubMed | Journal | |
| Nov 2005 | N. A. Zaitlen, H. M. Kang, M. L. Feolo, S. T. Sherry, E. Halperin, and E. Eskin. Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP. Genome Res, 15(11):1594– 1600, Nov 2005. | PubMed
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| 7 Oct 2005 | R. Overbeek, T. Begley, R. M. Butler, J. V. Choudhuri, H. Y. Chuang, M. Cohoon, V. de Crécy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E. D. Frank, S. Gerdes, E. M. Glass, A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M. Kubal, N. Larsen, B. Linke, A. C. McHardy, F. Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman, V. Portnoy, G. D. Pusch, D. A. Rodionov, C. Rückert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, and V. Vonstein. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res, 33(17):5691– 5702, 2005. | PubMed
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| Oct-Dec 2005 | S. Zhang, B. Haas, E. Eskin, and V. Bafna. Searching genomes for noncoding RNA using FastR. IEEE/ACM Trans Comput Biol Bioinform, 2(4):366– 379, Oct-Dec 2005. | PubMed | Journal | |
| Oct 2005 | S. S. Fong, A. R. Joyce, and B. Ø. Palsson. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res, 15(10):1365– 1372, Oct 2005. | PubMed
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| Epub 20 Sep 2005 | J. Chen, S. J. Swamidass, Y. Dou, J. Bruand, and P. Baldi. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics, 21(22):4133– 4139, Nov 2005. | PubMed | Journal | |
| 16 Sep 2005 | S. L. Werner, D. Barken, and A. Hoffmann. Stimulus specificity of gene expression programs determined by temporal control of IKK activity. Science, 309(5742):1857– 1861, Sep 2005. | PubMed | Journal | |
| 16 Sep 2005 | M. W. Covert, T. H. Leung, J. E. Gaston, and D. Baltimore. Achieving stability of lipopolysaccharide-induced NF-kappaB activation. Science, 309(5742):1854– 1857, Sep 2005. | PubMed | Journal | |
| 9 Sep 2005 | S. Ogawa, J. Lozach, C. Benner, G. Pascual, R. K. Tangirala, S. Westin, A. Hoffmann, S. Subramaniam, M. David, M. G. Rosenfeld, and C. K. Glass. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell, 122(5):707– 721, Sep 2005. | PubMed
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| Sep 2005 | S. S. Fong, A. R. Joyce, and B. Ø. Palsson. The econometrics of evolution. Nat Chem Biol, 1(4):191– 192, Sep 2005. | PubMed | Journal | |
| Aug 2005 | I. Thiele, T. D. Vo, N. D. Price, and B. Ø. Palsson. Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J Bacteriol, 187(16):5818– 5830, Aug 2005. | PubMed
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| 27 Jul 2005 | S. H. Payne. Metabolic pathways. In William F. Loomis and Adam Kuspa, Eds., Dictyostelium Genomics, pages 41– 57. Horizon Press, Far Hills, N.J., 2005. | Amazon | Publisher | |
| 15 Jul 2005 | S. Tanner, H. Shu, A. Frank, L. C. Wang, E. Zandi, M. Mumby, P. A. Pevzner, and V. Bafna. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem, 77(14):4626– 4639, Jul 2005. | PubMed | Journal | |
| Jul-Aug 2005 | A. Frank, S. Tanner, V. Bafna, and P. Pevzner. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res, 4(4):1287– 1295, Jul-Aug 2005. | PubMed | Journal | |
| Jul 2005 | A. Bashir, C. Ye, A. L. Price, and V. Bafna. Orthologous repeats and mammalian phylogenetic inference. Genome Res, 15(7):998– 1006, Jul 2005. | PubMed
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| Epub 29 Jun 2005 | T. H. Kim, L. O. Barrera, M. Zheng, C. Qu, M. A. Singer, T. A. Richmond, Y. Wu, R. D. Green, and B. Ren. A high-resolution map of active promoters in the human genome. Nature, 436(7052):876– 880, Aug 2005. | PubMed
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| 22 Jun 2005 | N. K. Devaraj, G. P. Miller, W. Ebina, B. Kakaradov, J. P. Collman, E. T. Kool, and C. E. Chidsey. Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers. J Am Chem Soc, 127(24):8600– 8601, Jun 2005. | PubMed | Journal | |
| Jun 2005 | S. J. Swamidass, J. Chen, J. Bruand, P. Phung, L. Ralaivola, and P. Baldi. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics, 21 Suppl 1:359– 368, Jun 2005. | PubMed | Journal | |
| Epub 17 May 2005 | T. H. Kim, L. O. Barrera, C. Qu, S. Van Calcar, N. D. Trinklein, S. J. Cooper, R. M. Luna, C. K. Glass, M. G. Rosenfeld, R. M. Myers, and B. Ren. Direct isolation and identification of promoters in the human genome. Genome Res, 15(6):830– 839, Jun 2005. | PubMed
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| May 2005 | R. Kelley and T. Ideker. Systematic interpretation of genetic interactions using protein networks. Nat Biotechnol, 23(5):561– 566, May 2005. | PubMed | Journal | |
| 1 Apr 2005 | D. Barken, C. J. Wang, J. Kearns, R. Cheong, A. Hoffmann, and A. Levchenko. Comment on "Oscillations in NF-kappaB signaling control the dynamics of gene expression". Science, 308(5718):52– 52, Apr 2005. | PubMed | Journal | |
| Epub 1 Feb 2005 | R. Sharan, S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R. M. Karp, and T. Ideker. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A, 102(6):1974– 1979, Feb 2005. | PubMed
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| Feb 2005 | J. A. Papin, T. Hunter, B. O. Palsson, and S. Subramaniam. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol, 6(2):99– 111, Feb 2005. | PubMed | Journal | |
| Jan 2005 | M. Tompa, N. Li, T. L. Bailey, G. M. Church, B. De Moor, E. Eskin, A. V. Favorov, M. C. Frith, Y. Fu, W. J. Kent, V. J. Makeev, A. A. Mironov, W. S. Noble, G. Pavesi, G. Pesole, M. Régnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol, 23(1):137– 144, Jan 2005. | PubMed | Journal | |
| Epub 30 Dec 2004 | I. Famili, R. Mahadevan, and B. O. Palsson. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J, 88(3):1616– 1625, Mar 2005. | PubMed
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| Epub 30 Nov 2004 | I. Thiele, N. D. Price, T. D. Vo, and B. Ø. Palsson. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem, 280(12):11683– 11695, Mar 2005. | PubMed | Journal |
2004
| Date | Publications | Links | ||
|---|---|---|---|---|
| 15 Dec 2004 | X. Zhu, R. Hart, M. S. Chang, J. W. Kim, S. Y. Lee, Y. A. Cao, D. Mock, E. Ke, B. Saunders, A. Alexander, J. Grossoehme, K. M. Lin, Z. Yan, R. Hsueh, J. Lee, R. H. Scheuermann, D. A. Fruman, W. Seaman, S. Subramaniam, P. Sternweis, M. I. Simon, and S. Choi. Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J Immunol, 173(12):7141– 7149, Dec 2004. | PubMed | ||
| Dec 2004 | J. A. Papin, J. L. Reed, and B. O. Palsson. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci, 29(12):641– 647, Dec 2004. | PubMed | Journal | |
| 29 Nov 2004 | A. C. Haugen, R. Kelley, J. B. Collins, C. J. Tucker, C. Deng, C. A. Afshari, J. M. Brown, T. Ideker, and B. Van Houten. Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol, 5(12), 2004. | PubMed
PMC | Journal | |
| Oct 2004 | N. D. Price, J. Schellenberger, and B. O. Palsson. Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys J, 87(4):2172– 2186, Oct 2004. | PubMed
PMC | Journal | |
| Aug 2004 | J. A. Papin, J. Stelling, N. D. Price, S. Klamt, S. Schuster, and B. O. Palsson. Comparison of network-based pathway analysis methods. Trends Biotechnol, 22(8):400– 405, Aug 2004. | PubMed | Journal | |
| Jul 2004 | J. A. Papin and B. O. Palsson. The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis. Biophys J, 87(1):37– 46, Jul 2004. | PubMed
PMC | Journal | |
| 21 Jun 2004 | S. J. Wiback, I. Famili, H. J. Greenberg, and B. Ø. Palsson. Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol, 228(4):437– 447, Jun 2004. | PubMed | Journal | |
| Jun 2004 | G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner. WebLogo: a sequence logo generator. Genome Res, 14(6):1188– 1190, Jun 2004. | PubMed
PMC | Journal | |
| 6 May 2004 | M. W. Covert, E. M. Knight, J. L. Reed, M. J. Herrgard, and B. O. Palsson. Integrating high-throughput and computational data elucidates bacterial networks. Nature, 429(6987):92– 96, May 2004. | PubMed | Journal | |
| 20 Apr 2004 | L. Barrera, C. Benner, Y. C. Tao, E. Winzeler, and Y. Zhou. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays. BMC Bioinformatics, 5:42– 42, Apr 2004. | PubMed
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| Epub 1 Apr 2004 | M. Chaisson, P. Pevzner, and H. Tang. Fragment assembly with short reads. Bioinformatics, 20(13):2067– 2074, Sep 2004. | PubMed | Journal | |
| 21 Mar 2004 | J. A. Papin and B. O. Palsson. Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol, 227(2):283– 297, Mar 2004. | PubMed | Journal | |
| Feb 2004 | M. J. Herrgård, M. W. Covert, and B. Ø. Palsson. Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol, 15(1):70– 77, Feb 2004. | PubMed | Journal | |
| 1 Jan 2004 | J. M. Chandonia, G. Hon, N. S. Walker, L. Lo Conte, P. Koehl, M. Levitt, and S. E. Brenner. The ASTRAL Compendium in 2004. Nucleic Acids Res, 32(Database issue):189– 192, Jan 2004. | PubMed
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2003
| Date | Publications | Links | ||
|---|---|---|---|---|
| 30 Dec 2003 | M. W. Covert, I. Famili, and B. O. Palsson. Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?. Biotechnol Bioeng, 84(7):763– 772, Dec 2003. | PubMed | Journal | |
| 21 Nov 2003 | N. D. Price, J. L. Reed, J. A. Papin, S. J. Wiback, and B. O. Palsson. Network-based analysis of metabolic regulation in the human red blood cell. J Theor Biol, 225(2):185– 194, Nov 2003. | PubMed | ||
| Epub 24 Oct 2003 | I. Famili, J. Forster, J. Nielsen, and B. O. Palsson. Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A, 100(23):13134– 13139, Nov 2003. | PubMed
PMC | Journal | |
| Epub 14 Oct 2003 | M. J. Herrgård, M. W. Covert, and B. Ø. Palsson. Reconciling gene expression data with known genome-scale regulatory network structures. Genome Res, 13(11):2423– 2434, Nov 2003. | PubMed
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| 26 Sep 2003 | J. Förster, I. Famili, B. O. Palsson, and J. Nielsen. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS, 7(2):193– 202, 2003. | PubMed | ||
| 7 Sep 2003 | I. Famili and B. O. Palsson. Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices. J Theor Biol, 224(1):87– 96, Sep 2003. | PubMed | ||
| Jul 2003 | I. Famili and B. O. Palsson. The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. Biophys J, 85(1):16– 26, Jul 2003. | PubMed
PMC | ||
| May 2003 | J. A. Papin, N. D. Price, S. J. Wiback, D. A. Fell, and B. O. Palsson. Metabolic pathways in the post-genome era. Trends Biochem Sci, 28(5):250– 258, May 2003. | PubMed | ||
| May 2003 | B. O. Palsson, N. D. Price, and J. A. Papin. Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends Biotechnol, 21(5):195– 198, May 2003. | PubMed | ||
| 7 Apr 2003 | M. W. Covert and B. O. Palsson. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J Theor Biol, 221(3):309– 325, Apr 2003. | PubMed | ||
| Apr 2003 | N. D. Price, J. A. Papin, C. H. Schilling, and B. O. Palsson. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol, 21(4):162– 169, Apr 2003. | PubMed | ||
| Feb 2003 | J. Förster, I. Famili, P. Fu, B. Ø. Palsson, and J. Nielsen. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res, 13(2):244– 253, Feb 2003. | PubMed
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| Feb 2003 | N. D. Price, J. L. Reed, J. A. Papin, I. Famili, and B. O. Palsson. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys J, 84(2 Pt 1):794– 804, Feb 2003. | PubMed
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2002
| Date | Publications | Links | ||
|---|---|---|---|---|
| Dec 2002 | J. A. Papin, N. D. Price, and B. Ø. Palsson. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res, 12(12):1889– 1900, Dec 2002. | PubMed
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| Nov 2002 | N. D. Price, I. Famili, D. A. Beard, and B. Ø. Palsson. Extreme pathways and Kirchhoff's second law. Biophys J, 83(5):2879– 2882, Nov 2002. | PubMed
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| Aug 2002 | C. H. Schilling, M. W. Covert, I. Famili, G. M. Church, J. S. Edwards, and B. O. Palsson. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol, 184(16):4582– 4593, Aug 2002. | PubMed
PMC | ||
| Epub 10 May 2002 | M. W. Covert and B. Ø. Palsson. Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem, 277(31):28058– 28064, Aug 2002. | PubMed | Journal | |
| May 2002 | N. D. Price, J. A. Papin, and B. Ø. Palsson. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res, 12(5):760– 769, May 2002. | PubMed
PMC | Journal | |
| 7 Mar 2002 | J. A. Papin, N. D. Price, J. S. Edwards, and B. Ø. Palsson B. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J Theor Biol, 215(1):67– 82, Mar 2002. | PubMed | Journal | |
| Mar 2002 | J. S. Edwards, M. Covert, and B. Palsson. Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol, 4(3):133– 140, Mar 2002. | PubMed |
2001
| Date | Publications | Links | ||
|---|---|---|---|---|
| 7 Nov 2001 | M. W. Covert, C. H. Schilling, and B. Palsson. Regulation of gene expression in flux balance models of metabolism. J Theor Biol, 213(1):73– 88, Nov 2001. | PubMed | Journal | |
| Mar 2001 | M. W. Covert, C. H. Schilling, I. Famili, J. S. Edwards, I. I. Goryanin, E. Selkov, and B. O. Palsson. Metabolic modeling of microbial strains in silico. Trends Biochem Sci, 26(3):179– 186, Mar 2001. | PubMed |
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