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Center for Systems Biology Publications

2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006


The publications below reference the Center for Systems Biology/P50 GM076547. Center publications are updated at the end of each quarter: March, June, September, and December. We are happy to provide full text copies of any Center publication. Please contact Jennifer Dougherty.

A complete list of Institute for Systems Biology publications can be found on the Institute website.

 2013. The following publications cite the P50GM076547/Center for Systems Biology
  1. Akiyoshi B, Nelson CR, Duggan N, Ceto S, Ranish JA, Biggins S (2013). The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein. PLoS Genet.  PMID: 23408894; PMCID: PMC3567142.
  2. Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL (2013). The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res. PMID: 23215161; PMC – In Process.
  3. Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, Lundberg E, Mias G, Menon R, Mu Z, Nice E, Paik YK, Uhlen M, Wells L, Wu SL, Yan F, Zhang F, Zhang Y, Snyder M, Omenn GS, Beavis RC, Hancock WS (2013). A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17. J Proteome Res.  PMID: 23259914; PMC – In Process.
  4. Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Antonio Vizcaíno J, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group (2013). The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford). PMID: 23482073; PMCID: PMC3594986.
  5. Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J (2013). Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proc Natl Acad Sci U S A. PMID: 23388641; PMCID: PMC3587231.
  6. Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS (2013). Metallochaperones regulate intracellular copper levels.  PLoS Comput Biol.  PMID: 23349626; PMCID: PMC3551603.
  7. Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L (2013). N-glycoproteome of E14.Tg2a mouse embryonic stem cells. PLoS One.  PMID: 23405203; PMCID: PMC3565968.
  8. Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW (2013).  A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell.  PMID: 23452847; PMC – In Process.

 2012. The following publications cite the P50GM076547/Center for Systems Biology
  1. Aitchison JD, Rout MP (2012). The yeast nuclear pore complex and transport through it. Genetics. PMID: 22419078; PMCID: PMC3296253.
  2. Ashworth J, Wurtmann EJ, Baliga NS (2012). Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Curr Opin Biotechnol. PMID: 22209016; PMCID: PMC3477774.
  3. Austin RJ, Smidansky HM, Holstein CA, Chang DK, Epp A, Josephson NC, Martin DB (2012). Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin. Proteomics. PMID: 22116683; PMCID: PMC3544294.
  4. Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Røntved CM, Aebersold R, Moritz RL, Bendixen E (2012). Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus uberis. J Proteome Res. PMID: 22256911; PMCID: PMC3342530.
  5. Boyle J, Kreisberg R, Bressler R, Killcoyne S (2012). Methods for visual mining of genomic and proteomic data atlases. BMC Bioinformatics. PMID: 22524279; PMCID: PMC3352268.
  6. Brusniak MY, Chu CS, Kusebauch U, Sartain MJ, Watts JD, Moritz RL (2012). An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology. Proteomics.  PMID: 22577019; PMC – In Process.
  7. Carter GW, Hays M, Sherman A, Galitski T (2012). Use of pleiotropy to model genetic interactions in a population. PLoS Genet.  PMID: 23071457; PMCID: PMC3469415.
  8. Deutsch EW (2012). File formats commonly used in mass spectrometry proteomics. Mol Cell Proteomics. PMID: 22956731; PMCID: PMC3518119.
  9. DuBois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD, Navarro M, Horn D, Aitchison JD, Rout MP, Field MC (2012). NUP-1 Is a Large Coiled-Coil Nucleoskeletal Protein in Trypanosomes with Lamina-Like Functions. PLOS Biology. PMID: 22479148; PMCID: PMC3313915.
  10. Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, Johnson CH, Kyriacou CP, O'Neill JS, Reddy AB (2012). Peroxiredoxins are conserved markers of circadian rhythms. Nature.  PMID: 22622569; PMCID: PMC3398137.
  11. Hood L, Balling R, Auffray C (2012). Revolutionizing medicine in the 21st century through systems approaches. Biotechnol J. PMID: 22815171; PMC – In Process.
  12. Hood L, Tian Q (2012). Systems approaches to biology and disease enable translational systems medicine. Genomics Proteomics Bioinformatics. PMID: 23084773; PMC – In Process.
  13. Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D (2012). The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics. PMID: 22375074; PMCID: PMC3394945.
  14. Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J (2012). Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC Bioinformatics. PMID: 23216909; PMCID: PMC3538679.
  15. London N, Ceto S, Ranish JA, Biggins S (2012). Phosphoregulation of Spc105 by Mps1 and PP1 regulates Bub1 localization to kinetochores. Curr Biol. PMID: 22521787; PMC – In Process.
  16. Luo J, Fishburn J, Hahn S, Ranish J (2012). An Integrated Chemical Cross-linking and Mass Spectrometry Approach to Study Protein Complex Architecture and Function. Mol Cell Proteomics. PMID: 22067100; PMCID: PMC3277749.
  17. Plaisier CL, Pan M, Baliga NS (2012). A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. PMID: 22745231; PMCID: PMC3483559.
  18. Plaisier CL, Baliga NS (2012). Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment Cell Melanoma Res. PMID: 22781216. 
  19. Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD (2012). Asymmetric Positive Feedback Loops Reliably Control Biological Responses. Mol Syst Biol.PMID: 22531117; PMCID: PMC3361002.
  20. Swearingen KE, Moritz RL (2012). High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics. Expert Rev Proteomics. PMID: 23194268; PMC – In Process.
  21. Thompson EG, Galitski T (2012). Quantifying and analyzing the network basis of genetic complexity. PLoS Comput Biol.  PMID: 22792055; PMCID: PMC3390359.

 

 2011. The following publications cite the P50GM076547/Center for Systems Biology
  1. Austin RJ, Kuestner RE, Chang DK, Madden KR, Martin DB (2011). SILAC compatible strain of Pichia pastoris for expression of isotopically labeled protein standards and quantitative proteomics. J Proteome Res. PMID: 21942632; PMCID: PMC3361967.
  2. Baumgardner LA, Shanmugam AK, Lam H, Eng JK, Martin DB (2011). Fast parallel tandem mass spectral library searching using GPU hardware acceleration. J Proteome Res. PMID: 21545112; PMCID: PMC3107871.
  3. Brooks AN, Turkarslan S, Beer KD, Lo FY, Baliga NS (2011). Adaptation of cells to new environments. Wiley Interdiscip Rev Syst Biol Med. PMID: 21197660; PMCID: PMC3081528.
  4. Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R (2011). ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics. PMID: 21414234. Book chapter.
  5. Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE (2011). RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res. PMID: 22199257; PMCID: PMC3315322.
  6. Cho JH, Gelinas R, Wang K, Etheridge A, Piper MG, Batte K, Dakhallah D, Price J, Bornman D, Zhang S, Marsh C, Galas D (2011). Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes. BMC Med Genomics. PMID: 21241464; PMCID: PMC3035594.
  7. Farrah T, Deutsch EW, Aebersold R (2011). Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods Mol Biol. PMID: 21468960. Book chapter.
  8. Farrah, T, Deutsch, EW, Omen, GS, Campbell, DS, Sun, Z, Bletz, JA, Mallick, P, Katz, JE, Malmstrom, J, Ossola, R, Watts, JD, Lin, B, Zhang, H, Mortiz, RL, Aebersold, R (2011) A high-confidence human plasma proteome reference set with estimated concentrations in PeptidleAtlas. Mol Cell Proteomics. PMCID: PMC3186192.
  9. Helsens, K, Brusniak, M, Deutsch, E, Moritz, R, Martens, L (2011). jTraML: An open source Java API for TraML, the PSI standard for sharing SRM transitions. J of Proteome Research. PMID: 21967198; PMCID: PMC3208355.
  10. Ideker T, Dutkowski J, Hood L (2011). Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. PMID: 21414478; PMCID: PMC3102020.
  11. Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I (2011). EPEPT: a web service for enhanced P-value estimation in permutation tests. BMC Bioinformatics. PMID: 22024252; PMCID: PMC3277916.
  12. Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I (2011). A regression model approach to enable cell morphology correction in high-throughput flow cytometry. Mol Syst Biol. PMID: 21952134; PMCID: PMC3202802.
  13. Moussay E, Wang K, Cho JH, van Moer K, Pierson S, Paggetti J, Nazarov PV, Palissot V, Hood LE, Berchem G, Galas DJ (2011). MicroRNA as biomarkers and regulators in B-cell chronic lymphocytic leukemia. Proc Natl Acad Sci. PMID: 21460253; PMCID: PMC3081030.
  14. Nadeau JH, Dudley AM (2011). Genetics. Systems genetics. Science. PubMed PMID: 21350153. Review
  15. Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H (2011). Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics. PMID: 22045680. Report..
  16. Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR (2011). Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem. PMID: 21341720; PMCID: PMC3217585.
  17. Plaisier CL, Bare JC, Baliga NS (2011). miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res. PMID: 21602264; PMCID: PMC3125776.
  18. Ratushny AV, Ramsey SA, Aitchison JD (2011). Mathematical modeling of biomolecular network dynamics. Methods Mol Biol. PMID: 21877294. PMC - In Process
  19. Ratushny AV, Shmulevich I, Aitchison JD (2011). Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues. PLoS Comput Biol. PMID: 21738459; PMCID: PMC3127798.
  20. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF (2011). Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. PMID: 21855840; PMCID: PMC3169815.
  21. Robinson CK, Webb K, Kaur A, Jaruga P, Dizdaroglu M, Baliga NS, Place A, Diruggiero J. (2011). A major role for nonenzymatic antioxidant processes in the radioresistance of Halobacterium salinarum. J Bacteriol. 2011 PMID: 21278285; PMCID: PMC3067647.
  22. Robinson T, Killcoyne S, Bressler R, Boyle J (2011). SAMQA: error classification and validation of high-throughput sequenced read data. BMC Genomics. PMID: 21851633; PMCID: PMC3170309.
  23. Schmid AK, Pan M, Sharma K, Baliga NS (2011). Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res. PMID: 21109526; PMCID: PMC3074139.
  24. Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI (2011). iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics. PMID: 21876204; PMCID: PMC3237071.
  25. Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD (2011). Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol. PMID: 21206489; PMC3049408.
  26. Smith JJ, Saleem RA, Aitchison JD (2011). Statistical analysis of dynamic transcriptional regulatory network structure. Methods Mol Biol. PMID: 21877289. PMC – In Process.
  27. Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL (2011). Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Mol Cell Proteomics. PMID: 22186714. PMC – In Process.
  28. Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS (2011). Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol. PMID: 22108796; PMCID: PMC3261711.
  29. Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD (2011). Role of the nuclear envelope in genome organization and gene expression. Wiley Interdiscip Rev Syst Biol Med. Review. PMID: 21305702; PMCID: PMC3050641.
  30. Yan W, Luo J, Robinson M, Eng J, Aebersold R, Ranish J (2011). Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures. Mol Cell Proteomics. PMID: 21169564; PMCID: PMC3047164.
  31. Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q (2011). A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A. PMID: 21220328; PMC3029739.

 2010. The following publications cite the P50GM076547/Center for Systems Biology
  1. Akiyoshi B, Sarangapani KK, Powers AF, Nelson CR, Reichow SL, Arellano-Santoyo H, Gonen T, Ranish JA, Asbury CL, Biggins S (2010). Tension directly stabilizes reconstituted kinetochore-microtubule attachments. Nature. PMID: 21107429. PMCID: PMC3108429.
  2. Bare JC, Koide T, Reiss DJ, Tenenbaum D, Baliga NS (2010). Integration and visualization of systems biology data in context of the genome. BMC Bioinformatics. 11:382. PMID: 20642854; PMCID: PMC2912892.
  3. Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I, Boyle J (2010). SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinformatics. 11:377. PMID: 20630057; PMCID: PMC2916924.
  4. Carter GW, Rush CG, Uygun F, Sakhanenko NA, Galas DJ, Galitski T (2010). A systems-biology approach to modular genetic complexity. Chaos. 20(2):026102. PMID: 20590331; PMCID: PMC2909309.
  5. Cheng L, Lu W, Kulkarni B, Pejovic T, Yan X, Chiang JH, Hood L, Odunsi K, Lin B (2010). Analysis of chemotherapy response programs in ovarian cancers by the next-generation sequencing technologies. Gynecol Oncol. 117(2):159-69. PMID: 20181382; PMCID: PMC2849907.
  6. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R (2010). A guided tour of the Trans-Proteomic Pipeline. Proteomics. 10(6):1150-9. Review. PMID: 20101611; PMCID: PMC3017125.
  7. Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R (2010). Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets. Proteomics. 10(6):1190-5. PMID: 20082347; PMCID: PMC3018683.
  8. Deutsch EW (2010). Mass spectrometer output file format mzML. Methods Mol Biol. 604:319-31. PMID: 20013381. PMCID: PMC3073315.
  9. Deutsch EW (2010). The PeptideAtlas Project. Methods Mol Biol. 604:285-96. PMID: 20013378. PMCID: PMC3076596.
  10. Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD (2010). QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. J Am Soc Mass Spectrom. 21(8):1417-22. PMID: 20451407; PMCID: PMC2914207.
  11. Eddy JA, Hood L, Price ND, Geman D (2010). Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol. 6(5):e1000792. PMID: 20523739; PMCID: PMC2877722.
  12. Erkkilä T, Lehmusvaara S, Ruusuvuori P, Visakorpi T, Shmulevich I, Lähdesmäki H (2010). Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics. 26(20):2571-7. PMID: 20631160; PMCID: PMC2951082.
  13. Facciotti MT, Pang WL, Lo FY, Whitehead K, Koide T, Masumura K, Pan M, Kaur A, Larsen DJ, Reiss DJ, Hoang L, Kalisiak E, Northen T, Trauger SA, Siuzdak G, Baliga NS (2010). Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. BMC Syst Biol. 4:64. PMID: 20470417; PMCID: PMC2880973.
  14. Falconnet D, Niemisto A, Taylor RJ, Ricicova M, Galitski T, Shmulevich I, Hansen CL. (2010). High-throughput tracking of single yeast cells in a microfluidic imaging matrix. Lab on a Chip 11(3):466-73. PMID: 21088765; PMCID: PMC3032636.
  15. Himeda CL, Ranish JA, Pearson RC, Crossley M, Hauschka SD (2010). KLF3 regulates muscle-specific gene expression and synergizes with serum response factor on KLF binding sites. Mol Cell Biol. 30(14):3430-43. PMID: 20404088; PMCID: PMC2897560.
  16. Holstein Sherwood CA, Gafken PR, Martin DB (2010). Collision energy optimization of b- and y-ions for multiple reaction monitoring mass spectrometry. J Proteome Res. PMID: 20968307. PMC - In Process.
  17. Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD (2010). Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem. 285(9):6739-49. PMID: 20026609; PMCID: PMC2825468.
  18. Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss DJ, DiRuggiero J, Baliga NS (2010). Coordination of frontline defense mechanisms under severe oxidative stress. Mol Syst Biol. 6:393. PMID: 20664639; PMCID: PMC2925529.
  19. Lee LW, Zhang S, Etheridge A, Ma L, Martin D, Galas D, Wang K (2010). Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA. PMID: 20876832; PMCID: PMC2957056.
  20. Munson MS, Spotts JM, Niemistö A, Selinummi J, Kralj JG, Salit ML, Ozinsky A (2010). Image-based feedback control for real-time sorting of microspheres in a microfluidic device. Lab Chip. 10(18):2402-10. PMID: 20593069; PMCID: PMC2928395.
  21. Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I. (2010). Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics. 26(17):2071-5. Epub 2010 Jul 27. PMID: 20663846; PMCID: PMC2922897.
  22. Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 328(5978):636-9. PMID: 20220176; PMCID: PMC3037280.
  23. Ruusuvuori P, Aijö T, Chowdhury S, Garmendia-Torres C, Selinummi J, Birbaumer M, Dudley AM, Pelkmans L, Yli-Harja O (2010). Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics. 11:248. PMID: 20465797. PMCID: PMC3098061.
  24. Saleem RA, Aitchison JD (2010). Systems cell biology of the mitotic spindle. J Cell Biol. 188(1):7-9. PMID: 20065087; PMCID: PMC2815928.
  25. Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD (2010). Genome-wide analysis of effectors of peroxisome biogenesis. PLoS One. 5(8). PMID: 20694151; PMCID: PMC2915925.
  26. Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD (2010). Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics. 9(9):2076-88. PMID: 20395639; PMCID: PMC2938103.
  27. Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT (2010). GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome. Mol Syst Biol. 6:353. PMID: 20212525; PMCID: PMC2858444.
  28. Sigmon I, Lee LW, Chang DK, Krusberski N, Cohen D, Eng JK, Martin DB (2010). ChromEval: a software application for the rapid evaluation of HPLC system performance in proteomic applications. Anal Chem. 82(12):5060-8. PMID: 20503988. PMC – In Process.
  29. Sípová H, Zhang S, Dudley AM, Galas D, Wang K, Homola J (2010). Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem. PMID: 21090631; PMCID: PMC3021551.
  30. Tenenbaum D, Bare JC, Baliga NS (2010). GTC: A web server for integrating systems biology data with web tools and desktop applications. Source Code Biol Med. PubMed PMID: 20626906; PMCID: PMC2917411.
  31. Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD (2010). Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing. Nucleic Acids Res. 38(5):1431-40. PMID: 20008511; PMCID: PMC2836552.
  32. Wang K, Lee I, Carlson G, Hood L, Galas D (2010). Systems biology and the discovery of diagnostic biomarkers. Dis Markers. 28(4):199-207. PMID: 20534905. PMCID: PMC3021550.
  33. Weber JA, Baxter DH, Zhang S, Huang DY, Huang KH, Lee MJ, Galas DJ, Wang K (2010). The microRNA spectrum in 12 body fluids. Clin Chem. PMID: 20847327. PMC - In Process.

 2009. The following publications cite the P50GM076547/Center for Systems Biology
  1. Akiyoshi B, Nelson CR, Ranish JA, Biggins S (2009). Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae. Genetics. 183(4):1591-5. PMID: 19822728; PMCID: PMC2787442.
  2. Akiyoshi B, Nelson CR, Ranish JA, Biggins S (2009). Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit. Genes Dev. 23(24):2887-99. PMID: 19948764; PMCID: PMC2800092.
  3. Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I (2009). Adaptable data management for systems biology investigations. BMC Bioinformatics. 10:79. PMID: 19265554. PMCID: PMC2670281.
  4. Carter GW, Galas DJ, Galitski T (2009). Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol. 5(4) :e1000347. PMID: 19343223; PMCID: PMC2909309.
  5. Diercks A, Kostner H, Ozinsky A (2009). Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS One. 4(7):e6326. PMID: 19633712; PMCID: PMC2711328.
  6. Diercks AH, Ozinsky A, Hansen CL, Spotts JM, Rodriguez DJ, Aderem A (2009). A microfluidic device for multiplexed protein detection in nano-liter volumes. Anal Biochem. 386(1):30-5. PMID: 19133224; PMCID: PMC2678059.
  7. Ghosh D, Yan X, Tian Q (2009). Gene regulatory networks in embryonic stem cells and brain development. Birth Defects Res C Embryo Today, 87(2):182-91. PMCID: PMC2996937.
  8. Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB (2009). Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. J Proteome Res. 8(3):1415-22. PMID: 19195997; PMCID: PMC2798736.
  9. Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I (2009). Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst Biol. 18;3:20. PMCID: 2652435.
  10. Hwang D, Lee IY, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R, Young R, Spicer D, Price ND, Hohmann JG, Dearmond SJ, Carlson GA, Hood LE (2009). A systems approach to prion disease. Mol Syst Biol. 5:252. PMID to 19308092; PMCID: PMC2671916.
  11. Killcoyne S, Boyle J (2009). Managing Chaos: Lessons Learned Developing Software in the Life Sciences. Comput Sci Eng. 11(6):20-29. PMID: 20700479; PMCID: PMC2917833.
  12. Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I (2009). Fewer permutations, more accurate P-values. Bioinformatics. 25(12):i161-8. PMID: 19477983; PMCID: PMC2687965.
  13. Koide T, Pang WL, Baliga NS (2009). The role of predictive modeling in rationally re-engineering biological systems. Nat Rev Microbiol. 7(4):297-305. PMID: 19252506; PMCID PMC2734281.
  14. Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS (2009). Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 5:285. PMID: 19536208; PMCID PMC2710873.
  15. Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L (2009). Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One. 4(8):e6589. PMID: 19668381; PMCID: PMC2720376.
  16. Liu Y, Warfield L, Zhang C, Luo J, Allen J, Lang WH, Ranish J, Shokat KM, Hahn S (2009). Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol. 29(17):4852-63. PMID: 19581288; PMCID: 2725703.
  17. Nykter M, Lähdesmäki H, Rust A, Thorsson V, Shmulevich I (2009). A data integration framework for prediction of transcription factor targets. Ann N Y Acad Sci.1158:205-14. PMID: 19348642; PMCID: PMC2771581.
  18. Pascal LE, Goo YA, Vêncio RZ, Page LS, Chambers AA, Liebeskind ES, Takayama TK, True LD, Liu AY (2009). Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific genes. BMC Cancer. 9:317. PMID: 19737398; PMCID: PMC2745432.
  19. Peterson A, Hohmann L, Huang L, Kim B, Eng JK, Martin DB (2009). Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics. J Proteome Res. 8(8) :4161-8. PMID: 19601632; PMCID: PMC2757279.
  20. Saleem RA, Aitchison JD. Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae (2009). J Vis Exp. 12;(32). PMID: 19823167; PMCID: PMC2865974
  21. Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS (2009). A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol. 5:282. PMID: 19536205; PMCID: PMC2710871.
  22. Shmulevich I, Aitchison JD. Deterministic and stochastic models of genetic regulatory networks (2009). Methods Enzymol. 467:335-56. PMID: 19897099;
  23. Selinummi J, Ruusuvuori P, Podolsky I, Ozinsky A, Gold E, Yli-Harja O, Aderem A, Shmulevich I (2009). Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS One 22;4 (10):e7497; PMCID: 2760782.
  24. Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N, Aebersold R, Lam H, Martin DB (2009). MaRiMba: a software application for spectral library-based MRM transition list assembly. J Proteome Res. 8(10) :4396-405. PMID: 19603829; PMCID: PMC2837355.
  25. Sherwood CA, Eastham A, Lee LW, Risler J, Vitek O, Martin DB (2009). Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res. 8(9):4243-51. PMID: 19603825; PMCID: PMC2802215.
  26. Sherwood CA, Eastham A, Lee LW, Risler J, Mirzaei H, Falkner JA, Martin DB (2009). Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets. J Proteome Res. 8(7):3746-51. PMID: 19405522; PMCID: PMC2811718.
  27. Smith JJ, Aitchison JD (2009). Regulation of peroxisome dynamics. Curr Opin Cell Biol.:119-26. Review. PMID: 19188056; PMCID: PMC2681484.
  28. Taylor RJ, Falconnet D, Niemistö A, Ramsey SA, Prinz S, Shmulevich I, Galitski T, Hansen CL (2009). Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform. Proc Natl Acad Sci U S A. 106(10):3758-63. PMID: 19223588; PMCID: PMC264426.
  29. Tu LC, Foltz G, Lin E, Hood L, Tian Q (2009). Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther. 4(2):147-53. PMID: 19442199; PMCID: PMC3034385.
  30. Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD (2009). Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes. Mol Cell Biol. 29(9):2346-58. PMID: 19273605: PMCID: PMC2668375.
  31. Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ (2009). Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci U S A.106(11):4402-7. PMID: 19246379; PMCID: PMC2657429.
  32. Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS (2009). Diurnally entrained anticipatory behavior in archaea. PLoS One. 4(5):e5485. PMID: 19424498; PMCID PMC 2734281.

 2008. The following publications cite the P50GM076547/Center for Systems Biology
  1. Balleza E, Alvarez-Buylla E, Chaos A, Kauffman SA, Shmulevich I, Aldana M (2008). Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms, PLoS ONE, Vol. 3, No. 6, e2456. PMCID: PMC2423472.
  2. Boyle J, Cavnor C, Killcoyne S, Shmulevich I (2008). Systems biology driven software design for the research enterprise, BMC Bioinformatics, Vol. 9, No. 295. PMCID: PMC2478690.
  3. Deutsch EW, Lam H, Aebersold R (2008). Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 33(1):18-25. PMID: 18212004.
  4. Deutsch EW, Lam H, Aebersold R (2008). PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5):429-34. PMID: 18451766; PMCID: 2373374.
  5. Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ (2008). Saccharomyces cerevisiae Yta7 Regulates Histone Gene Expression, Genetics. PMID: 18493054; PMCID: PMC2390607.
  6. Himeda CL, Ranish JA, Hauschka SD (2008). Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes, Mol. Cell Biol. PMID: 18710939; PMCID: PMC2577440.
  7. Hood LE, Rowen L, Galas DJ, Aitchison JD (2008). Systems Biology at the Institute for Systems Biology, Briefings in Functional Genomics and Proteomics.
  8. Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy K, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H (2008). The Innate Immune Database (IIDB), BMC Immunology, Vol. 9, No. 7. PMID: 18321385; PMCID: PMC2268913.
  9. Lähdesmäki H, Shmulevich I (2008). Learning the Structure of Dynamic Bayesian Networks from Time Series and Steady State Measurements, Machine Learning, Vol. 71, 185-217. PMCID: PMC2766792.
  10. Lähdesmäki H, Rust AG, Shmulevich I (2008). Probabilistic inference of transcription factor binding from multiple data sources, PLoS ONE, Vol. 3, No. 3, e1820. PMID: 18364997; PMCID: PMC2268002.
  11. Li R, Guo Y, Ming Han B, Yan X, Utleg AG, Li W, Chun Tu L, Wang J, Hood LE, Xia S, Lin B (2008). Proteomics cataloguing analysis of human expressed prostatic secretions reveals rich source of biomarker candidates. Proteomics-Clinical Applications. Volume 2, Issue 4, 543 – 555. PMID: 20559448; PMCID: PMC2886281.
  12. Lin B, Utleg A, Gravdal K, White J, Halvorsen O, Lu W, True L, Vessella R, Lange P, Nelson P, Hood LE, Kalland K, Akslen L (2007). WDR19 expression is increased in prostate cancer compared to normal cells, but low intensity expression in cancers is associated with shorter time to biochemical failures and local recurrence. Clinical Cancer Research 14, 1397-1406. PMID: 18316261.
  13. Liu W, Lähdesmäki H, Dougherty ER, Shmulevich I (2008). Inference of Boolean Networks using Sensitivity Regularization, EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541. PMID: 18604289; PMCID: PMC2441825.
  14. Marelli M, Nesvizhskii AI, Aitchison JD. Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions: an example in peroxisomes (2008). Methods Mol Biol. 432:357-71. PMID: 18370030.
  15. Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M (2008). MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics. 7(11):2270-8. PMID: 18641041; PMCID: PMC2577205.
  16. Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O, Shmulevich I (2008). Gene Expression Dynamics in the Macrophage Exhibit Criticality, Proceedings of the National Academy of Sciences of the USA, Vol. 105, No. 6, 1897-1900. PMID: 18250330; PMCID: PMC2538855.
  17. Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I (2008). Critical networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, Vol. 100, 058702. PMID: 18352443.
  18. Pascal LE, True LD, Campbell DS, Deutsch EW, Risk M, Coleman IM, Eichner LJ, Nelson PS, Liu AY (2008). Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. BMC Genomics. 9:246. PMID: 18501003; PMCID: 2413246.
  19. Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM , Long-O’Donnell R, Rachubinski RA, Aitchison JD (2008). Genome-wide analysis of signaling networks regulating fatty acid- induced gene expression and organelle biogenesis. The Journal of Cell Biology. PMID: 18426976; PMCID: PMC2315675.
  20. Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold E, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I (2008). Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics, PLoS Computational Biology, Vol. 4, No. 3, e1000021. PMCID: PMC2265556.
  21. Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD (2008). Control of Transcriptional Variability by Overlapping Feed-Forward Regulatory Motifs, Biophys J. PMID: 18621837; PMCID: PMC2553142.
  22. Reiss DJ, Facciotti MT, Baliga NS (2008). Model-based deconvolution of genome-wide DNA binding. Bioinformatics. 24(3):396-403. PMID: 18056063.
  23. Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A (2008). CTCF physically links cohesin to chromatin, Proc Natl Acad Sci U S A, 105(24):8309-14. PMID: 18550811; PMCID: PMC2448833.
  24. Tabb DL, Ma ZQ, Martin DB, Ham AJ L, Chambers MC (2008). DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring, Journal of Proteome Research. PMID: 18630943; PMCID: PMC2810657.
  25. Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS (2008). Halobacterium salinarum NRC-1 Peptide Atlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage. J Proteome Res. PMID: 18652504; PMCID: PMC2643335

 2007. The following publications cite the P50GM076547/Center for Systems Biology
  1. Bare JC, Shannon P, Schmid A, Baliga NS. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics. 2007 Nov 19; 8(1), 456. PMID: 18021453.
  2. Bong K, Nesvizhskii AI, Rani PG, Hahn S, Aebersold R, Ranish, JA. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. (2007). PNAS 41(104): 16068-73.
  3. Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson T, Shannon P, Johnson MH, Bare CJ, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, DiRuggiero J, Johnson CH, Hood L, Baliga NS. A predictive model for transcriptional control of physiology in a free living cell. Cell. 2007 Dec 28; 131 (7): 1354-65. PMID: 18160043.
  4. Carter GW, Prinz S, Neou C, Shelby JP, Marzolf B, Thorsson V, Galitski T. (2007). Prediction of phenotype and gene expression for combinations of mutations. Mol. Syst. Biol. 3:96.
  5. Carter GW, Thorsson V, Galitski T. (2007). Integrated network modeling of molecular and genetic interactions. In, Sourcebook of Models for Biomedical Research, (ed. M Conn, Humana). Book chapter.
  6. Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007; 104(11): 4630-4635. PMID: 17360575.
  7. P. Krawitz, I. Shmulevich, Basin Entropy in Boolean Network Ensembles, Physical Review Letters, Vol. 98, No. 15, pp. 158701(1-4), 2007.
  8. P. Krawitz, I. Shmulevich, Entropy of complex relevant components in Boolean networks, Physical Review E, Vol. 76, 036115, 2007.
  9. Makhnevych, T., Ptak, C., Lusk, C. P., Aitchison, J. D., Wozniak, R. W. (2007). The role of karyopherins in the regulated sumoylation of septins. J Cell Biol 177, 39-49.
  10. A. Niemisto, T. Korpelainen, R. Saleem, O. Yli-Harja, J. Aitchison, I. Shmulevich, A K-Means Segmentation Method for Finding 2-D Object Areas Based on 3-D Image Stacks Obtained by Confocal Microscopy, 29th International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France, August 23-26, 2007.
  11. Oeffinger, M, Wei, KE, Rogers, R, Degrasse, JA, Chait, BT, Aitchison, JD, Rout, MP. (2007). Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods 4, 951-956.
  12. N. D. Price, J. Trent, A. K. El-Naggar, D. Cogdell, E. Taylor, K. K. Hunt, R. E. Pollock, L. Hood, I. Shmulevich, W. Zhang, Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas, Proceedings of the National Academy of Sciences of the USA, Vol. 104, No. 9, pp- 3414-3419, 2007.
  13. Prinz S, Aldridge C, Ramsey SA, Taylor RJ, Galitski T. (2007). Control of Signaling in a MAP-kinase Pathway by an RNA-Binding Protein. PLoS ONE 2:e249.
  14. Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS. The anatomy of microbial cell state transitions in response to oxygen. Genome Research. 2007 Oct; 17(10): 1399-413. Epub 2007 Sep 4. PMID: 17785531.
  15. J. Selinummi, A. Niemistö, R. Saleem, G. W. Carter, J. Aitchison, O. Yli-Harja, I. Shmulevich, and J. Boyle, A Case Study on 3-D Reconstruction and Shape Description of Peroxisomes in Yeast, IEEE International Conference on Signal Processing and Communication (ICSPC07), Dubai, United Arab Emirates (UAE), November 24-27, 2007.
  16. Smith, J. J., Ramsey, S. A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R. A., Rachubinski, R. A., Aitchison, J. D. (2007). Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol Syst Biol 3, 115.
  17. Sun B, Ranish J.A., Utleg A.G., White J.T., Yan X., Lin B, Hood L.E. (2007). Shotgun Glycopeptide-Capture Approach Coupled With Mass Spectrometry for Comprehensive Glycoproteomics. Molecular Cellular Proteomics 6:141-149.
  18. Taylor RJ, Siegel AF, Galitski T. (2007). Network motif analysis of multi-mode genetic-interaction networks. Genome Biology 2007 8:R160.
  19. Tu L.C., Yan X., Hood L.E., Lin B. (2007). Proteomic analysis of the interactome of N-myc downstream regulated gene 1 and its interaction with the androgen program in prostrate cancer cells. Mol Cell Proteomics, 6(4): 575-588. Epub 2007.
  20. R. Vencio, I. Shmulevich, ProbCD: enrichment analysis accounting for categorization uncertainty, BMC Bioinformatics, Vol 8, No. 383, 2007.
  21. R. Vêncio, L. Varuzza, C. Pereira, H. Brentani, I. Shmulevich, Simcluster: clustering enumeration gene expression data on the simplex space, BMC Bioinformatics, Vol. 8, No. 246, 2007.


 2006. The following publications cite the P50GM076547/Center for Systems Biology
  1. Ramsey, S. A., Smith, J. J., Orrell, D., Marelli, M., Petersen, T. W., de Atauri, P., Bolouri, H., Aitchison, J. D. (2006). Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 38, 1082-1087.
  2. Saleem, R. A., Smith, J. J., Aitchison, J. D. (2006). Proteomics of the peroxisome. Biochim Biophys Acta 1763, 1541-1551.
  3. Taverna, S. D., Ilin, S., Rogers, R. S., Tanny, J. C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L. P., Chait, B. T., Patel, D. J., Aitchison, J. D., Tackett, A. J., Allis, C. D. (2006). Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 24, 785-796.
  4. Whitehead K., Kish A., Pan M., Kaur A., Reiss D.J., King N., Hohmann L., DiRuggiero J., Baliga N. (2006). An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol, 2, 47.

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