1. ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens–Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs Nicoletti, Paola; Bansal, Mukesh; Lefebvre, Celine; Guarnieri, Paolo; Shen, Yufeng; Pe’er, Itsik; Califano, Andrea; Floratos, Aristidis 2015 Articles Drugs--Side effectsATP-binding cassette transportersGene expressionGenetic regulationApoptosisToxic epidermal necrolysisBiology--ClassificationBioinformaticsGenetics
2. Aberrantly Expressed CeRNAs Account for Missing Genomic Variability of Cancer Genes via MicroRNA-Mediated Interactions Chiu, Hua-Sheng 2014 Theses CarcinogenesisOncogenesBioinformaticsRNABiology--ClassificationGenetics
3. A classification-based framework for predicting and analyzing gene regulatory response Kundaje, Anshul; Middendorf, Manuel; Wiggins, Chris H.; Shah, Mihir; Freund, Yoav; Leslie, Christina 2006 Articles BioinformaticsGenetics
4. A haplotype inference algorithm for trios based on deterministic sampling Wang, Xiaodong; Anastassiou, Dimitris; Iliandis, Alexandros; Watkinson, John 2010 Articles GeneticsBioinformatics
5. A method to identify differential expression profiles of time-course gene data with Fourier transformation Kim, Jaehee; Ogden, Robert T.; Kim, Haseong 2013 Articles Gene expression--Data processingGenetics--Data processingFourier analysisBioinformaticsGene expressionGeneticsBiology
6. A Novel Platform to Perform Cancer-Relevant Synthetic Dosage Lethality Screens in Saccharomyces cerevisiae Dittmar, John 2013 Theses BioinformaticsBiologyGenetics
7. Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach Ogundijo, Oyetunji Enoch; Wang, Xiaodong 2017 Articles BioinformaticsBayesian statistical decision theoryMonte Carlo methodGenealogyGenetics
8. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data Saal, Lao H.; Troein, Carl; Vallon-Christersson, Johan; Gruvberger, Sofia; Borg, Åke; Peterson, Carsten 2002 Articles BioinformaticsDNA microarraysCytologyGenetics
9. Bos taurus genome assembly Liu, Yue; Qin, Xiang; Song, Xing-Zhi; Jiang, Huaiyang; Shen, Yufeng; Durbin, K James; Lien, Sigbjørn; Kent, Matthew; Sodeland, Marte; Ren, Yanru; Zhang, Lan; Sodergren, Erica; Havlak, Paul; Worley, Kim; Weinstock, George; Gibbs, Richard 2009 Articles BioinformaticsGenetics
10. ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding Margolin, Adam; Palomero Vazquez, M. Teresa; Ferrando, Adolfo A.; Califano, Andrea; Stolovitzky, Gustavo 2007 Articles BioinformaticsGene regulatory networksHuman genetics--VariationGeneticsBiology
11. Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses Ulgen, Ayse; Li, Wentian 2005 Articles Microsatellites (Genetics)Linkage (Genetics)Single nucleotide polymorphismsBioinformaticsGeneticsEpidemiology
12. Comparison of the power between microsatellite and single-nucleotide polymorphism markers for linkage and linkage disequilibrium mapping of an electrophysiological phenotype Lin, Hsiu-Fen; Juo, Suh-Hang; Cheng, Rong 2005 Articles Microsatellites (Genetics)Gene mappingGenetic polymorphismsGeneticsBioinformaticsEpidemiology
13. Computational Inferences of Mutations Driving Mesenchymal Differentiation in Glioblastoma Chen, James C. 2013 Theses Mutation (Biology)Mesenchymal stem cells--DifferentiationSystems biologyRetinoblastomaBioinformaticsGeneticsBiology
14. Confounding effects in gene expression and their impact on downstream analysis Lachmann, Alexander 2016 Theses Genetic regulationGenetic regulation--Data processingGene expressionGene expression--Data processingBioinformaticsGene regulatory networksGenetics
15. Correlating measurements across samples improves accuracy of large-scale expression profile experiments Alvarez, Mariano; Sumazin, Pavel; Rajbhandari, Presha; Califano, Andrea 2009 Articles GeneticsBioinformatics
16. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data Gao, Feng; Foat, Barrett; Bussemaker, Harmen J. 2004 Articles BioinformaticsGenetics
17. De novo likelihood-based measures for comparing genome assemblies Ghodsi, Mohammadreza; Hill, Christopher; Astrovskaya, Irina; Lin, Henry; Sommer, Dan; Koren, Sergey; Pop, Mihai 2013 Articles Nucleotide sequence--SoftwareBiotechnology--ResearchGenomicsGeneticsBioinformaticsBiomedical engineering
18. Detecting transcriptionally active regions using genomic tiling arrays Halasz, Gabor; van Batenburg, Marinus F.; Perusse, Joelle; Hua, Sujun; Lu, Xiang-Jun; White, Kevin P.; Bussemaker, Harmen J. 2006 Articles Genetic transcriptionDNA probesGenomicsDNA microarraysGeneticsBioinformatics
19. Discriminative topological features reveal biological network mechanisms Middendorf, Manuel; Ziv, Etay; Adams, Carter; Hom, Jennifer C.; Koytcheff, Robin; Levovitz, Chaya; Woods, Gregory; Chen, Linda; Wiggins, Chris H. 2004 Articles BioinformaticsGeneticsBiological models
20. Electronic Health Record-Derived Phenotyping Models to Improve Genomic Research in Stroke Thangaraj, Phyllis Mary 2020 Theses BioinformaticsGeneticsCerebrovascular diseaseCerebrovascular disease--Risk factorsMedical records--Data processingMachine learning--Industrial applications
21. ErmineJ: Tool for functional analysis of gene expression data sets Lee, Homin; Braynen, William; Keshav, Kiran; Pavlidis, Paul 2005 Articles Hypergeometric distributionGene expression--Data processingBioinformaticsDNA microarrays--Data processingGenetics
22. Evaluation of high-throughput functional categorization of human disease genes Chen, James L.; Liu, Yang; Sam, Lee T.; Li, Jianrong; Lussier, Yves 2007 Articles Medical geneticsBioinformaticsGeneticsPathology
23. Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data Iliadis, Alexandros; Anastassiou, Dimitris; Wang, Xiaodong 2012 Articles GeneticsBioinformatics
24. Gene functional similarity search tool (GFSST) Zhang, Peisen; Zhang, Jinghui; Sheng, Huitao; Russo, James J.; Osborne, Brian; Buetow, Kenneth 2006 Articles GenesDatabase searchingBioinformaticsInformation storage and retrieval systems--ScienceGenetics
25. Gene Prediction Using Multinomial Probit Regression with Bayesian Gene Selection Zhou, Xiaobo; Wang, Xiaodong; Dougherty, Edward R 2004 Articles GeneticsBioinformatics
26. Genetics of ABCA4-associated Diseases and Retinitis Pigmentosa Xie, Yajing 2016 Theses Retinitis pigmentosaRetinitis pigmentosa--Genetic aspectsMedical geneticsRetinal degenerationGeneticsBioinformatics
27. Genomic and machine-learning analysis of germline variants in cancer Madubata, Chioma 2018 Theses BioinformaticsCytologyGeneticsMachine learningGerm cellsCancer
28. Identifying functional relationships among human genes by systematic analysis of biological literature Tao, Yong-Chuan; Leibel, Rudolph L. 2002 Articles Information storage and retrieval systems--BiologyMedicine--ResearchBiological literatureHuman gene mappingBioinformaticsGeneticsInformation science
29. Identifying genes required for the formation of neurons from skin cells using forward genetic screens and whole genome sequencing in C. elegans Minevich, Gregory 2015 Theses Neurons--GrowthNeural stem cellsDevelopmental neurobiologyGene mappingGeneticsNeurosciencesBioinformatics
30. Identifying metabolic enzymes with multiple types of association evidence Kharchenko, Peter; Chen, Lifeng; Freund, Yoav; Vitkup, Dennis; Church, George 2006 Articles EnzymesBioinformaticsSequence alignment (Bioinformatics)Genetics
31. Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information Giorgi, Federico M.; Lopez, Gonzalo; Woo, Jung H.; Bisikirska, Brygida; Califano, Andrea; Bansal, Mukesh 2014 Articles Gene expressionGenetic algorithmsTranscription factorsBioinformaticsGeneticsMolecular biology
32. Integration of Germline and Somatic Variation in Tumor Data Dewal, Ninad Pradeep 2011 Theses BioinformaticsComputer scienceGeneticsTumorsGerm cellsSomatic cells
33. Investigating the utility of exome sequencing for kidney disease Groopman, Emily 2019 Theses GeneticsBioinformaticsMedicineKidneys--DiseasesExomes
34. Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference Lehner, Ben; Calixto, Andrea; Crombie, Catriona; Tischler, Julia; Fortunato, Angelo; Chalfie, Martin; Fraser, Andrew 2006 Articles Caenorhabditis elegansGenomicsRNA intereferenceGeneticsBioinformaticsBiology
35. Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA Jajamovich, Guido H.; Iliadis, Alexandros; Anastassiou, Dimitris; Wang, Xiaodong 2013 Articles BiometryDNA--Data processingGenetics—ResearchBioinformaticsGeneticsBiology
36. Maximum parsimony xor haplotyping by sparse dictionary selection Elmas, Abdulkadir; Jajamovich, Guido H.; Wang, Xiaodong 2013 Articles Biometry--ResearchBioinformatics--MethodologyGenomics--Data processingGenetics—ResearchGeneticsBioinformaticsMolecular biology
37. Mechanisms Underlying Phenotypic Heterogeneity in Simplex Autism Spectrum Disorders Chiang, Andrew Hann 2021 Theses GeneticsBiologyBioinformaticsAutism spectrum disorders--Genetic aspectsPhenotypeMutagenesis
38. Metaseq: Privacy Preserving Meta-analysis of Sequencing-based Association Studies Singh, Angad Pal; Zafer, Samreen; Pe'er, Itsik 2013 Articles BioinformaticsGeneticsComputer science
39. Model based analysis of real-time PCR data from DNA binding dye protocols Alvarez, Mariano Javier; Vila-Ortiz, Guillermo; Salibe, Mariano; Podhajcer, Osvaldo; Pitossi, Fernando 2007 Articles Polymerase chain reactionMessenger RNABioinformaticsGenetics
40. Molecular and genetic effect of coding variants in human Zhao, Yige 2024 Theses GeneticsHuman genetics--VariationBioinformaticsHuman genomeAllelomorphismMachine learningAutism--Research
41. Mosaicism and the genetic architecture of congenital heart disease Hsieh, Alexander Lin 2020 Theses BioinformaticsGeneticsCongenital heart diseaseMosaicismDiseases--Causes and theories of causation
42. Novel computational analysis of protein binding array data identifies direct targets of Nkx2.2 in the pancreas Hill, Jonathon; Anderson, Keith; Mastracci, Teresa; Kaestner, Klaus; Sussel, Lori 2011 Articles GeneticsBioinformatics
43. OGA: an ontological tool of human phenotypes with genetic associations Herrera-Galeano, Jesus; Hirschberg, David L.; Mokashi, Vishwesh; Solka, Jeffrey 2013 Articles PhenotypeGene mappingGenomesBioinformaticsOntology--MethodologyGenomes--Data processingGenetics--Data processingGenetics
44. Optimal Step Length EM Algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping Zhang, Peisen; Sheng, Huitao; Morabia, Alfredo; Gilliam, T. Conrad 2003 Articles Expectation-maximization algorithmsLipoprotein lipaseGenetic markersLinkage (Genetics)--Computer programsBioinformaticsGenetics
45. PAGE: Parametric Analysis of Gene Set Enrichment Kim, Seon-Young; Volsky, David Julian 2005 Articles Bioinformatics--MethodologyStatisticsDNA microarrays--Data processingBioinformaticsGeneticsBiometry
46. Pathogenic Mutations in Cancer-Predisposing Genes: A Survey of 300 Patients with Whole-Genome Sequencing and Lifetime Electronic Health Records He, Karen Y.; Zhao, Yiqing; McPherson, Elizabeth W.; Li, Quan; Wang, Kai; Xia, Fan; Weng, Chunhua; He, Max M. 2016 Articles Human geneticsCancer--Genetic aspectsHuman genetics--Data processingMedical records--Data processingGenomicsMedicineGeneticsBioinformatics
47. Pathway analysis of genome-wide data improves warfarin dose prediction Klein, Teri E.; Altman, Russ B.; Johnson, Julie A.; Perera, Minoli; Daneshjou, Roxana; Tatonetti, Nicholas P.; Karczewski, Konrad J.; Sagreiya, Hersh; Bourgeois, Stephane; Drozda, Katarzyna; Burmester, James K.; Tsunoda, Tatsuhiko; Nakamura, Yusuke; Kubo, Michiaki; Tector, Matthew; Limdi, Nita A.; Cavallari, Larisa H. 2013 Articles GeneticsBioinformatics
48. Post-transcriptional gene expression regulation in developmental disorders Kitaygorodsky, Alexander 2021 Theses BioinformaticsGeneticsComputer scienceGene expressionGenomesNeural networks (Neurobiology)
49. Predicting genes for orphan metabolic activities using phylogenetic profiles Chen, Lifeng; Vitkup, Dennis 2006 Articles Biological systems--Mathematical modelsPhylogenyMetabolism--RegulationBioinformaticsGeneticsMicrobiology
50. Quantifying Pathogen Surveillance Using Temporal Genomic Data Chan, Joseph Minhow; Rabadan, Raul 2013 Articles BioinformaticsMolecular biologyCommunicable diseasesGenetics
51. Quantitative Approaches to the Genomics of Clonal Evolution Zairis, Sakellarios 2018 Theses GeneticsBioinformaticsMathematicsGenomicsClones (Plants)Evolution (Biology)
52. Reconstruction of novel transcription factor regulons through inference of their binding sites Elmas, Abdulkadir; Wang, Xiaodong; Samoilov, Michael S. 2015 Articles Comparative genomicsBioinformaticsGenomics--Data processingComputational biologyTranscription factorsElectrical engineeringGeneticsMolecular biologyMathematics
53. SAVI: a statistical algorithm for variant frequency identification Trifonov, Vladimir; Pasqualucci, Laura; Tiacci, Enrico; Falini, Brunangelo; Rabadan, Raul 2013 Articles Bayesian statistical decision theorySequence alignment (Bioinformatics)Gene frequency--Statistical methodsGeneticsBioinformaticsBiometry
54. SeqMule: automated pipeline for analysis of human exome/genome sequencing data Guo, Yunfei; Ding, Xiaolei; Shen, Yufeng; Lyon, Gholson J.; Wang, Kai 2015 Articles Genomes--Data processingGeneticsSoftware engineeringBioinformaticsSystems biology
55. Systems Genetics of DNA Damage Tolerance – Cisplatin, RAD5 & CRISPR-mediated Nonsense Bryant, Eric Edward 2019 Theses GeneticsBioinformaticsBiology--ClassificationDNA damageCisplatinCRISPR (Genetics)
56. Transcriptome reconstruction and annotation of cynomolgus and African green monkey Lee, Albert Kim; Khiabanian, Hossein; Kugelman, Jeffrey; Elliott, Oliver T.; Nagle, Elyse; Yu, Guo-Yun; Warren, Travis; Palacios, Gustavo; Rabadan, Raul 2014 Articles BioinformaticsGenetics
57. Variable window binding for mutually exclusive alternative splicing Anastassiou, Dimitris; Liu, Hairuo; Varadan, Vinay 2006 Articles RNA splicingLocus of controlExons (Genetics)Messenger RNAGeneticsBioinformatics
58. Whole-genome linkage analysis in mapping alcoholism genes using single-nucleotide polymorphisms and microsatellites Wang, Shuang; Huang, Song; Liu, Nianjun; Chen, Liang; Oh, Cheongeun; Zhao, Hongyu 2005 Articles Microsatellites (Genetics)Gene mappingAlcoholism--Genetic aspectsSingle nucleotide polymorphismsBiometryBioinformaticsGenetics