Updated 1/12/17

  1. Ashworth J, Bernard B, Reynolds S, Plaisier CL, Shmulevich I, Baliga NS (2014). Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers. Nucleic Acids Res. PMID: 25378323; PMCID: PMC4245936.
  2. Ashworth J, Plaisier CL, Lo FY, Reiss DJ, Baliga NS (2014). Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction. PLoS One. PMID: 25255272; PMCID: PMC4177876.
  3. Bare JC, Baliga NS (2014). Architecture for interoperable software in biology. Brief Bioinform. PMID: 23235920; PMCID: PMC4103535.
  4. Beer KD, Wurtmann EJ, Pinel N, Baliga NS (2014). Model organisms retain an “ecological memory” of complex ecologically relevant environmental variation.  Appl Environ Microbiol. PMID: 24413600; PMCID: PMC3957629.
  5. Brooks AN, Reiss DJ, Allard A, Wu WJ, Salvanha DM, Plaisier CL, Chandrasekaran S, Pan M, Kaur A, Baliga NS (2014). A system-level model for the microbial regulatory genome. Mol Syst Biol. PMID: 25028489; PMCID: PMC4299497.
  6. Bundgaard L, Jacobsen S, Sørensen MA, Sun Z, Deutsch EW, Moritz RL, Bendixen E (2014). The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research. Proteomics. PMID: 24436130; PMCID: PMC4340707.
  7. Carpp LN, Rogers RS, Moritz RL, Aitchison JD (2014). Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection. Mol Cell Proteomics. PMID: 24855065; PMCID: PMC4223476.
  8. Cary GA, Yoon SH, Torres CG, Wang K, Hays M, Ludlow C, Goodlett DR, Dudley AM (2014). Identification and characterization of a drug-sensitive strain enables puromycin-based translational assays in Saccharomyces cerevisiae. Yeast. PMID: 24610064; PMCID: PMC4013229.
  9. Chiang JH, Cheng WS, Hood L, Tian Q (2014). An epigenetic biomarker panel for glioblastoma multiforme personalized medicine through DNA methylation analysis of human embryonic stem cell-like signature. OMICS. PMID: 24601786; PMCID: PMC4012637.
  10. Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD (2014). Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic Acids Res. PMID: 24185701; PMCID: PMC3919619.
  11. Garmendia-Torres C, Skupin A, Michael SA, Ruusuvuori P, Kuwada NJ, Falconnet D, Cary GA, Hansen C, Wiggins PA, Dudley AM (2014). Unidirectional P-Body Transport during the Yeast Cell Cycle. PLoS One. PMID: 24918601; PMCID: PMC4053424.
  12. Ghaffarizadeh A, Flann NS, Podgorski GJ (2014). Multistable switches and their role in cellular differentiation networks. BMC Bioinformatics. PMID: 25078021; PMCID: PMC4110729.
  13. Ghaffarizadeh A, Podgorski GJ, Flann NS (2014). Modeling and visualizing cell type switching. Comput Math Methods Med. PMID: 24834107; PMCID: PMC4009162.
  14. Gierman HJ, Fortney K, Roach JC, Coles NS, Li H, Glusman G, Markov GJ, Smith JD, Hood L, Coles LS, Kim SK (2014). Whole-genome sequencing of the world’s oldest people. PLoS One. PMID: 25390934; PMCID: PMC4229186.
  15. Glusman G, Cox HC, Roach JC. Whole-genome haplotyping approaches and genomic medicine (2014). Genome Med. PMID: 25473435; PMCID: PMC4254418.Han Y, Luo J, Ranish J, Hahn S (2014). Architecture of the Saccharomyces cerevisiae SAGA transcription coactivator complex. EMBO J. PMID: 25216679; PMCID: PMC4283410.
  16. He Y, Chevillet JR, Liu G, Kim TK, Wang K (2014). The effects of microRNA on the absorption, distribution, metabolism and excretion of drugs. Br J Pharmacol. PMID: 25296724; PMCID: PMC4439871.
  17. Holden JM, Koreny L, Kelly S, Chait BT, Rout MP, Field MC, Obado SO (2014). Touching from a distance. Nucleus. PMID: 25482119; PMCID: PMC4152344.
  18. Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Chiang JH, Kelly S, Chait BT, Aitchison JD, Rout MP, Field MC (2014). Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. Mol Biol Cell. PMID: 24600046; PMCID: PMC4004592.
  19. Knutson BA, Luo J, Ranish J, Hahn S (2014). Architecture of the Saccharomyces cerevisiae RNA polymerase I Core Factor complex. Nat Struct Mol Biol. PMID: 25132180; PMCID: PMC4219626.
  20. Krishna A, Biryukov M, Trefois C, Antony PM, Hussong R, Lin J, Heinäniemi M, Glusman G, Köglsberger S, Boyd O, van den Berg BH, Linke D, Huang D, Wang K, Hood L, Tholey A, Schneider R, Galas DJ, Balling R, May P (2014). Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease. BMC Genomics. PMID: 25528190; PMCID: PMC4367834.
  21. Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL (2014). Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. Curr Protoc Bioinformatics. PMID: 24939129; PMCID: PMC4331073.
  22. Kusebauch U, Ortega C, Ollodart A, Rogers RS, Sherman DR, Moritz RL, Grundner C (2014). Mycobacterium tuberculosis supports protein tyrosine phosphorylation. Proc Natl Acad Sci U S A. PMID: 24927537; PMCID: PMC4078798.
  23. Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS (2014). Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res. PMID: 24364385; PMCID: PMC3928647.
  24. Lausted C, Lee I, Zhou Y, Qin S, Sung J, Price ND, Hood L, Wang K (2014). Systems approach to neurodegenerative disease biomarker discovery. Annu Rev Pharmacol Toxicol. PMID: 24160693. Book Chapter.
  25. Lehman A, Stittrich AB, Glusman G, Zong Z, Li H, Eydoux P, Senger C, Lyons C, Roach JC, Patel M (2014). Diffuse angiopathy in Adams-Oliver syndrome associated with truncating DOCK6 mutations. Am J Med Genet A. PMID: 25091416; PMCID: PMC4167472.
  26. Li H, Glusman G, Huff C, Caballero J, Roach JC (2014). Accurate and robust prediction of genetic relationship from whole-genome sequences. PLoS One. PMID: 24586241; PMCID: PMC3938395.
  27. Mast FD, Ratushny AV, Aitchison JD (2014). Systems cell biology. J Cell Biol. Review. PMID: 25225336; PMCID: PMC4164942.
  28. Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M (2013). Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim Biophys Acta. PMID: 23429179; PMCID: PMC3898906.
  29. Mohamadlou H, Shope JC, Flann NS (2014). Maximizing Kolmogorov Complexity for accurate and robust bright field cell segmentation. BMC Bioinformatics. PMID: 24475950; PMCID: PMC3922779.
  30. Mojtahedi M, Fouquier d’Hérouël A, Huang S (2014). Direct elicitation of template concentration from quantification cycle (Cq) distributions in digital PCR. Nucleic Acids Res. PMID: 25104023; PMCID: PMC4176345.
  31. Muller EE, Pinel N, Laczny CC, Hoopmann MR, Narayanasamy S, Lebrun LA, Roume H, Lin J, May P, Hicks ND, Heintz-Buschart A, Wampach L, Liu CM, Price LB, Gillece JD, Guignard C, Schupp JM, Vlassis N, Baliga NS, Moritz RL, Keim PS, Wilmes P (2014). Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nat Commun. PMID: 25424998; PMCID: PMC4263124.
  32. Ptak C, Aitchison JD, Wozniak RW (2014). The multifunctional nuclear pore complex: a platform for controlling gene expression. Curr Opin Cell Biol. PMID: 24657998; PMCID: PMC4061258.
  33. Peterson EJ, Reiss DJ, Turkarslan S, Minch KJ, Rustad T, Plaisier CL, Longabaugh WJ, Sherman DR, Baliga NS (2014). A high-resolution network model for global gene regulation in Mycobacterium tuberculosis. Nucleic Acids Res. PMID: 25232098; PMCID: PMC4191388.
  34. Plaisier CL, Lo FY, Ashworth J, Brooks AN, Beer KD, Kaur A, Pan M, Reiss DJ, Facciotti MT, Baliga NS (2014). Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. BMC Syst Biol. PMID: 25394904; PMCID: PMC4236453.
  35. Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND (2014). MediaDB: a database of microbial growth conditions in defined media. PLoS One. PMID: 25098325; PMCID: PMC4123892.
  36. Rustad TR, Minch KJ, Ma S, Winkler JK, Hobbs S, Hickey M, Brabant W, Turkarslan S, Price ND, Baliga NS, Sherman DR (2014). Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network. Genome Biol. PMID: 25380655; PMCID: PMC4249609.
  37. Ruusuvuori P, Lin J, Scott AC, Tan Z, Sorsa S, Kallio A, Nykter M, Yli-Harja O, Shmulevich I, Dudley AM (2014). Quantitative analysis of colony morphology in yeast. Biotechniques. PMID: 24447135; PMCID: PMC3996921.
  38. Sangar V, Funk CC, Kusebauch U, Campbell DS, Moritz RL, Price ND (2014). Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells. Mol Cell Proteomics. PMID: 24997998; PMCID: PMC4188991.
  39. Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM (2014). Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature. PMID: 24284630; PMCID: PMC4077721.
  40. Schubert J, Siekierska A, Langlois M, May P, Huneau C, Becker F, Muhle H, Suls A, Lemke JR, de Kovel CG, Thiele H, Konrad K, Kawalia A, Toliat MR, Sander T, Rüschendorf F, Caliebe A, Nagel I, Kohl B, Kecskés A, Jacmin M, Hardies K, Weckhuysen S, Riesch E, Dorn T, Brilstra EH, Baulac S, Møller RS, Hjalgrim H, Koeleman BP; EuroEPINOMICS RES Consortium., Jurkat-Rott K, Lehman-Horn F, Roach JC, Glusman G, Hood L, Galas DJ, Martin B, de Witte PA, Biskup S, De Jonghe P, Helbig I, Balling R, Nürnberg P, Crawford AD, Esguerra CV, Weber YG, Lerche H (2014). Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes. Nat Genet. PMID: 25362483.
  41. Sun B, Hood L (2014). Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res. PMID: 24754784; PMCID: PMC4053080.
  42. Surmann K, Michalik S, Hildebrandt P, Gierok P, Depke M, Brinkmann L, Bernhardt J, Salazar MG, Sun Z, Shteynberg D, Kusebauch U, Moritz RL, Wollscheid B, Lalk M, Völker U, Schmidt F (2014). Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells. Front Microbiol. PMID: 25136337; PMCID: PMC4117987.
  43. Taylor AF, Amundsen SK, Guttman M, Lee KK, Luo J, Ranish J, Smith GR (2014). Control of RecBCD enzyme activity by DNA binding- and Chi hotspot-dependent conformational changes. J Mol Biol. PMID: 25073102; PMCID: PMC4188757.
  44. Tien JF, Umbreit NT, Zelter A, Riffle M, Hoopmann MR, Johnson RS, Fonslow BR, Yates JR 3rd, MacCoss MJ, Moritz RL, Asbury CL, Davis TN (2014). Kinetochore biorientation in Saccharomyces cerevisiae requires a tightly folded conformation of the Ndc80 complex. Genetics. PMID: 25230952; PMCID: PMC4256767.
  45. Tyler AL, Crawford DC, Pendergrass SA (2014). Detecting and Characterizing Pleiotropy: New Methods for Uncovering the Connection Between the Complexity of Genomic Architecture and Multiple phenotypes. Pac Symp Biocomput. PMID: 25072629; PMCID: PMC4108263.
  46. Vialas V, Sun Z, Loureiro y Penha CV, Carrascal M, Abián J, Monteoliva L,Deutsch EW, Aebersold R, Moritz RL, Gil C (2014). A Candida albicans PeptideAtlas. J Proteomics. PMID: 23811049; PMCID: PMC3951211.
  47. Wang L, Limbo O, Fei J, Chen L, Kim B, Luo J, Chong J, Conaway RC, Conaway JW, Ranish JA, Kadonaga JT, Russell P, Wang D (2014). Regulation of the Rhp26ERCC6/CSB chromatin remodeler by a novel conserved leucine latch motif. Proc Natl Acad Sci U S A. PMID: 25512493; PMCID: PMC4284531.
  48. Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS (2014). An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol. PMID: 24612392; PMCID: PMC4060883.