My Bibliography

select

Linderman MD, Wallace J, van der Heyde A, Wieman E, Brey D, Shi Y, Hansen P, Shamsi Z, Liu J, Gelb BD, Bashir A. NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data. Bioinformatics. 2024 Mar 4;40(3). doi: 10.1093/bioinformatics/btae129. PubMed PMID: 38444093; PubMed Central PMCID: PMC10955255.

select

Linderman MD, Paudyal C, Shakeel M, Kelley W, Bashir A, Gelb BD. NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. Gigascience. 2021 Jul 1;10(7). doi: 10.1093/gigascience/giab046. PubMed PMID: 34195837; PubMed Central PMCID: PMC8246072.

select

Linderman MD, Suckiel SA, Thompson N, Weiss DJ, Roberts JS, Green RC. Development and Validation of a Comprehensive Genomics Knowledge Scale. Public Health Genomics. 2021;24(5-6):291-303. doi: 10.1159/000515006. Epub 2021 May 31. PubMed PMID: 34058740; PubMed Central PMCID: PMC8962920.

select

Linderman MD, McElroy L, Chang L. MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration. BMC Med Genomics. 2019 Nov 27;12(1):172. doi: 10.1186/s12920-019-0615-3. PubMed PMID: 31775760; PubMed Central PMCID: PMC6882182.

select

Linderman MD, Chia D, Wallace F, Nothaft FA. DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark. BMC Bioinformatics. 2019 Oct 11;20(1):493. doi: 10.1186/s12859-019-3108-7. PubMed PMID: 31604420; PubMed Central PMCID: PMC6787990.

select

Zoltick ES, Linderman MD, McGinniss MA, Ramos E, Ball MP, Church GM, Leonard DGB, Pereira S, McGuire AL, Caskey CT, Sanderson SC, Schadt EE, Nielsen DE, Crawford SD, Green RC. Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium. Genome Med. 2019 Feb 27;11(1):10. doi: 10.1186/s13073-019-0619-9. PubMed PMID: 30808425; PubMed Central PMCID: PMC6391825.

select

Linderman MD, Sanderson SC, Bashir A, Diaz GA, Kasarskis A, Zinberg R, Mahajan M, Suckiel SA, Zweig M, Schadt EE. Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years. BMC Med Genomics. 2018 Jan 30;11(1):5. doi: 10.1186/s12920-018-0319-0. PubMed PMID: 29382336; PubMed Central PMCID: PMC5791365.

select

Belbin GM, Odgis J, Sorokin EP, Yee MC, Kohli S, Glicksberg BS, Gignoux CR, Wojcik GL, Van Vleck T, Jeff JM, Linderman M, Schurmann C, Ruderfer D, Cai X, Merkelson A, Justice AE, Young KL, Graff M, North KE, Peters U, James R, Hindorff L, Kornreich R, Edelmann L, Gottesman O, Stahl EE, Cho JH, Loos RJ, Bottinger EP, Nadkarni GN, Abul-Husn NS, Kenny EE. Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system. Elife. 2017 Sep 12;6. doi: 10.7554/eLife.25060. PubMed PMID: 28895531; PubMed Central PMCID: PMC5595434.

select

Rasmussen-Torvik LJ, Almoguera B, Doheny KF, Freimuth RR, Gordon AS, Hakonarson H, Hawkins JB, Husami A, Ivacic LC, Kullo IJ, Linderman MD, Manolio TA, Obeng AO, Pellegrino R, Prows CA, Ritchie MD, Smith ME, Stallings SC, Wolf WA, Zhang K, Scott SA. Concordance between Research Sequencing and Clinical Pharmacogenetic Genotyping in the eMERGE-PGx Study. J Mol Diagn. 2017 Jul;19(4):561-566. doi: 10.1016/j.jmoldx.2017.04.002. Epub 2017 May 11. PubMed PMID: 28502727; PubMed Central PMCID: PMC5500823.

select

Bichoupan K, Tandon N, Martel-Laferriere V, Patel NM, Sachs D, Ng M, Schonfeld EA, Pappas A, Crismale J, Stivala A, Khaitova V, Gardenier D, Linderman M, Olson W, Perumalswami PV, Schiano TD, Odin JA, Liu LU, Dieterich DT, Branch AD. Factors associated with success of telaprevir- and boceprevir-based triple therapy for hepatitis C virus infection. World J Hepatol. 2017 Apr 18;9(11):551-561. doi: 10.4254/wjh.v9.i11.551. PubMed PMID: 28469811; PubMed Central PMCID: PMC5395804.

select

Sanderson SC, Linderman MD, Suckiel SA, Zinberg R, Wasserstein M, Kasarskis A, Diaz GA, Schadt EE. Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project. Eur J Hum Genet. 2017 Feb;25(3):280-292. doi: 10.1038/ejhg.2016.178. Epub 2017 Jan 4. PubMed PMID: 28051073; PubMed Central PMCID: PMC5315514.

select

Suckiel SA, Linderman MD, Sanderson SC, Diaz GA, Wasserstein M, Kasarskis A, Schadt EE, Zinberg RE. Impact of Genomic Counseling on Informed Decision-Making among ostensibly Healthy Individuals Seeking Personal Genome Sequencing: the HealthSeq Project. J Genet Couns. 2016 Oct;25(5):1044-53. doi: 10.1007/s10897-016-9935-z. Epub 2016 Feb 22. PubMed PMID: 26898680.

select

Scott SA, Collet JP, Baber U, Yang Y, Peter I, Linderman M, Sload J, Qiao W, Kini AS, Sharma SK, Desnick RJ, Fuster V, Hajjar RJ, Montalescot G, Hulot JS. Exome sequencing of extreme clopidogrel response phenotypes identifies B4GALT2 as a determinant of on-treatment platelet reactivity. Clin Pharmacol Ther. 2016 Sep;100(3):287-94. doi: 10.1002/cpt.401. Epub 2016 Jun 20. PubMed PMID: 27213804; PubMed Central PMCID: PMC4982803.

select

Anchang B, Hart TD, Bendall SC, Qiu P, Bjornson Z, Linderman M, Nolan GP, Plevritis SK. Visualization and cellular hierarchy inference of single-cell data using SPADE. Nat Protoc. 2016 Jul;11(7):1264-79. doi: 10.1038/nprot.2016.066. Epub 2016 Jun 16. PubMed PMID: 27310265.

select

Uzilov AV, Ding W, Fink MY, Antipin Y, Brohl AS, Davis C, Lau CY, Pandya C, Shah H, Kasai Y, Powell J, Micchelli M, Castellanos R, Zhang Z, Linderman M, Kinoshita Y, Zweig M, Raustad K, Cheung K, Castillo D, Wooten M, Bourzgui I, Newman LC, Deikus G, Mathew B, Zhu J, Glicksberg BS, Moe AS, Liao J, Edelmann L, Dudley JT, Maki RG, Kasarskis A, Holcombe RF, Mahajan M, Hao K, Reva B, Longtine J, Starcevic D, Sebra R, Donovan MJ, Li S, Schadt EE, Chen R. Development and clinical application of an integrative genomic approach to personalized cancer therapy. Genome Med. 2016 Jun 1;8(1):62. doi: 10.1186/s13073-016-0313-0. PubMed PMID: 27245685; PubMed Central PMCID: PMC4888213.

select

Linderman MD, Nielsen DE, Green RC. Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium. J Pers Med. 2016 Mar 25;6(2). doi: 10.3390/jpm6020014. Review. PubMed PMID: 27023617; PubMed Central PMCID: PMC4932461.

select

Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC. Toward clinical genomics in everyday medicine: perspectives and recommendations. Expert Rev Mol Diagn. 2016;16(5):521-32. doi: 10.1586/14737159.2016.1146593. Epub 2016 Feb 24. PubMed PMID: 26810587; PubMed Central PMCID: PMC4841021.

select

Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, Wasserstein M, Kasarskis A, Schadt EE. Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project. Eur J Hum Genet. 2016 Jan;24(1):14-20. doi: 10.1038/ejhg.2015.118. Epub 2015 Jun 3. PubMed PMID: 26036856; PubMed Central PMCID: PMC4795230.

select

Gaulton KJ, Ferreira T, Lee Y, Raimondo A, Mägi R, Reschen ME, Mahajan A, Locke A, Rayner NW, Robertson N, Scott RA, Prokopenko I, Scott LJ, Green T, Sparso T, Thuillier D, Yengo L, Grallert H, Wahl S, Frånberg M, Strawbridge RJ, Kestler H, Chheda H, Eisele L, Gustafsson S, Steinthorsdottir V, Thorleifsson G, Qi L, Karssen LC, van Leeuwen EM, Willems SM, Li M, Chen H, Fuchsberger C, Kwan P, Ma C, Linderman M, Lu Y, Thomsen SK, Rundle JK, Beer NL, van de Bunt M, Chalisey A, Kang HM, Voight BF, Abecasis GR, Almgren P, Baldassarre D, Balkau B, Benediktsson R, Blüher M, Boeing H, Bonnycastle LL, Bottinger EP, Burtt NP, Carey J, Charpentier G, Chines PS, Cornelis MC, Couper DJ, Crenshaw AT, van Dam RM, Doney AS, Dorkhan M, Edkins S, Eriksson JG, Esko T, Eury E, Fadista J, Flannick J, Fontanillas P, Fox C, Franks PW, Gertow K, Gieger C, Gigante B, Gottesman O, Grant GB, Grarup N, Groves CJ, Hassinen M, Have CT, Herder C, Holmen OL, Hreidarsson AB, Humphries SE, Hunter DJ, Jackson AU, Jonsson A, Jørgensen ME, Jørgensen T, Kao WH, Kerrison ND, Kinnunen L, Klopp N, Kong A, Kovacs P, Kraft P, Kravic J, Langford C, Leander K, Liang L, Lichtner P, Lindgren CM, Lindholm E, Linneberg A, Liu CT, Lobbens S, Luan J, Lyssenko V, Männistö S, McLeod O, Meyer J, Mihailov E, Mirza G, Mühleisen TW, Müller-Nurasyid M, Navarro C, Nöthen MM, Oskolkov NN, Owen KR, Palli D, Pechlivanis S, Peltonen L, Perry JR, Platou CG, Roden M, Ruderfer D, Rybin D, van der Schouw YT, Sennblad B, Sigurðsson G, Stančáková A, Steinbach G, Storm P, Strauch K, Stringham HM, Sun Q, Thorand B, Tikkanen E, Tonjes A, Trakalo J, Tremoli E, Tuomi T, Wennauer R, Wiltshire S, Wood AR, Zeggini E, Dunham I, Birney E, Pasquali L, Ferrer J, Loos RJ, Dupuis J, Florez JC, Boerwinkle E, Pankow JS, van Duijn C, Sijbrands E, Meigs JB, Hu FB, Thorsteinsdottir U, Stefansson K, Lakka TA, Rauramaa R, Stumvoll M, Pedersen NL, Lind L, Keinanen-Kiukaanniemi SM, Korpi-Hyövälti E, Saaristo TE, Saltevo J, Kuusisto J, Laakso M, Metspalu A, Erbel R, Jöcke KH, Moebus S, Ripatti S, Salomaa V, Ingelsson E, Boehm BO, Bergman RN, Collins FS, Mohlke KL, Koistinen H, Tuomilehto J, Hveem K, Njølstad I, Deloukas P, Donnelly PJ, Frayling TM, Hattersley AT, de Faire U, Hamsten A, Illig T, Peters A, Cauchi S, Sladek R, Froguel P, Hansen T, Pedersen O, Morris AD, Palmer CN, Kathiresan S, Melander O, Nilsson PM, Groop LC, Barroso I, Langenberg C, Wareham NJ, O'Callaghan CA, Gloyn AL, Altshuler D, Boehnke M, Teslovich TM, McCarthy MI, Morris AP. Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. Nat Genet. 2015 Dec;47(12):1415-25. doi: 10.1038/ng.3437. Epub 2015 Nov 9. PubMed PMID: 26551672; PubMed Central PMCID: PMC4666734.

select

Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, Suckiel S, Shah H, Mahajan M, Diaz GA, Schadt EE. How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study. Genet Med. 2015 Nov;17(11):866-74. doi: 10.1038/gim.2014.203. Epub 2015 Jan 29. PubMed PMID: 25634025.

select

Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, Mahajan M, Shah H, Suckiel S, Zweig M, Schadt EE. Preparing the next generation of genomicists: a laboratory-style course in medical genomics. BMC Med Genomics. 2015 Aug 12;8:47. doi: 10.1186/s12920-015-0124-y. PubMed PMID: 26264128; PubMed Central PMCID: PMC4534145.

select

Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, Naidich TP, Rodenburg RJ, Houten SM, Schadt EE. Novel, compound heterozygous, single-nucleotide variants in MARS2 associated with developmental delay, poor growth, and sensorineural hearing loss. Hum Mutat. 2015 Jun;36(6):587-92. doi: 10.1002/humu.22781. Epub 2015 Apr 8. PubMed PMID: 25754315; PubMed Central PMCID: PMC4439286.

select

Bichoupan K, Martel-Laferriere V, Sachs D, Ng M, Schonfeld EA, Pappas A, Crismale J, Stivala A, Khaitova V, Gardenier D, Linderman M, Perumalswami PV, Schiano TD, Odin JA, Liu L, Moskowitz AJ, Dieterich DT, Branch AD. Costs of telaprevir-based triple therapy for hepatitis C: $189,000 per sustained virological response. Hepatology. 2014 Oct;60(4):1187-95. doi: 10.1002/hep.27340. Epub 2014 Aug 25. PubMed PMID: 25065814; PubMed Central PMCID: PMC4190678.

select

Bunyavanich S, Schadt EE, Himes BE, Lasky-Su J, Qiu W, Lazarus R, Ziniti JP, Cohain A, Linderman M, Torgerson DG, Eng CS, Pino-Yanes M, Padhukasahasram B, Yang JJ, Mathias RA, Beaty TH, Li X, Graves P, Romieu I, Navarro Bdel R, Salam MT, Vora H, Nicolae DL, Ober C, Martinez FD, Bleecker ER, Meyers DA, Gauderman WJ, Gilliland F, Burchard EG, Barnes KC, Williams LK, London SJ, Zhang B, Raby BA, Weiss ST. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. BMC Med Genomics. 2014 Aug 2;7:48. doi: 10.1186/1755-8794-7-48. PubMed PMID: 25085501; PubMed Central PMCID: PMC4127082.

select

Webb BD, Brandt T, Liu L, Jalas C, Liao J, Fedick A, Linderman MD, Diaz GA, Kornreich R, Trachtman H, Mehta L, Edelmann L. A founder mutation in COL4A3 causes autosomal recessive Alport syndrome in the Ashkenazi Jewish population. Clin Genet. 2014 Aug;86(2):155-60. doi: 10.1111/cge.12247. Epub 2013 Sep 2. PubMed PMID: 23927549.

select

Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE. Analytical validation of whole exome and whole genome sequencing for clinical applications. BMC Med Genomics. 2014 Apr 23;7:20. doi: 10.1186/1755-8794-7-20. PubMed PMID: 24758382; PubMed Central PMCID: PMC4022392.

select

Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE. Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome Med. 2013;5(12):113. doi: 10.1186/gm518. eCollection 2013. PubMed PMID: 24373383; PubMed Central PMCID: PMC3971344.

select

Chen Z, Tang H, Qayyum R, Schick UM, Nalls MA, Handsaker R, Li J, Lu Y, Yanek LR, Keating B, Meng Y, van Rooij FJ, Okada Y, Kubo M, Rasmussen-Torvik L, Keller MF, Lange L, Evans M, Bottinger EP, Linderman MD, Ruderfer DM, Hakonarson H, Papanicolaou G, Zonderman AB, Gottesman O, Thomson C, Ziv E, Singleton AB, Loos RJ, Sleiman PM, Ganesh S, McCarroll S, Becker DM, Wilson JG, Lettre G, Reiner AP. Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. Hum Mol Genet. 2013 Jun 15;22(12):2529-38. doi: 10.1093/hmg/ddt087. Epub 2013 Feb 26. PubMed PMID: 23446634; PubMed Central PMCID: PMC3658166.

select

Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP. CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data. Bioinformatics. 2012 Sep 15;28(18):2400-1. doi: 10.1093/bioinformatics/bts425. Epub 2012 Jul 10. PubMed PMID: 22782546; PubMed Central PMCID: PMC3436846.

select

Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol. 2011 Oct 2;29(10):886-91. doi: 10.1038/nbt.1991. PubMed PMID: 21964415; PubMed Central PMCID: PMC3196363.

select

Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology. Nat Rev Genet. 2011 Mar;12(3):224. doi: 10.1038/nrg2857-c2. Epub 2011 Feb 8. PubMed PMID: 21301474.

select

Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP. Computational solutions to large-scale data management and analysis. Nat Rev Genet. 2010 Sep;11(9):647-57. doi: 10.1038/nrg2857. Review. PubMed PMID: 20717155; PubMed Central PMCID: PMC3124937.

select

Linderman MD, Bruggner R, Athalye V, Meng TH, Bani Asadi N, Nolan GP. High-throughput Bayesian network learning using heterogeneous multicore computers. Proceedings of the 24th ACM International Conference on Supercomputing. 2010; :95-104. doi: 10.1145/1810085.1810101.

select

Linderman MD, Ho M, Dill DL, Meng TH, Nolan GP. Towards program optimization through automated analysis of numerical precision. Proceedings of the 8th annual IEEE/ACM international symposium on Code generation and optimization. 2010; :230-237. doi: 10.1145/1772954.1772987.

select

Linderman MD, Balfour J, Meng TH, Dally WJ. Embracing heterogeneity: parallel programming for changing hardware. Proceedings of the First USENIX conference on Hot topics in parallelism. 2009; :3-3.

select

Linderman MD, Collins JD, Wang H, Meng TH. Merge: a programming model for heterogeneous multi-core systems. Proceedings of the 13th international conference on Architectural support for programming languages and operating systems. 2008; :287-296. doi: 10.1145/1346281.1346318.

select

Santhanam G, Linderman MD, Gilja V, Afshar A, Ryu SI, Meng TH, Shenoy KV. HermesB: a continuous neural recording system for freely behaving primates. IEEE Trans Biomed Eng. 2007 Nov;54(11):2037-50. doi: 10.1109/TBME.2007.895753. PubMed PMID: 18018699.

select

Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV. Neural recording stability of chronic electrode arrays in freely behaving primates. Conf Proc IEEE Eng Med Biol Soc. 2006;2006:4387-91. doi: 10.1109/IEMBS.2006.260814. PubMed PMID: 17946626.

select

Gilja V, Linderman MD, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV. Multiday electrophysiological recordings from freely behaving primates. Conf Proc IEEE Eng Med Biol Soc. 2006;2006:5643-6. doi: 10.1109/IEMBS.2006.260412. PubMed PMID: 17947159.

select

Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV. An autonomous, broadband, multi-channel neural recording system for freely behaving primates. Conf Proc IEEE Eng Med Biol Soc. 2006;2006:1212-5. doi: 10.1109/IEMBS.2006.260813. PubMed PMID: 17946450.

select

Shenoy KV, Santhanam G, Ryu SI, Afshar A, Yu BM, Gilja V, Linderman MD, Kalmar RS, Cunningham JP, Kemere CT, Batista AP, Churchland MM, Meng TH. Increasing the performance of cortically-controlled prostheses. Conf Proc IEEE Eng Med Biol Soc. 2006;Suppl:6652-6. doi: 10.1109/IEMBS.2006.260912. Review. PubMed PMID: 17959477.