Jacob Kocher - Related publications

2009-2014 Department of Biomedical Sciences and Pathobiology Virginia Polytechnic and State University, United States 
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50 most relevant papers in past 60 days:
Year Citation  Score
2020 Wei J, Rybczynska AA, Meng P, Terpstra M, Saber A, Sietzema J, Timens W, Schuuring E, Hiltermann TJN, Groen HJM, van der Wekken AJ, van den Berg A, Kok K. An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients. Cancers. 12. PMID 33019710 DOI: 10.3390/cancers12102843   
2020 Polprasert C, Takeuchi Y, Makishima H, Wudhikarn K, Kakiuchi N, Tangnuntachai N, Assanasen T, Sitthi W, Muhamad H, Lawasut P, Kongkiatkamon S, Bunworasate U, Izutsu K, Shiraishi Y, Chiba K, et al. Frequent mutations in HLA and related genes in extranodal NK/T cell lymphomas. Leukemia & Lymphoma. 1-9. PMID 32964767 DOI: 10.1080/10428194.2020.1821011   
2020 Smith J, Lipkin E, Soller M, Fulton JE, Burt DW. Mapping QTL Associated with Resistance to Avian Oncogenic Marek's Disease Virus (MDV) Reveals Major Candidate Genes and Variants. Genes. 11. PMID 32872585 DOI: 10.3390/genes11091019   
2020 Zhang J, Chen G, Zhang J, Zhang P, Ye Y. Construction of a prognostic model based on nine immune-related genes and identification of small molecule drugs for hepatocellular carcinoma (HCC). American Journal of Translational Research. 12: 5108-5130. PMID 33042409   
2020 Taber A, Christensen E, Lamy P, Nordentoft I, Prip F, Lindskrog SV, Birkenkamp-Demtröder K, Okholm TLH, Knudsen M, Pedersen JS, Steiniche T, Agerbæk M, Jensen JB, Dyrskjøt L. Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis. Nature Communications. 11: 4858. PMID 32978382 DOI: 10.1038/s41467-020-18640-0   
2020 Fu AX, Lui KN, Tang CS, Ng RK, Lai FP, Lau ST, Li Z, Gracia-Barcelo MM, Sham P, Tam PK, Ngan ES, Yip KY. Whole-genome analysis of noncoding genetic variations identifies multi-scale regulatory element perturbations associated with Hirschsprung disease. Genome Research. PMID 32948616 DOI: 10.1101/gr.264473.120   
2020 Aref-Eshghi E, Kerkhof J, Carere DA, Volodarsky M, Bhai P, Colaiacovo S, Saleh M, Caudle M, Karp N, Prasad C, Balci T, Lin H, Campbell C, Siu VM, Sadikovic B. Clinical and technical assessment of MedExome vs. NGS panels in patients with suspected genetic disorders in Southwestern Ontario. Journal of Human Genetics. PMID 33093641 DOI: 10.1038/s10038-020-00860-3   
2020 Sun R, Xu M, Li X, Gaynor S, Zhou H, Li Z, Bossé Y, Lam S, Tsao MS, Tardon A, Chen C, Doherty J, Goodman G, Bojesen SE, Landi MT, et al. Integration of multiomic annotation data to prioritize and characterize inflammation and immune-related risk variants in squamous cell lung cancer. Genetic Epidemiology. PMID 32924180 DOI: 10.1002/gepi.22358   
2020 Seroussi E, Blum SE, Krifucks O, Shirak A, Jacoby S, Leitner G. Basal Levels of CD18 Antigen Presenting Cells in Cow Milk Associate with Copy Number Variation of Fc Gamma Receptors. Genes. 11. PMID 32824852 DOI: 10.3390/genes11080952   
2020 Xu S, Feng W, Lu Z, Yu CY, Shao W, Nakshatri H, Reiter JL, Gao H, Chu X, Wang Y, Liu Y. regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data. Frontiers in Bioengineering and Biotechnology. 8: 886. PMID 32850739 DOI: 10.3389/fbioe.2020.00886   
2020 Gao W, Cheng L, He S, Li W, Zhou C, Zhou B, Liu J, Xu J, Yu X, Zhu H. Multiomics integrative analysis for gene signatures and prognostic values of mA regulators in pancreatic adenocarcinoma: a retrospective study in The Cancer Genome Atlas project. Aging. 12. PMID 33082301 DOI: 10.18632/aging.103942   
2020 Wang H, Wang MS, Wang Y, Huang YQ, Shi JP, Ding ZL, Wang WJ. Prognostic value of immune related genes in lung adenocarcinoma. Oncology Letters. 20: 259. PMID 32989393 DOI: 10.3892/ol.2020.12122   
2020 Ferraro NM, Strober BJ, Einson J, Abell NS, Aguet F, Barbeira AN, Brandt M, Bucan M, Castel SE, Davis JR, Greenwald E, Hess GT, Hilliard AT, Kember RL, Kotis B, ... , ... , et al. Transcriptomic signatures across human tissues identify functional rare genetic variation. Science (New York, N.Y.). 369. PMID 32913073 DOI: 10.1126/science.aaz5900   
2020 Suhre K, McCarthy MI, Schwenk JM. Genetics meets proteomics: perspectives for large population-based studies. Nature Reviews. Genetics. PMID 32860016 DOI: 10.1038/s41576-020-0268-2   
2020 Hegde N, Doddamani D, Kushalappa AC. Identification and functional characterisation of late blight resistance polymorphic genes in Russet Burbank potato cultivar. Functional Plant Biology : Fpb. PMID 32741427 DOI: 10.1071/FP19327   
2020 Chen J, Madireddi S, Nagarkar D, Migdal M, Vander Heiden J, Chang D, Mukhyala K, Selvaraj S, Kadel EE, Brauer MJ, Mariathasan S, Hunkapiller J, Jhunjhunwala S, Albert ML, Hammer C. In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales. Briefings in Bioinformatics. PMID 32940337 DOI: 10.1093/bib/bbaa223   
2020 Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, Jain M, Metsu S, Olsen H, Paten B, Ritz B, Kooy RF, Gecz J, Sharp AJ. A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions. American Journal of Human Genetics. PMID 32937144 DOI: 10.1016/j.ajhg.2020.08.019   
2020 Ghoussaini M, Mountjoy E, Carmona M, Peat G, Schmidt EM, Hercules A, Fumis L, Miranda A, Carvalho-Silva D, Buniello A, Burdett T, Hayhurst J, Baker J, Ferrer J, Gonzalez-Uriarte A, et al. Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Research. PMID 33045747 DOI: 10.1093/nar/gkaa840   
2020 Qin N, Li Y, Wang C, Zhu M, Dai J, Hong T, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojesen SE, Landi MT, Johansson M, Risch A, et al. Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between lung adenocarcinoma and squamous cell carcinoma. Frontiers of Medicine. PMID 32889700 DOI: 10.1007/s11684-020-0779-4   
2020 Pan Q, Liu YJ, Bai XF, Han XL, Jiang Y, Ai B, Shi SS, Wang F, Xu MC, Wang YZ, Zhao J, Chen JX, Zhang J, Li XC, Zhu J, et al. VARAdb: a comprehensive variation annotation database for human. Nucleic Acids Research. PMID 33095866 DOI: 10.1093/nar/gkaa922   
2020 Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Lin AE, ... , et al. Inherited causes of clonal haematopoiesis in 97,691 whole genomes. Nature. PMID 33057201 DOI: 10.1038/s41586-020-2819-2   
2020 Nguyen ND, Jin T, Wang D. Varmole: A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes. Bioinformatics (Oxford, England). PMID 33031552 DOI: 10.1093/bioinformatics/btaa866   
2020 Li M, Wang H, Liao H, Shen J, Wu Y, Wu Y, Weng Q, Zhu C, Geng X, Lan F, Xia Y, Zhang B, Zou H, Zhang N, Zhou Y, et al. Mutation Revealed from Myofibroblastoma-Discordant Monozygotic Twins Leads to p53/p21 Deficit and WEE1 Inhibitor Sensitivity. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). 7: 2001041. PMID 33042742 DOI: 10.1002/advs.202001041   
2020 Loo SL, Ong A, Kyaw W, Thibaut LM, Lan R, Tanaka MM. A comparative examination of non-synonymous polymorphism counts in bacterial genomes. Applied and Environmental Microbiology. PMID 33097502 DOI: 10.1128/AEM.02002-20   
2020 Huh SJ, Oh SY, Lee S, Lee JH, Kim SH, Pak MK, Kim HJ. Mutational analysis of extranodal marginal zone lymphoma using next generation sequencing. Oncology Letters. 20: 205. PMID 32963611 DOI: 10.3892/ol.2020.12068   
2020 Cheasley D, Nigam A, Zethoven M, Hunter S, Etemadmoghadam D, Semple T, Allan P, Carey MS, Fernandez ML, Dawson A, Köbel M, Huntsman DG, Page CL, Mes-Masson AM, Provencher D, et al. Genomic analysis of low-grade serous ovarian carcinoma to identify key drivers and therapeutic vulnerabilities. The Journal of Pathology. PMID 32901952 DOI: 10.1002/path.5545   
2020 Zhou RR, Wang L, Zhao SD. Estimation and inference for the indirect effect in high-dimensional linear mediation models. Biometrika. 107: 573-589. PMID 32831353 DOI: 10.1093/biomet/asaa016   
2020 Owen KA, Price A, Ainsworth H, Aidukaitis BN, Bachali P, Catalina MD, Dittman JM, Howard TD, Kingsmore KM, Labonte AC, Marion MC, Robl RD, Zimmerman KD, Langefeld CD, Grammer AC, et al. Analysis of Trans-Ancestral SLE Risk Loci Identifies Unique Biologic Networks and Drug Targets in African and European Ancestries. American Journal of Human Genetics. PMID 33031749 DOI: 10.1016/j.ajhg.2020.09.007   
2020 Zhou Q, Li Z, Song L, Mu D, Wang J, Tian L, Liao Y. Whole-exome mutational landscape of metastasis in patient-derived hepatocellular carcinoma cells. Genes & Diseases. 7: 380-391. PMID 32884992 DOI: 10.1016/j.gendis.2020.05.003   
2020 Karimnezhad A, Palidwor GA, Thavorn K, Stewart DJ, Campbell PA, Lo B, Perkins TJ. Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data. Bmc Medical Genomics. 13: 156. PMID 33059707 DOI: 10.1186/s12920-020-00803-z   
2020 Mulvey B, Lagunas T, Dougherty JD. Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts. Biological Psychiatry. PMID 32843144 DOI: 10.1016/j.biopsych.2020.06.011   
2020 Słowiński P, Li M, Restrepo P, Alomran N, Spurr LF, Miller C, Tsaneva-Atanasova K, Horvath A. GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions. Frontiers in Bioengineering and Biotechnology. 8: 1021. PMID 33042959 DOI: 10.3389/fbioe.2020.01021   
2020 Barbeira AN, Melia OJ, Liang Y, Bonazzola R, Wang G, Wheeler HE, Aguet F, Ardlie KG, Wen X, Im HK. Fine-mapping and QTL tissue-sharing information improves the reliability of causal gene identification. Genetic Epidemiology. PMID 32964524 DOI: 10.1002/gepi.22346   
2020 Silva RCO, Júnior AHPDS, Gurgel APAD, Junior MRB, Santos DL, de Lima RCP, Batista MVA, Pena LJ, Chagas BS, Freitas AC. Structural and functional impacts of E5 genetic variants of human papillomavirus type 31. Virus Research. 198143. PMID 32871208 DOI: 10.1016/j.virusres.2020.198143   
2020 Vanni I, Tanda ET, Dalmasso B, Pastorino L, Andreotti V, Bruno W, Boutros A, Spagnolo F, Ghiorzo P. Non-BRAF Mutant Melanoma: Molecular Features and Therapeutical Implications. Frontiers in Molecular Biosciences. 7: 172. PMID 32850962 DOI: 10.3389/fmolb.2020.00172   
2020 Li Y, Burgman B, McGrail DJ, Sun M, Qi D, Shukla SA, Wu E, Capasso A, Lin SY, Wu CJ, Eckhardt SG, Mills GB, Li B, Sahni N, Yi SS. Integrated Genomic Characterization of the Human Immunome in Cancer. Cancer Research. PMID 32855206 DOI: 10.1158/0008-5472.CAN-20-0384   
2020 Cui Y, Cheng X, Chen Q, Song B, Chiu A, Gao Y, Dawson T, Chao L, Zhang W, Li D, Zeng Z, Yu J, Li Z, Fei T, Peng S, et al. CRISP-view: a database of functional genetic screens spanning multiple phenotypes. Nucleic Acids Research. PMID 33010154 DOI: 10.1093/nar/gkaa809   
2020 Tamura R, Toda M. Historic Overview of Genetic Engineering Technologies for Human Gene Therapy. Neurologia Medico-Chirurgica. 60: 483-491. PMID 32908085 DOI: 10.2176/nmc.ra.2020-0049   
2020 Chen SY, Oliveira HR, Schenkel FS, Pedrosa VB, Melka MG, Brito LF. Using imputed whole-genome sequence variants to uncover candidate mutations and genes affecting milking speed and temperament in Holstein cattle. Journal of Dairy Science. PMID 32952011 DOI: 10.3168/jds.2020-18897   
2020 Rashid NU, Li Q, Yeh JJ, Ibrahim JG. Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction. Journal of the American Statistical Association. 115: 1125-1138. PMID 33012902 DOI: 10.1080/01621459.2019.1671197   
2020 Jones MR, Peng PC, Coetzee SG, Tyrer J, Reyes ALP, Corona RI, Davis B, Chen S, Dezem F, Seo JH, Kar S, Dareng E, , Berman BP, Freedman ML, et al. Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. American Journal of Human Genetics. PMID 32946763 DOI: 10.1016/j.ajhg.2020.08.021   
2020 Cavani L, Braz CU, Giglioti R, Okino CH, Gulias-Gomes CC, Caetano AR, Oliveira MCS, Cardoso FF, de Oliveira HN. Genomic Study of Infection Level and Its Association With Tick Count in Hereford and Braford Cattle. Frontiers in Immunology. 11: 1905. PMID 33013839 DOI: 10.3389/fimmu.2020.01905   
2020 Brandt M, Gokden A, Ziosi M, Lappalainen T. A polyclonal allelic expression assay for detecting regulatory effects of transcript variants. Genome Medicine. 12: 79. PMID 32912286 DOI: 10.1186/s13073-020-00777-8   
2020 Kulkarni R, Chopra R, Chagoya J, Simpson CE, Baring MR, Hillhouse A, Puppala N, Chamberlin K, Burow MD. Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes. Genes. 11. PMID 33080972 DOI: 10.3390/genes11101220   
2020 Fikere M, Barbulescu DM, Malmberg MM, Spangenberg GC, Cogan NOI, Daetwyler HD. Meta-analysis of GWAS in canola blackleg (Leptosphaeria maculans) disease traits demonstrates increased power from imputed whole-genome sequence. Scientific Reports. 10: 14300. PMID 32868838 DOI: 10.1038/s41598-020-71274-6   
2020 Kammers K, Taub M, Rodriguez B, Yanek LR, Ruczinski I, Martin J, Kanchan K, Battle A, Cheng L, Wang ZZ, Johnson AD, Leek J, Faraday N, Becker L, Mathias R. Transcriptional profile of platelets and iPSC-derived megakaryocytes from whole genome and RNA sequencing. Blood. PMID 33094331 DOI: 10.1182/blood.2020006115   
2020 Almazni I, Stapley RJ, Khan AO, Morgan NV, . A comprehensive bioinformatic analysis of 126 patients with an inherited platelet disorder to identify both sequence and copy number genetic variants. Human Mutation. PMID 32935436 DOI: 10.1002/humu.24114   
2020 Saha I, Ghosh N, Maity D, Sharma N, Mitra K. Inferring the genetic variability in Indian SARS-CoV-2 genomes using consensus of multiple sequence alignment techniques. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 104522. PMID 32889094 DOI: 10.1016/j.meegid.2020.104522   
2020 Gutierrez MJ, Nino G, Hong X, Wang X. Epigenomics and Early Life Human Humoral Immunity: Novel Paradigms and Research Opportunities. Frontiers in Immunology. 11: 1766. PMID 32983086 DOI: 10.3389/fimmu.2020.01766   
2020 Au PYB, Eaton A, Dyment DA. Genetic mechanisms of neurodevelopmental disorders. Handbook of Clinical Neurology. 173: 307-326. PMID 32958182 DOI: 10.1016/B978-0-444-64150-2.00024-1