2011 Publications –
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Deutsch EW (2010). Mass spectrometer output file format mzML. Methods Mol Biol. 604:319-31. PMID: 20013381.
  8. Deutsch EW (2010). The PeptideAtlas Project. Methods Mol Biol. 604:285-96. PMID: 20013378.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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 (accepted for publication).
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. Saleem RA, Aitchison JD (2010). Systems cell biology of the mitotic spindle. J Cell Biol. 188(1):7-9. PMID: 20065087; PMCID: PMC2812858.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.