Updated 1/12/17, 6/26/17, 2/21/18

  1. Baker QB, Podgorski GJ, Vargis E, Flann NS (2017). A computational study of VEGF production by patterned retinal epithelial cell colonies as a model for neovascular macular degeneration. J Biol Eng. PMID: 28775765; PMCID: PMC5540422.
  2. Bargaje R, Trachana K, Shelton MN, McGinnis CS, Zhou JX, Chadick C, Cook S, Cavanaugh C, Huang S, Hood L (2017). Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells. Proc Natl Acad Sci U S A. PMID: 28167799; PMCID: PMC5338498.
  3. Cromie GA, Tan Z, Hays M, Jeffery EW, Dudley AM (2017). Dissecting Gene Expression Changes Accompanying a Ploidy-Based Phenotypic Switch. G3 (Bethesda). PMID: 27836908; PMCID: PMC5217112.
  4. Cromie GA, Tan Z, Hays M, Sirr A, Jeffery EW, Dudley AM (2017). Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in Saccharomyces cerevisiae. G3 (Bethesda). PMID: 28673928; PMCID: PMC5555487.
  5. Davis D, Doloman A, Podgorski GJ, Vargis E, Flann NS (2017). Exploiting Self-organization in Bioengineered Systems: A Computational Approach. Front Bioeng Biotechnol. PMID: 28503548; PMCID: PMC5408088.
  6. Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA (2017). The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. PMID: 27924013; PMCID: PMC5210636.
  7. Ghaffarizadeh A, Podgorski GJ, Flann NS (2017). Applying attractor dynamics to infer gene regulatory interactions involved in cellular differentiation. Biosystems. PMID: 28254369; PMC In Process.
  8. Ghosh D, Funk CC, Caballero J, Shah N, Rouleau K, Earls JC, Soroceanu L, Foltz G, Cobbs CS, Price ND, Hood L (2017). A Cell-Surface Membrane Protein Signature for Glioblastoma. Cell Syst. PMID: 28365151; PMCID:PMC5512565
  9. Herricks T, Dilworth DJ, Mast FD, Li S, Smith JJ, Ratushny AV, Aitchison JD (2017). One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY! G3 (Bethesda). PMID: 27856698; PMCID: PMC5217116.
  10. Herricks T, Mast FD, Li S, Aitchison JD (2017). ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth. J Vis Exp. PMID: 28715382; PMCID: PMC5608540.
  11. Joesch-Cohen LM, Glusman G (2017). Differences between the genomes of lymphoblastoid cell lines and blood-derived samples. Adv Genomics Genet. PMID: 28736497; PMCID: PMC5520659.
  12. Kessler A, Dankwa S, Bernabeu M, Harawa V, Danziger SA, Duffy F, Kampondeni SD, Potchen MJ, Dambrauskas N, Vigdorovich V, Oliver BG, Hochman SE, Mowrey WB, MacCormick IJC, Mandala WL, Rogerson SJ, Sather DN, Aitchison JD, Taylor TE, Seydel KB, Smith JD, Kim K (2017). Linking EPCR-Binding PfEMP1 to Brain Swelling in Pediatric Cerebral Malaria. Cell Host Microbe. PMID: 29107642; PMCID: PMC5783720.
  13. Michalik S, Depke M, Murr A, Gesell Salazar M, Kusebauch U, Sun Z, Meyer TC, Surmann K, Pförtner H, Hildebrandt P, Weiss S, Palma Medina LM, Gutjahr M, Hammer E, Becher D, Pribyl T, Hammerschmidt S, Deutsch EW, Bader SL, Hecker M, Moritz RL, Mäder U, Völker U, Schmidt F (2017). A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions. Sci Rep. PMID: 28887440; PMCID: PMC5591248.
  14. Price ND, Magis AT, Earls JC, Glusman G, Levy R, Lausted C, McDonald DT, Kusebauch U, Moss CL, Zhou Y, Qin S, Moritz RL, Brogaard K, Omenn GS, Lovejoy JC, Hood L (2017). A wellness study of 108 individuals using personal, dense, dynamic data clouds. Nat Biotechnol. PMID: 28714965; PMCID: PMC5568837.
  15. Sen P, Luo J, Hada A, Hailu SG, Dechassa ML, Persinger J, Brahma S, Paul S, Ranish J, Bartholomew B (2017). Loss of Snf5 Induces Formation of an Aberrant SWI/SNF Complex. Cell Rep. PMID: 28249160; PMCID: PMC5424545.
  16. Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS (2017). Mechanism for microbial population collapse in a fluctuating resource environment. Mol Syst Biol. PMID: 28320772; PMCID: PMC5371734.
  17. Zhou JX, Taramelli R, Pedrini E, Knijnenburg T, Huang S (2017). Extracting Intercellular Signaling Network of Cancer Tissues using Ligand-Receptor Expression Patterns from Whole-tumor and Single-cell Transcriptomes. Sci Rep. PMID: 28821810; PMCID: PMC5562796.
  18. Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A (2017). The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria. Front Microbiol. Review. PMID: 29201016; PMCID: PMC5696578.