Updated 4/13/16, 1/12/2017

  1. Aitchison JD, Rout MP (2015). The interactome challenge. J Cell Biol. PMID: 26572620; PMCID: PMC4657177.
  2. Ament SA, Szelinger S, Glusman G, Ashworth J, Hou L, Akula N, Shekhtman T, Badner JA, Brunkow ME, Mauldin DE, Stittrich AB, Rouleau K, Detera-Wadleigh SD, Nurnberger JI Jr, Edenberg HJ, Gershon ES, Schork N; Bipolar Genome Study, Price ND, Gelinas R, Hood L, Craig D, McMahon FJ, Kelsoe JR, Roach JC (2015). Rare variants in neuronal excitability genes influence risk for bipolar disorder. Proc Natl Acad Sci U S A. PMID: 25730879; PMCID: PMC4371952.
  3. Bennett KL, Wang X, Bystrom CE, Chambers MC, Andacht TM, Dangott LJ, Elortza F, Leszyk J, Molina H, Moritz RL, Phinney BS, Thompson JW, Bunger MK, Tabb DL (2015). The 2012/2013 ABRF Proteomic Research Group Study: Assessing Longitudinal Intralaboratory Variability in Routine Peptide Liquid Chromatography Tandem Mass Spectrometry Analyses. Mol Cell Proteomics. PMID: 26435129; PMCID: PMC4762617.
  4. Cary GA, Vinh DB, May P, Kuestner R, Dudley AM (2015). Proteomic Analysis of Dhh1 Complexes Reveals a Role for Hsp40 Chaperone Ydj1 in Yeast P-Body Assembly. G3 (Bethesda). PMID: 26392412; PMCID: PMC4632068.
  5. Chandrasekaran S, Rittschof CC, Djukovic D, Gu H, Raftery D, Price ND, Robinson GE (2015). Aggression is associated with aerobic glycolysis in the honey bee brain(1). Genes Brain Behav. PMID: 25640316; PMCID: PMC4449359.
  6. Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS (2015). Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.BMC Syst Biol. PMID: 25881257; PMCID: PMC4407105.
  7. Depke M, Michalik S, Rabe A, Surmann K, Brinkmann L, Jehmlich N, Bernhardt J, Hecker M, Wollscheid B, Sun Z, Moritz RL, Völker U, Schmidt F (2015). A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies. Proteomics. PMID: 26224020. PMC Journal – In Process.
  8. Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL (2015). Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl. PMID: 25631240; PMCID: PMC4506239.
  9. Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS, Moritz RL (2015). State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet. JProteome Res. PMID: 26139527; PMCID: PMC4755269.
  10. Eddy JA, Funk CC, Price ND (2015). Fostering synergy between cell biology and systems biology. Trends Cell Biol. PMID: 26013981; PMCID: PMC4758507
  11. Geman D, Ochs M, Price ND, Tomasetti C, Younes L (2015). An argument for mechanism-based statistical inference in cancer. Hum Genet. Review. PMID: 25381197; PMCID: PMC4612627.
  12. Gillespie MA, Gold ES, Ramsey SA, Podolsky I, Aderem A, Ranish JA (2015). An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. EMBO J. PMID: 25755249; PMCID: PMC4426483.
  13. Glusman G, Severson A, Dhankani V, Robinson M, Farrah T, Mauldin DE, Stittrich AB, Ament SA, Roach JC, Brunkow ME, Bodian DL, Vockley JG, Shmulevich I, Niederhuber JE, Hood L (2015). Identification of copy number variants in whole-genome data using Reference Coverage Profiles. Front Genet. PMID: 25741365; PMCID: PMC4330915.
  14. Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J (2015). Rapid, optimized interactomic screening. Nat Methods. PMID: 25938370; PMCID: PMC4449307.
  15. He Y, Chevillet JR, Liu G, Kim TK, Wang K (2015). The effects of microRNA on the absorption, distribution, metabolism and excretion of drugs. Br J Pharmacol. Review. PMID: 25296724; PMCID: PMC4439871.
  16. Heavner BD, Price ND (2015). Transparency in metabolic network reconstruction enables scalable biological discovery. Curr Opin Biotechnol. PMID: 25562137; PMCID: PMC4490137.
  17. Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL (2015). Kojak: efficient analysis of chemically cross-linked protein complexes. J Proteome Res. PMID: 25812159; PMCID: PMC4428575.
  18. Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND (2015). Data-driven integration of genome-scale regulatory and metabolic network models. Front Microbiol. Review. PMID: 25999934; PMCID: PMC4419725.
  19. Imam S, Schäuble S, Valenzuela J, López García de Lomana A, Carter W, Price ND, Baliga NS (2015). A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. Plant J. PMID: 26485611; PMCID: PMC4715634.
  20. Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR (2015). Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry. J Proteomics Bioinform. PMID: 26962293; PMCID: PMC4780416.
  21. Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X (2015). Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev. PMID: 25792597; PMCID: PMC4378192.
  22. Keller A, Bader SL, Shteynberg D, Hood L, Moritz RL (2015). Automated Validation of Results and Removal of Fragment Ion Interferences in Targeted Analysis of Data-independent Acquisition Mass Spectrometry (MS) using SWATHProphet. Mol Cell Proteomics. PMID: 25713123; PMCID: PMC4424409.
  23. Lee JM, Kim KH, Shin A, Chao MJ, Abu Elneel K, Gillis T, Mysore JS, Kaye JA, Zahed H, Kratter IH, Daub AC, Finkbeiner S, Li H, Roach JC, Goodman N, Hood L, Myers RH, MacDonald ME, Gusella JF (2015). Sequence-Level Analysis of the Major European Huntington Disease Haplotype. Am J Hum Genet. PMID: 26320893; PMCID: PMC4564985.
  24. López García de Lomana A, Schäuble S, Valenzuela J, Imam S, Carter W, Bilgin DD, Yohn CB, Turkarslan S, Reiss DJ, Orellana MV, Price ND, Baliga NS (2015). Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii. Biotechnol Biofuels. PMID: 26633994; PMCID: PMC4667458.
  25. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J (2015). Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell. PMID: 26340423; PMCID: PMC4560838.
  26. Ma S, Minch KJ, Rustad TR, Hobbs S, Zhou SL, Sherman DR, Price ND (2015). Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis. PLoS Comput Biol. PMID: 26618656; PMCID: PMC4664399.
  27. Mast FD, Rachubinski RA, Aitchison JD (2015). Signaling dynamics and peroxisomes. Curr Opin Cell Biol. Review. PMID: 26042681; PMCID: PMC4529763.
  28. Meester JA, Southgate L, Stittrich AB, Venselaar H, Beekmans SJ, den Hollander N, Bijlsma EK, Helderman-van den Enden A, Verheij JB, Glusman G, Roach JC, Lehman A, Patel MS, de Vries BB, Ruivenkamp C, Itin P, Prescott K, Clarke S, Trembath R, Zenker M, Sukalo M, Van Laer L, Loeys B, Wuyts W (2015). Heterozygous Loss-of-Function Mutations in DLL4 Cause Adams-Oliver Syndrome. Am J Hum Genet. PMID: 26299364; PMCID: PMC4564989.
  29. Minch KJ, Rustad TR, Peterson EJ, Winkler J, Reiss DJ, Ma S, Hickey M, Brabant W, Morrison B, Turkarslan S, Mawhinney C, Galagan JE, Price ND, Baliga NS, Sherman DR (2015). The DNA-binding network of Mycobacterium tuberculosis. Nat Commun. PMID: 25581030; PMCID: PMC4301838.
  30. Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW (2015). Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. J Proteome Res. PMID: 26155816; PMCID: PMC4755311.
  31. Raman AV, Baliga NS (2015). The universe under a microscope. Environ Microbiol Rep. PMID: 25721591. PMC Journal – In Process.
  32. Reiss DJ, Plaisier CL, Wu WJ, Baliga NS (2015). cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. Nucleic Acids Res. PMID: 25873626; PMCID: PMC4513845.
  33. Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL (2015). reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra. J Am Soc Mass Spectrom. PMID: 26419769; PMCID: PMC4750398.
  34. Simeonidis E, Price ND (2015). Genome-scale modeling for metabolic engineering. J Ind Microbiol Biotechnol. PMID: 25578304; PMCID: PMC4455951.
  35. Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL (2015). Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline. Mol Cell Proteomics. PMID: 25418363; PMCID: PMC4350034.
  36. Stittrich AB, Ashworth J, Shi M, Robinson M, Mauldin D, Brunkow ME, Biswas S, Kim JM, Kwon KS, Jung JU, Galas D, Serikawa K, Duerr RH, Guthery SL, Peschon J, Hood L, Roach JC, Glusman G (2015). Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals. Hum Genome Var. PMID: 27081563; PMCID: PMC4785573.
  37. Swearingen KE, Winget JM, Hoopmann MR, Kusebauch U, Moritz RL (2015). Decreased Gap Width in a Cylindrical High-Field Asymmetric Waveform Ion Mobility Spectrometry Device Improves Protein Discovery. Anal Chem. PMID: 26560994; PMCID: PMC4777518.
  38. Thompson AW, Crow MJ, Wadey B, Arens C, Turkarslan S, Stolyar S, Elliott N, Petersen TW, van den Engh G, Stahl DA, Baliga NS (2015). A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities. J Microbiol Methods. PMID: 26187776. PMC Journal – In Process.
  39. Turkarslan S, Peterson EJ, Rustad TR, Minch KJ, Reiss DJ, Morrison R, Ma S, Price ND, Sherman DR, Baliga NS (2014). A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Sci Data. PMID: 25977815; PMCID: PMC4413241.
  40. Viollet L, Glusman G, Murphy KJ, Newcomb TM, Reyna SP, Sweney M, Nelson B, Andermann F, Andermann E, Acsadi G, Barbano RL, Brown C, Brunkow ME, Chugani HT, Cheyette SR, Collins A, DeBrosse SD, Galas D, Friedman J, Hood L, Huff C, Jorde LB, King MD, LaSalle B, Leventer RJ, Lewelt AJ, Massart MB, Mérida MR 2nd, Ptáček LJ, Roach JC, Rust RS, Renault F, Sanger TD, Sotero de Menezes MA, Tennyson R, Uldall P, Zhang Y, Zupanc M, Xin W, Silver K, Swoboda KJ (2015). Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry. PLoS One. PMID: 25996915; PMCID: PMC4440742.
  41. Winget JM, Watts JD, Hoopmann MR, DiColandrea T, Robinson MK, Huggins T, Bascom CC, Isfort RJ, Moritz RL (2015). Quantitative proteogenomic profiling of epidermal barrier formation in vitro. J Dermatol Sci. PMID: 25862149; PMCID: PMC4424144.
  42. Zelter A, Bonomi M, Kim Jo, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN (2015). The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling. Nat Commun. PMID: 26560693; PMCID: PMC4660060.