Experts and Doctors on computational biology in Boston, Massachusetts, United States

Summary

Locale: Boston, Massachusetts, United States
Topic: computational biology

Top Publications

  1. Paulo J, Urrutia R, Banks P, Conwell D, Steen H. Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states. J Proteome Res. 2011;10:4835-44 pubmed publisher
  2. Hendricks A, Dupuis J, Gupta M, Logue M, Lunetta K. A comparison of gene region simulation methods. PLoS ONE. 2012;7:e40925 pubmed publisher
    ..We recommend using Hapgen to simulate replicate haplotypes from a gene region. Hapgen produces moderate sampling variation between the replicates while retaining the overall unique LD structure of the gene region. ..
  3. Zhang B, Jia W, Matsuda K, Kweon S, Matsuo K, Xiang Y, et al. Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk. Nat Genet. 2014;46:533-42 pubmed publisher
    ..11, 10q21.1 and 10q24.2. Furthermore, we replicated 22 previously reported CRC-associated loci. Our study provides insights into the genetic basis of CRC and suggests the involvement of new biological pathways. ..
  4. Karpathakis A, Dibra H, Pipinikas C, Feber A, Morris T, Francis J, et al. Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor. Clin Cancer Res. 2016;22:250-8 pubmed publisher
    ..We have demonstrated that these tumors are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression-free survival. ..
  5. Estrada B, Choe S, Gisselbrecht S, Michaud S, Raj L, Busser B, et al. An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet. 2006;2:e16 pubmed
    ..This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system. ..
  6. Iliopoulos D, Bimpaki E, Nesterova M, Stratakis C. MicroRNA signature of primary pigmented nodular adrenocortical disease: clinical correlations and regulation of Wnt signaling. Cancer Res. 2009;69:3278-82 pubmed publisher
  7. Rapoport B. Metabolic factors limiting performance in marathon runners. PLoS Comput Biol. 2010;6:e1000960 pubmed publisher
    ..The present analysis also sheds physiologically principled light on important standards in marathon running that until now have remained empirically defined: The qualifying times for the Boston Marathon. ..
  8. Seyedsayamdost M, Cleto S, Carr G, Vlamakis H, João Vieira M, Kolter R, et al. Mixing and matching siderophore clusters: structure and biosynthesis of serratiochelins from Serratia sp. V4. J Am Chem Soc. 2012;134:13550-3 pubmed publisher
    ..These results highlight how modular siderophore gene clusters can be mixed and matched during evolution to generate structural diversity in siderophores. ..
  9. Savage V, Deeds E, Fontana W. Sizing up allometric scaling theory. PLoS Comput Biol. 2008;4:e1000171 pubmed publisher

More Information

Publications107 found, 100 shown here

  1. Pratt J, Zeng Q, Ravnic D, Huss H, Rawn J, Mentzer S. Hierarchical clustering of monoclonal antibody reactivity patterns in nonhuman species. Cytometry A. 2009;75:734-42 pubmed publisher
    ..We conclude that our computational algorithm is a potentially useful tool for both Mab classification and molecular taxonomy in nonhuman experimental systems. ..
  2. Dreze M, Monachello D, Lurin C, Cusick M, Hill D, Vidal M, et al. High-quality binary interactome mapping. Methods Enzymol. 2010;470:281-315 pubmed publisher
    ..This chapter describes a high-quality, high-throughput binary protein-protein interactome mapping pipeline that includes these features. ..
  3. Cherepanov P, Devroe E, Silver P, Engelman A. Identification of an evolutionarily conserved domain in human lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) that binds HIV-1 integrase. J Biol Chem. 2004;279:48883-92 pubmed
    ..LEDGF/p75 and HRP2 are predicted to share a similar domain organization and have an evident evolutionary and likely functional relationship. ..
  4. Zhang W, Ntai I, Kelleher N, Walsh C. tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A. 2011;108:12249-53 pubmed publisher
  5. Shen H, Shanmugasundaram K, Simon N, Cai C, Wang H, Chen S, et al. In silico discovery of androgen receptor antagonists with activity in castration resistant prostate cancer. Mol Endocrinol. 2012;26:1836-46 pubmed publisher
  6. Adam R, Eaton S, Estrada C, Nimgaonkar A, Shih S, Smith L, et al. Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cells. Physiol Genomics. 2004;20:36-44 pubmed
    ..Moreover, they suggest that mechanical and growth factor signals converge on common transcriptional regulators that include members of the AP-1 family. ..
  7. Kubota K, Anjum R, Yu Y, Kunz R, Andersen J, Kraus M, et al. Sensitive multiplexed analysis of kinase activities and activity-based kinase identification. Nat Biotechnol. 2009;27:933-40 pubmed publisher
    ..Finally, we introduce a strategy to identify the kinase, and even associated protein complex members, responsible for phosphorylation events of interest. ..
  8. Gao B, Stuart L, Feener E. Label-free quantitative analysis of one-dimensional PAGE LC/MS/MS proteome: application on angiotensin II-stimulated smooth muscle cells secretome. Mol Cell Proteomics. 2008;7:2399-409 pubmed publisher
  9. Fletcher C, Coyne M, Comstock L. Theoretical and experimental characterization of the scope of protein O-glycosylation in Bacteroides fragilis. J Biol Chem. 2011;286:3219-26 pubmed publisher
  10. Vasudevan S. Functional validation of microRNA-target RNA interactions. Methods. 2012;58:126-34 pubmed publisher
  11. Haserick J, Klein J, Costello C, Samuelson J. Cryptosporidium parvum vaccine candidates are incompletely modified with O-linked-N-acetylgalactosamine or contain N-terminal N-myristate and S-palmitate. PLoS ONE. 2017;12:e0182395 pubmed publisher
    ..The significance of these post-translational modifications is discussed with regards to the function of these proteins and the design of serological tests and vaccines. ..
  12. Deo R, Hunter L, Lewis G, Pare G, Vasan R, Chasman D, et al. Interpreting metabolomic profiles using unbiased pathway models. PLoS Comput Biol. 2010;6:e1000692 pubmed publisher
    ..Given the involvement of transporters in human disease, metabolite profiling may contribute to improved disease classification via the interrogation of specific transporter activities. ..
  13. Börnigen D, Tyekucheva S, Wang X, Rider J, Lee G, Mucci L, et al. Computational Reconstruction of NF?B Pathway Interaction Mechanisms during Prostate Cancer. PLoS Comput Biol. 2016;12:e1004820 pubmed publisher
  14. Nishihara R, Glass K, Mima K, Hamada T, Nowak J, Qian Z, et al. Biomarker correlation network in colorectal carcinoma by tumor anatomic location. BMC Bioinformatics. 2017;18:304 pubmed publisher
    ..Our findings highlight the importance of considering multiple correlated pathways for therapeutic targets especially in proximal colon cancer. ..
  15. Beausoleil S, Jedrychowski M, Schwartz D, Elias J, Villen J, Li J, et al. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A. 2004;101:12130-5 pubmed
    ..From 967 proteins, 2,002 phosphorylation sites were determined by tandem MS. This unprecedented large collection of sites permitted a detailed accounting of known and unknown kinase motifs and substrates. ..
  16. Schirmer C, Malek A. Estimation of wall shear stress dynamic fluctuations in intracranial atherosclerotic lesions using computational fluid dynamics. Neurosurgery. 2008;63:326-34; discussion 334-5 pubmed publisher
  17. Moffitt K, Malley R, Lu Y. Identification of protective pneumococcal T(H)17 antigens from the soluble fraction of a killed whole cell vaccine. PLoS ONE. 2012;7:e43445 pubmed publisher
    ..We propose that, by providing protection against pneumococcal colonization, one or more of these proteins may serve as components of a multivalent pneumococcal vaccine. ..
  18. Morelli X, Palma P, Guerlesquin F, Rigby A. A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data. Protein Sci. 2001;10:2131-7 pubmed
    ..The potential utility of this novel NMR and simulated docking approach in current structural genomic initiatives is discussed. ..
  19. Walsh C. Natural insights for chemical biologists. Nat Chem Biol. 2005;1:122-4 pubmed
    ..Chemical biologists studying natural-product pathways encoded in genomes have unearthed new chemistry and insights into the evolution of biologically active metabolites. ..
  20. Tragante V, Barnes M, Ganesh S, Lanktree M, Guo W, Franceschini N, et al. Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. Am J Hum Genet. 2014;94:349-60 pubmed publisher
    ..In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification. ..
  21. Sheu S, Kaya T, Waxman D, Vajda S. Exploring the binding site structure of the PPAR gamma ligand-binding domain by computational solvent mapping. Biochemistry. 2005;44:1193-209 pubmed
    ..The number of probe clusters retained by these sites depends on the properties of the bound agonist, providing information on the origin of correlations between ligand and coactivator binding. ..
  22. Vijai J, Wang Z, Berndt S, Skibola C, Slager S, de Sanjose S, et al. A genome-wide association study of marginal zone lymphoma shows association to the HLA region. Nat Commun. 2015;6:5751 pubmed publisher
    ..95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. This is the first evidence that genetic variation in the major histocompatibility complex influences MZL susceptibility. ..
  23. Yin L, Tagde A, Gali R, Tai Y, Hideshima T, Anderson K, et al. MUC1-C is a target in lenalidomide resistant multiple myeloma. Br J Haematol. 2017;178:914-926 pubmed publisher
    ..These findings, and the demonstration that expression of MUC1 and CD44 significantly correlate in microarrays from primary MM cells, provide support for combining GO-203 with LEN in the treatment of MM and in LEN-resistance. ..
  24. Lazaro E, Kadie C, Stamegna P, Zhang S, Gourdain P, Lai N, et al. Variable HIV peptide stability in human cytosol is critical to epitope presentation and immune escape. J Clin Invest. 2011;121:2480-92 pubmed publisher
    ..Our results identify sequence motifs able to alter the amount of peptide available for loading onto MHC-I, suggesting potential new strategies to modulate epitope production from vaccine immunogens. ..
  25. Xu Y, Wang Z, Li C, Chou K. iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC. Med Chem. 2017;13:544-551 pubmed publisher
    ..aporc.org/iPreny-PseAAC/, by which users can easily get their desired results without needing to go through the mathematical details involved in this paper. ..
  26. Ghadie M, Lambourne L, Vidal M, Xia Y. Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PLoS Comput Biol. 2017;13:e1005717 pubmed publisher
    ..Our prediction method complements experimental efforts, and demonstrates that integrating structural domain information with interactomes provides insights into the functional impact of alternative splicing. ..
  27. Liu X, Fortin P, Walsh C. Andrimid producers encode an acetyl-CoA carboxyltransferase subunit resistant to the action of the antibiotic. Proc Natl Acad Sci U S A. 2008;105:13321-6 pubmed publisher
    ..This observation allowed for bioinformatic identification of several Vibrio cholerae strains in which accD genes encode the Met<-->Leu switches, and their occurrences correlate predictively with sensitivities to andrimid in vivo. ..
  28. Qureshi A, Chaoji V, Maiguel D, Faridi M, Barth C, Salem S, et al. Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling. PLoS ONE. 2009;4:e7627 pubmed publisher
  29. Sigoillot F, Lyman S, Huckins J, Adamson B, Chung E, Quattrochi B, et al. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods. 2012;9:363-6 pubmed publisher
    ..GESS analysis results can enhance the validation rate in RNAi screens. ..
  30. Jogler C, Waldmann J, Huang X, Jogler M, Glöckner F, Mascher T, et al. Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics. J Bacteriol. 2012;194:6419-30 pubmed publisher
  31. Lee J, Whittington M, Kopell N. Top-down beta rhythms support selective attention via interlaminar interaction: a model. PLoS Comput Biol. 2013;9:e1003164 pubmed publisher
    ..The predicted critical roles of these cells in attentional gain provide a potential mechanism by which cholinergic drive can support selective attention. ..
  32. Liu Y, Hu Z, Delisi C. Mutated Pathways as a Guide to Adjuvant Therapy Treatments for Breast Cancer. Mol Cancer Ther. 2016;15:184-9 pubmed publisher
    ..These results suggest that patient profiling using these pathway groups can potentially enable the development of personalized treatment plans that may be more accurate and specific than those currently available. ..
  33. Bulyk M, McGuire A, Masuda N, Church G. A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res. 2004;14:201-8 pubmed
    ..This approach may be useful in analyzing binding sites in a variety of organisms. ..
  34. Schirmer C, Malek A. Prediction of complex flow patterns in intracranial atherosclerotic disease using computational fluid dynamics. Neurosurgery. 2007;61:842-51; discussion 852 pubmed
  35. Aryee M, Gutiérrez Pabello J, Kramnik I, Maiti T, Quackenbush J. An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). BMC Bioinformatics. 2009;10:409 pubmed publisher
    ..The open-source R package betr is available through Bioconductor. BETR has also been incorporated in the freely-available, open-source MeV software tool available from http://www.tm4.org/mev.html. ..
  36. Larremore D, Clauset A, Buckee C. A network approach to analyzing highly recombinant malaria parasite genes. PLoS Comput Biol. 2013;9:e1003268 pubmed publisher
    ..Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences. ..
  37. Vinayagam A, ZIRIN J, Roesel C, Hu Y, Yilmazel B, Samsonova A, et al. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. Nat Methods. 2014;11:94-9 pubmed publisher
  38. Ernst J, Ghanem L, Bar Joseph Z, McNamara M, Brown J, Steinman R. IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. PLoS ONE. 2009;4:e7469 pubmed publisher
    ..These findings support a model of IL-3 action through mRNA stability control and suggest that aberrant stabilization of an mRNA network linked to IL-3 contributes to leukemic cell growth. ..
  39. Thaden J, Lory S, Gardner T. Quorum-sensing regulation of a copper toxicity system in Pseudomonas aeruginosa. J Bacteriol. 2010;192:2557-68 pubmed publisher
    ..This work identifies a cellular function for PA4778 and four other previously unannotated genes (PA3515, PA3516, PA3517, and PA3518) and suggests a potential role for copper in the quorum response. We propose to name PA4778 cueR...
  40. Shchedrina V, Everley R, Zhang Y, Gygi S, Hatfield D, Gladyshev V. Selenoprotein K binds multiprotein complexes and is involved in the regulation of endoplasmic reticulum homeostasis. J Biol Chem. 2011;286:42937-48 pubmed publisher
    ..These data suggest that SelK is involved in the Derlin-dependent ERAD of glycosylated misfolded proteins and that the function defined by the prototypic SelK is the widespread function of selenium in eukaryotes. ..
  41. Sinha A, Armstrong S. iCanPlot: visual exploration of high-throughput omics data using interactive Canvas plotting. PLoS ONE. 2012;7:e31690 pubmed publisher
    ..We illustrate the power of iCanPlot by showing an example of how it can be used to interpret histone modifications in the context of gene expression. ..
  42. Gulbahce N, Yan H, Dricot A, Padi M, Byrdsong D, Franchi R, et al. Viral perturbations of host networks reflect disease etiology. PLoS Comput Biol. 2012;8:e1002531 pubmed publisher
    ..The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia...
  43. Henzy J, Coffin J. Betaretroviral envelope subunits are noncovalently associated and restricted to the mammalian class. J Virol. 2013;87:1937-46 pubmed publisher
    ..We discuss implications of these findings for retroviral evolution, cross-species transmissions, and recombination events involving the env gene...
  44. Kosuri S, Church G. Large-scale de novo DNA synthesis: technologies and applications. Nat Methods. 2014;11:499-507 pubmed publisher
    ..In addition, we discuss emerging applications enabled by large-scale de novo DNA constructs, as well as the challenges and opportunities that lie ahead. ..
  45. Cha Y, Han M, Cha H, Zoldan J, Burkart A, Jung J, et al. Metabolic control of primed human pluripotent stem cell fate and function by the miR-200c-SIRT2 axis. Nat Cell Biol. 2017;19:445-456 pubmed publisher
  46. Dankwa S, Chaand M, Kanjee U, Jiang R, Nobre L, Goldberg J, et al. Genetic Evidence for Erythrocyte Receptor Glycophorin B Expression Levels Defining a Dominant Plasmodium falciparum Invasion Pathway into Human Erythrocytes. Infect Immun. 2017;85: pubmed publisher
    ..The collective data suggest that the GPA and GPB receptors are of greater importance than the GPC receptor, supporting a hierarchy of erythrocyte receptor usage in P. falciparum. ..
  47. Gymrek M, Willems T, Reich D, Erlich Y. Interpreting short tandem repeat variations in humans using mutational constraint. Nat Genet. 2017;49:1495-1501 pubmed publisher
    ..Constraint scores identified known pathogenic variants with early-onset effects. Our metric will provide a valuable tool for prioritizing pathogenic STRs in medical genetics studies. ..
  48. Ellis T, Wang X, Collins J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol. 2009;27:465-71 pubmed publisher
    ..We use this network to control the timing of yeast sedimentation, illustrating how the plug-and-play nature of our design can be readily applied to biotechnology. ..
  49. Lee J, Park I, Gao Y, Li J, Li Z, Daley G, et al. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 2009;5:e1000718 pubmed publisher
    ..We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells. ..
  50. Thomas M, Lieberman J, Lal A. Desperately seeking microRNA targets. Nat Struct Mol Biol. 2010;17:1169-74 pubmed publisher
    ..Bioinformatic analysis of over-represented pathways and nodes in protein-DNA interactomes formed from experimental candidate miRNA gene target lists can focus attention on biologically significant target genes. ..
  51. Hwang H, Vreven T, Pierce B, Hung J, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins. 2010;78:3104-10 pubmed publisher
  52. Markowitz J, Ivie E, Kligler L, Gardner T. Long-range order in canary song. PLoS Comput Biol. 2013;9:e1003052 pubmed publisher
    ..The neural basis of these long-range correlations may provide insight into how complex behaviors are assembled from more elementary, stereotyped modules...
  53. Ibrahim E, Hims M, Shomron N, Burge C, Slaugenhaupt S, Reed R. Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Hum Mutat. 2007;28:41-53 pubmed
  54. Fusaro V, Patil P, Gafni E, Wall D, Tonellato P. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol. 2011;7:e1002147 pubmed publisher
    ..amazon.com/importexport/). More information about cloud computing, detailed cost analysis, and security can be found in references. ..
  55. Klann J, Murphy S. Computing health quality measures using Informatics for Integrating Biology and the Bedside. J Med Internet Res. 2013;15:e75 pubmed publisher
    ..It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers. ..
  56. Wang Z, McGlynn K, Rajpert De Meyts E, Bishop D, Chung C, Dalgaard M, et al. Meta-analysis of five genome-wide association studies identifies multiple new loci associated with testicular germ cell tumor. Nat Genet. 2017;49:1141-1147 pubmed publisher
  57. Hu Y, Hines L, Weng H, Zuo D, Rivera M, Richardson A, et al. Analysis of genomic and proteomic data using advanced literature mining. J Proteome Res. 2003;2:405-12 pubmed
    ..Interestingly, this only held true for estrogen receptor (ER) positive tumors, not ER negative. MedGene identified a set of relatively understudied, yet highly expressed genes in ER negative tumors worthy of further examination. ..
  58. Tremblay L, Dunaway Mariano D, Allen K. Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily. Biochemistry. 2006;45:1183-93 pubmed
    ..The ability to catabolize other related secondary metabolites indicates that there is regulation at the genetic level. ..
  59. Parry D, Xu J, Ruvkun G. A whole-genome RNAi Screen for C. elegans miRNA pathway genes. Curr Biol. 2007;17:2013-22 pubmed
  60. Kharchenko P, Tolstorukov M, Park P. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008;26:1351-9 pubmed publisher
    ..We also analyze the relationship between the depth of sequencing and characteristics of the detected binding positions, and provide a method for estimating the sequencing depth necessary for a desired coverage of protein binding sites. ..
  61. Yang J, Niemierko A, Bajcsy R, Xu D, Athey B, Zhang A, et al. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. BMC Genomics. 2010;11 Suppl 3:I1 pubmed publisher
    ..Joydeep Ghosh (UT Austin), Dr. Aidong Zhang (Buffalo) and Dr. Zhi-Hua Zhou (Nanjing) for their significant contributions to the field of intelligent biological medicine. ..
  62. Zakka L, Reche P, Ahmed A. The molecular basis for the presence of two autoimmune diseases occurring simultaneously--preliminary observations based on computer analysis. Autoimmunity. 2012;45:253-63 pubmed publisher
    ..While other explanations and mechanisms exist, the authors suggest that epitope spreading may be one possible mechanism, amongst others, that may result in the simultaneous presence of two separate pathogenic autoantibodies. ..
  63. Marks D, Colwell L, Sheridan R, Hopf T, Pagnani A, Zecchina R, et al. Protein 3D structure computed from evolutionary sequence variation. PLoS ONE. 2011;6:e28766 pubmed publisher
  64. Grossberg S, Pilly P. How entorhinal grid cells may learn multiple spatial scales from a dorsoventral gradient of cell response rates in a self-organizing map. PLoS Comput Biol. 2012;8:e1002648 pubmed publisher
    ..Spatial and temporal representations may hereby arise from homologous mechanisms, thereby embodying a mechanistic "neural relativity" that may clarify how episodic memories are learned...
  65. Kasinathan S, Orsi G, Zentner G, Ahmad K, Henikoff S. High-resolution mapping of transcription factor binding sites on native chromatin. Nat Methods. 2014;11:203-9 pubmed publisher
    ..Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. ..
  66. Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014;506:376-81 pubmed publisher
  67. Medema M, Kottmann R, Yilmaz P, Cummings M, Biggins J, Blin K, et al. Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015;11:625-31 pubmed publisher
  68. Glover J, Man T, Barkauskas D, Hall D, Tello T, Sullivan M, et al. Osteosarcoma enters a post genomic era with in silico opportunities: Generation of the High Dimensional Database for facilitating sarcoma biology research: A report from the Children's Oncology Group and the QuadW Foundation. PLoS ONE. 2017;12:e0181204 pubmed publisher
  69. Rual J, Klitgord N, Achaz G. Novel insights into RNAi off-target effects using C. elegans paralogs. BMC Genomics. 2007;8:106 pubmed
    ..elegans. Our predictive methods would improve the design of dsRNA and ultimately the use of RNAi as a therapeutic tool upon experimental verification. ..
  70. Pujana M, Han J, Starita L, Stevens K, Tewari M, Ahn J, et al. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet. 2007;39:1338-49 pubmed
    ..Our network modeling strategy should be useful for the discovery of additional cancer-associated genes. ..
  71. Warner J, Philippakis A, Jaeger S, He F, Lin J, Bulyk M. Systematic identification of mammalian regulatory motifs' target genes and functions. Nat Methods. 2008;5:347-53 pubmed publisher
    ..This approach is general and can be applied readily to any cell type, gene expression pattern or organism of interest. ..
  72. Lazebnik M, Tussie Luna M, Roy A. Determination and functional analysis of the consensus binding site for TFII-I family member BEN, implicated in Williams-Beuren syndrome. J Biol Chem. 2008;283:11078-82 pubmed publisher
  73. Livny J, Teonadi H, Livny M, Waldor M. High-throughput, kingdom-wide prediction and annotation of bacterial non-coding RNAs. PLoS ONE. 2008;3:e3197 pubmed publisher
    ..Annotation of candidate loci by SIPHT provides clues into the potential biological function of thousands of previously confirmed and candidate regulatory RNAs and affords new insights into the evolution of bacterial riboregulation. ..
  74. Zhu C, Byers K, McCord R, Shi Z, Berger M, Newburger D, et al. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009;19:556-66 pubmed publisher
    ..These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes. ..
  75. Riemer A, Keskin D, Zhang G, Handley M, Anderson K, Brusic V, et al. A conserved E7-derived cytotoxic T lymphocyte epitope expressed on human papillomavirus 16-transformed HLA-A2+ epithelial cancers. J Biol Chem. 2010;285:29608-22 pubmed publisher
    ..These data underscore the importance of precisely defining CTL epitopes on tumor cells and offer a paradigm for T cell-based vaccine design. ..
  76. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010;11:685-96 pubmed publisher
    ..This Review focuses on the methodological considerations for characterizing somatic genome alterations in cancer and the future prospects for these approaches. ..
  77. Bradshaw M, Smith M. Contribution of unfolding and intermolecular architecture to fibronectin fiber extensibility. Biophys J. 2011;101:1740-8 pubmed publisher
    ..These data have implications for Fn-dependent mechanotransduction and give insight into how the molecular architecture of natural materials permits such remarkable extensibility. ..
  78. Serang O, Mollinari M, Garcia A. Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids. PLoS ONE. 2012;7:e30906 pubmed publisher
    ..Our method achieves state-of-the-art performance on both data sets and can be trivially adapted to use models that utilize prior information about any platform or species. ..
  79. Qiao D, Yip W, Lange C. Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data. BMC Bioinformatics. 2012;13:100 pubmed publisher
    ..The SpeedGene algorithm enables the storage and the analysis of next generation sequencing data in current hardware environment, making system upgrades unnecessary. ..
  80. Nibert M, Duncan R. Bioinformatics of recent aqua- and orthoreovirus isolates from fish: evolutionary gain or loss of FAST and fiber proteins and taxonomic implications. PLoS ONE. 2013;8:e68607 pubmed publisher
    ..In addition, an apparent evolutionary correlation was found between the gain or loss of NS-FAST and outer-fiber proteins among more distally branching members of this taxon. ..
  81. Bonham K, Stefan M. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology. PLoS Comput Biol. 2017;13:e1005134 pubmed publisher
    ..Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance...
  82. MacConaill L, Aldred M, Lu X, LaFramboise T. Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. BMC Genomics. 2007;8:211 pubmed
    ..Software to perform generalized genotyping from SNP array data is freely available online 1. ..
  83. Tian W, Zhang L, Tasan M, Gibbons F, King O, Park J, et al. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biol. 2008;9 Suppl 1:S7 pubmed publisher
    ..Performance was evaluated by cross-validation and by literature examination of the top-scoring novel predictions. These quantitative predictions should help prioritize experimental study of yeast gene functions. ..
  84. Zhang X, Sebastiani P, Liu G, Schembri F, Zhang X, Dumas Y, et al. Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. Physiol Genomics. 2010;41:1-8 pubmed publisher
    ..Our findings suggest that nasal epithelial gene expression may serve as a relatively noninvasive surrogate to measure physiological responses to cigarette smoke and/or other inhaled exposures in large-scale epidemiological studies. ..
  85. Chang H, McGeachie M, Alterovitz G, Ramoni M. Mapping transcription mechanisms from multimodal genomic data. BMC Bioinformatics. 2010;11 Suppl 9:S2 pubmed publisher
    ..The application of our method to the leukemia study explains how genetic variants and gene expression are linked to leukemia. ..
  86. Jun G, Moncaster J, Koutras C, Seshadri S, Buros J, McKee A, et al. δ-Catenin is genetically and biologically associated with cortical cataract and future Alzheimer-related structural and functional brain changes. PLoS ONE. 2012;7:e43728 pubmed publisher
    ..Our findings suggest that genetic variation in delta catenin may underlie both cortical lens opacities in mid-life and subsequent MRI and cognitive changes that presage the development of AD. ..
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