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Jesse J. Salk, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
mutations and human cancer
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Serrano IM, Hirose M, Valentine CC, Roesner S, Schmidt E, Pratt G, Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout ageing. Nature Ecology & Evolution. PMID 38361161 DOI: 10.1038/s41559-024-02338-3  0.426
2023 Smith-Roe SL, Hobbs CA, Hull V, Todd Auman J, Recio L, Streicker MA, Rivas MV, Pratt GA, Lo FY, Higgins JE, Schmidt EK, Williams LN, Nachmanson D, Valentine Iii CC, Salk JJ, et al. Adopting duplex sequencing technology for genetic toxicity testing: A proof-of-concept mutagenesis experiment with N-ethyl-N-nitrosourea (ENU)-exposed rats. Mutation Research. Genetic Toxicology and Environmental Mutagenesis. 891: 503669. PMID 37770135 DOI: 10.1016/j.mrgentox.2023.503669  0.394
2023 Marchetti F, Cardoso R, Chen CL, Douglas GR, Elloway J, Escobar PA, Harper T, Heflich RH, Kidd D, Lynch AM, Myers MB, Parsons BL, Salk JJ, Settivari RS, Smith-Roe SL, et al. Error-corrected next generation sequencing - Promises and challenges for genotoxicity and cancer risk assessment. Mutation Research. Reviews in Mutation Research. 792: 108466. PMID 37643677 DOI: 10.1016/j.mrrev.2023.108466  0.467
2023 Cho E, Swartz CD, Williams A, V Rivas M, Recio L, Witt KL, Schmidt EK, Yaplee J, Smith TH, Van P, Lo FY, Valentine CC, Salk JJ, Marchetti F, Smith-Roe SL, et al. Error-corrected duplex sequencing enables direct detection and quantification of mutations in human TK6 cells with strong inter-laboratory consistency. Mutation Research. Genetic Toxicology and Environmental Mutagenesis. 889: 503649. PMID 37491114 DOI: 10.1016/j.mrgentox.2023.503649  0.402
2023 Dodge AE, LeBlanc DPM, Zhou G, Williams A, Meier MJ, Van P, Lo FY, Valentine Iii CC, Salk JJ, Yauk CL, Marchetti F. Duplex sequencing provides detailed characterization of mutation frequencies and spectra in the bone marrow of MutaMouse males exposed to procarbazine hydrochloride. Archives of Toxicology. PMID 37341741 DOI: 10.1007/s00204-023-03527-y  0.436
2023 Lynch AM, Zanoni TB, Salk JJ, Martincorena I, Young RR, Kucab J, Valentine CC, Yauk C, Escobar PA, Witt KL, Frötschl R, Reed SH, Ashford A. Next Generation Sequencing Workshop at the Royal Society of Medicine (London, May 2022): How genomics is on the path to modernizing Genetic Toxicology. Mutagenesis. PMID 37300447 DOI: 10.1093/mutage/gead012  0.335
2023 Smith-Roe SL, Hobbs CA, Hull V, Auman JT, Recio L, Streicker MA, Rivas MV, Pratt GA, Lo FY, Higgins JE, Schmidt EK, Williams LN, Nachmanson D, Valentine CC, Salk JJ, et al. Adopting Duplex Sequencing™ Technology for Genetic Toxicity Testing: A Proof-of-Concept Mutagenesis Experiment with N-Ethyl-N-Nitrosourea (ENU)-Exposed Rats. Biorxiv : the Preprint Server For Biology. PMID 37214853 DOI: 10.1101/2023.05.08.539833  0.384
2023 Wilson TE, Ahmed S, Higgins J, Salk JJ, Glover TW. svCapture: efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing. Nar Genomics and Bioinformatics. 5: lqad042. PMID 37181851 DOI: 10.1093/nargab/lqad042  0.316
2023 Serrano IM, Hirose M, Valentine C, Austin S, Schmidt E, Pratt G, Williams L, Salk J, Ibrahim S, Sudmant PH. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging. Biorxiv : the Preprint Server For Biology. PMID 36945529 DOI: 10.1101/2023.03.06.531392  0.446
2022 LeBlanc DPM, Meier M, Lo FY, Schmidt E, Valentine C, Williams A, Salk JJ, Yauk CL, Marchetti F. Duplex sequencing identifies genomic features that determine susceptibility to benzo(a)pyrene-induced in vivo mutations. Bmc Genomics. 23: 542. PMID 35902794 DOI: 10.1186/s12864-022-08752-w  0.5
2021 Zhang Y, Kohrn BF, Yang M, Nachmanson D, Soong TR, Lee IH, Tao Y, Clevers H, Swisher EM, Brentnall TA, Loeb LA, Kennedy SR, Salk JJ, Naxerova K, Risques RA. PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34330826 DOI: 10.1073/pnas.2023373118  0.645
2020 Valentine CC, Young RR, Fielden MR, Kulkarni R, Williams LN, Li T, Minocherhomji S, Salk JJ. Direct quantification of in vivo mutagenesis and carcinogenesis using duplex sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 33318186 DOI: 10.1073/pnas.2013724117  0.54
2020 Short NJ, Kantarjian H, Kanagal-Shamanna R, Sasaki K, Ravandi F, Cortes J, Konopleva M, Issa GC, Kornblau SM, Garcia-Manero G, Garris R, Higgins J, Pratt G, Williams LN, Valentine CC, ... ... Salk JJ, et al. Ultra-accurate Duplex Sequencing for the assessment of pretreatment ABL1 kinase domain mutations in Ph+ ALL. Blood Cancer Journal. 10: 61. PMID 32457305 DOI: 10.1038/S41408-020-0329-Y  0.533
2020 Higgins J, Williams LN, Valentine CC, Pratt G, Kanagal-Shamanna R, Short NJ, Ueda M, Storb R, Radich JP, Salk JJ. Abstract PR04: Clonal landscapes of hematologic malignancies redefined by ultrasensitive duplex sequencing Clinical Cancer Research. 26. DOI: 10.1158/1557-3265.Liqbiop20-Pr04  0.538
2020 Lo FY, Valentine C, Schmidt E, Williams L, Boot A, Rozen S, Salk J. Abstract 3147: Non-invasive detection of aristolochic acid exposure using ultra-sensitive duplex sequencing Clinical Trials. DOI: 10.1158/1538-7445.Am2020-3147  0.316
2019 Loeb LA, Kohrn BF, Loubet-Senear KJ, Dunn YJ, Ahn EH, O'Sullivan JN, Salk JJ, Bronner MP, Beckman RA. Extensive subclonal mutational diversity in human colorectal cancer and its significance. Proceedings of the National Academy of Sciences of the United States of America. PMID 31806761 DOI: 10.1073/Pnas.1910301116  0.693
2019 Salk JJ, Kennedy SR. Next-Generation Genotoxicology: Using Modern Sequencing Technologies to Assess Somatic Mutagenesis and Cancer Risk. Environmental and Molecular Mutagenesis. PMID 31595553 DOI: 10.1002/Em.22342  0.481
2019 Salk JJ, Loubet-Senear K, Maritschnegg E, Valentine CC, Williams LN, Higgins JE, Horvat R, Vanderstichele A, Nachmanson D, Baker KT, Emond MJ, Loter E, Tretiakova M, Soussi T, Loeb LA, et al. Ultra-Sensitive TP53 Sequencing for Cancer Detection Reveals Progressive Clonal Selection in Normal Tissue over a Century of Human Lifespan. Cell Reports. 28: 132-144.e3. PMID 31269435 DOI: 10.1016/J.Celrep.2019.05.109  0.711
2019 Higgins J, Pratt G, Valentine CC, Williams LN, Salk JJ. Redefining "Gold Standard": Ultra-Sensitive Characterization of Commercial DNA Standards with Duplex Sequencing Blood. 134: 2093-2093. DOI: 10.1182/Blood-2019-131428  0.518
2019 Short NJ, Kantarjian HM, Kanagal-Shamanna R, Sasaki K, Ravandi F, Cortes JE, Konopleva MY, Issa GC, Kornblau SM, Garcia-Manero G, Rivera V, Garris R, Higgins J, Pratt G, Williams LN, ... ... Salk JJ, et al. Ultra-Accurate Assessment of Pretreatment ABL1 Kinase Domain (KD) Mutations in Patients (pts) with Newly Diagnosed Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia (Ph+ ALL) Using Duplex Sequencing (DS) Blood. 134: 2578-2578. DOI: 10.1182/Blood-2019-125131  0.437
2019 Higgins J, Pratt G, Valentine CC, Williams LN, Ueda M, Storb R, Radich JP, Salk JJ. Characterization of Clonal Dynamics after Hematopoietic Cell Transplantation Using Ultra-Sensitive Duplex Sequencing Blood. 134: 2483-2483. DOI: 10.1182/Blood-2019-122490  0.433
2019 Valentine CC, Fielden M, Young R, Higgins J, Williams L, Li T, Kulkarni R, Minocherhomji S, Risques R, Danaher P, Salk J. Abstract 4649: Duplex Sequencing detects rare subclonal variants that mark early carcinogenesis and preneoplastic clonal evolution Cancer Research. 79: 4649-4649. DOI: 10.1158/1538-7445.Am2019-4649  0.588
2019 Higgins JE, Williams LN, Hourigan CS, Radich JP, Salk JJ. Abstract 422: Duplex sequencing for MRD detection in acute myeloid leukemia Cancer Research. 79: 422-422. DOI: 10.1158/1538-7445.Am2019-422  0.604
2019 Short N, Kantarjian H, Sasaki K, Kanagal-Shamanna R, Ravandi F, Cortes J, Konopleva M, Issa G, Kornblau S, Garcia-Manero G, Rivera V, Garris R, Salk J, Prichard J, Radich J, et al. Duplex Sequencing Identifies Low Level ABL1 Kinase Domain Mutations in Untreated Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Clinical Lymphoma Myeloma and Leukemia. 19: S186. DOI: 10.1016/J.Clml.2019.07.025  0.423
2018 Nachmanson D, Lian S, Schmidt EK, Hipp MJ, Baker KT, Zhang Y, Tretiakova M, Loubet-Senear K, Kohrn BF, Salk JJ, Kennedy SR, Risques RA. Targeted genome fragmentation with CRISPR/Cas9 enables fast and efficient enrichment of small genomic regions and ultra-accurate sequencing with low DNA input (CRISPR-DS). Genome Research. PMID 30232196 DOI: 10.1101/Gr.235291.118  0.481
2018 Salk JJ, Schmitt MW, Loeb LA. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. Nature Reviews. Genetics. PMID 29576615 DOI: 10.1038/Nrg.2017.117  0.668
2018 Short NJ, Kantarjian HM, Sasaki K, Ravandi F, Cortes JE, Konopleva MY, Issa GC, Kanagal-Shamanna R, Kornblau SM, Garcia-Manero G, Rivera V, Garris RE, Salk J, Prichard J, Radich JP, et al. Ultrasensitive Duplex Sequencing of Pretreatment ABL1 Kinase Domain Mutations in Patients with Newly Diagnosed Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Blood. 132: 1548-1548. DOI: 10.1182/Blood-2018-99-115369  0.478
2018 Higgins JE, Williams LN, Buckley SA, Hourigan CS, Radich JP, Salk JJ. Duplex Sequencing Accurately Detects Variants below 1/100,000 in Genes Recurrently Mutated in Acute Myeloid Leukemia Blood. 132: 2769-2769. DOI: 10.1182/Blood-2018-99-115071  0.589
2017 Baker KT, Salk JJ, Brentnall TA, Risques RA. Precancer in Ulcerative Colitis: The Role of the Field Effect and its Clinical Implications. Carcinogenesis. PMID 29087436 DOI: 10.1093/Carcin/Bgx117  0.373
2017 Salk JJ, Maritschnegg E, Speiser P, Zeillinger R, Risques R, Loeb LA. Abstract 3041: Duplex Sequencing detects cancer-associated mutations arising during normal aging: Clonal evolution over a century of human lifetime Cancer Research. 77: 3041-3041. DOI: 10.1158/1538-7445.Am2017-3041  0.676
2017 Young R, Salk J, Fielden M, Valentine C, Kulkarni R, Minocherhomii S. Application of duplex sequencing for in vivo mutation analysis in the cII transgene and endogenous genes in Big Blue ® mice Toxicology Letters. 280: S253. DOI: 10.1016/J.Toxlet.2017.07.702  0.346
2016 Fox EJ, Salk JJ, Loeb LA. Exploring the implications of distinct mutational signatures and mutation rates in aging and cancer. Genome Medicine. 8: 30. PMID 26987311 DOI: 10.1186/S13073-016-0286-Z  0.674
2016 Krimmel JD, Salk JJ, Risques RA. Cancer-like mutations in non-cancer tissue: towards a better understanding of multistep carcinogenesis Translational Cancer Research. 5. DOI: 10.21037/10644  0.608
2016 Schmitt MW, Salk JJ, Fox EJ, Pritchard JR, Hodgson JG, Rivera VM, Becker PS, Radich JP, Loeb LA. Abstract 2395: Direct assessment of sequence heterogeneity in human cancers by Duplex Sequencing Cancer Research. 76: 2395-2395. DOI: 10.1158/1538-7445.Am2016-2395  0.706
2015 Schmitt MW, Loeb LA, Salk JJ. The influence of subclonal resistance mutations on targeted cancer therapy. Nature Reviews. Clinical Oncology. PMID 26483300 DOI: 10.1038/Nrclinonc.2015.175  0.532
2014 Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, Salk JJ, Ahn EH, Prindle MJ, Kuong KJ, Shen JC, Risques RA, Loeb LA. Corrigendum: Detecting ultralow-frequency mutations by Duplex Sequencing. Nature Protocols. 9: 2903. PMID 25411958 DOI: 10.1038/Nprot1214-2903D  0.601
2014 Kennedy SR, Schmitt MW, Fox EJ, Kohrn BF, Salk JJ, Ahn EH, Prindle MJ, Kuong KJ, Shen JC, Risques RA, Loeb LA. Detecting ultralow-frequency mutations by Duplex Sequencing. Nature Protocols. 9: 2586-606. PMID 25299156 DOI: 10.1038/Nprot.2014.170  0.651
2014 Naxerova K, Brachtel E, Salk JJ, Seese AM, Power K, Abbasi B, Snuderl M, Chiang S, Kasif S, Jain RK. Hypermutable DNA chronicles the evolution of human colon cancer. Proceedings of the National Academy of Sciences of the United States of America. 111: E1889-98. PMID 24753616 DOI: 10.1073/Pnas.1400179111  0.519
2014 Schmitt MW, Fox EJ, Salk JJ. Risks of double-counting in deep sequencing. Proceedings of the National Academy of Sciences of the United States of America. 111: E1560. PMID 24706907 DOI: 10.1073/Pnas.1400941111  0.386
2013 Salk JJ, Bansal A, Lai LA, Crispin DA, Ussakli CH, Horwitz MS, Bronner MP, Brentnall TA, Loeb LA, Rabinovitch PS, Risques RA. Clonal expansions and short telomeres are associated with neoplasia in early-onset, but not late-onset, ulcerative colitis. Inflammatory Bowel Diseases. 19: 2593-602. PMID 24097228 DOI: 10.1097/Mib.0B013E3182A87640  0.578
2013 Kennedy SR, Salk JJ, Schmitt MW, Loeb LA. Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. Plos Genetics. 9: e1003794. PMID 24086148 DOI: 10.1371/Journal.Pgen.1003794  0.681
2013 Loeb LA, Fox EJ, Kennedy SR, Kuong J, Schmitt MW, Salk JJ. Abstract 1789A: Duplex DNA sequencing detects subclonal and ultra-rare mutations in human tumors. Cancer Research. 73. DOI: 10.1158/1538-7445.Am2013-1789A  0.641
2012 Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proceedings of the National Academy of Sciences of the United States of America. 109: 14508-13. PMID 22853953 DOI: 10.1073/Pnas.1208715109  0.666
2012 Ericson NG, Kulawiec M, Vermulst M, Sheahan K, O'Sullivan J, Salk JJ, Bielas JH. Decreased mitochondrial DNA mutagenesis in human colorectal cancer. Plos Genetics. 8: e1002689. PMID 22685414 DOI: 10.1371/Journal.Pgen.1002689  0.734
2010 Salk JJ, Horwitz MS. Passenger mutations as a marker of clonal cell lineages in emerging neoplasia. Seminars in Cancer Biology. 20: 294-303. PMID 20951806 DOI: 10.1016/J.Semcancer.2010.10.008  0.54
2010 Kulawiec M, Salk JJ, Ericson NG, Wanagat J, Bielas JH. Generation, function, and prognostic utility of somatic mitochondrial DNA mutations in cancer. Environmental and Molecular Mutagenesis. 51: 427-39. PMID 20544883 DOI: 10.1002/Em.20582  0.581
2010 Loh E, Salk JJ, Loeb LA. Optimization of DNA polymerase mutation rates during bacterial evolution. Proceedings of the National Academy of Sciences of the United States of America. 107: 1154-9. PMID 20080608 DOI: 10.1073/Pnas.0912451107  0.695
2010 Salk JJ, Fox EJ, Loeb LA. Mutational heterogeneity in human cancers: origin and consequences. Annual Review of Pathology. 5: 51-75. PMID 19743960 DOI: 10.1146/Annurev-Pathol-121808-102113  0.672
2010 Salk JJ, Salipante SJ, Risques RA, Crispin DA, Li L, Bronner MP, Rabinovitch PS, Horwitz MS, Loeb LA, Brentnall TA. Abstract 4707: Clonal expansions as a biomarker of preneoplastic processes in ulcerative colitis Cancer Research. 70: 4707-4707. DOI: 10.1158/1538-7445.Am10-4707  0.566
2009 Salk JJ, Salipante SJ, Risques RA, Crispin DA, Li L, Bronner MP, Brentnall TA, Rabinovitch PS, Horwitz MS, Loeb LA. Clonal expansions in ulcerative colitis identify patients with neoplasia. Proceedings of the National Academy of Sciences of the United States of America. 106: 20871-6. PMID 19926851 DOI: 10.1073/Pnas.0909428106  0.656
2009 Fox EJ, Salk JJ, Loeb LA. Cancer genome sequencing--an interim analysis. Cancer Research. 69: 4948-50. PMID 19509220 DOI: 10.1158/0008-5472.Can-09-1231  0.634
2006 Salk JJ, Sanchez JA, Pierce KE, Rice JE, Soares KC, Wangh LJ. Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)-PCR. Analytical Biochemistry. 353: 124-32. PMID 16540077 DOI: 10.1016/J.Ab.2006.02.012  0.309
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