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Items: 48

1.

MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration.

Linderman MD, McElroy L, Chang L.

BMC Med Genomics. 2019 Nov 27;12(1):172. doi: 10.1186/s12920-019-0615-3.

2.

DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark.

Linderman MD, Chia D, Wallace F, Nothaft FA.

BMC Bioinformatics. 2019 Oct 11;20(1):493. doi: 10.1186/s12859-019-3108-7.

3.

Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium.

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; PeopleSeq Consortium.

Genome Med. 2019 Feb 27;11(1):10. doi: 10.1186/s13073-019-0619-9.

4.

Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years.

Linderman MD, Sanderson SC, Bashir A, Diaz GA, Kasarskis A, Zinberg R, Mahajan M, Suckiel SA, Zweig M, Schadt EE.

BMC Med Genomics. 2018 Jan 30;11(1):5. doi: 10.1186/s12920-018-0319-0.

5.

Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system.

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.

Elife. 2017 Sep 12;6. pii: e25060. doi: 10.7554/eLife.25060.

6.

Concordance between Research Sequencing and Clinical Pharmacogenetic Genotyping in the eMERGE-PGx Study.

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.

J Mol Diagn. 2017 Jul;19(4):561-566. doi: 10.1016/j.jmoldx.2017.04.002. Epub 2017 May 11.

7.

Factors associated with success of telaprevir- and boceprevir-based triple therapy for hepatitis C virus infection.

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.

World J Hepatol. 2017 Apr 18;9(11):551-561. doi: 10.4254/wjh.v9.i11.551.

8.

Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project.

Sanderson SC, Linderman MD, Suckiel SA, Zinberg R, Wasserstein M, Kasarskis A, Diaz GA, Schadt EE.

Eur J Hum Genet. 2017 Feb;25(3):280-292. doi: 10.1038/ejhg.2016.178. Epub 2017 Jan 4.

9.

Visualization and cellular hierarchy inference of single-cell data using SPADE.

Anchang B, Hart TD, Bendall SC, Qiu P, Bjornson Z, Linderman M, Nolan GP, Plevritis SK.

Nat Protoc. 2016 Jul;11(7):1264-79. doi: 10.1038/nprot.2016.066. Epub 2016 Jun 16.

PMID:
27310265
10.

Development and clinical application of an integrative genomic approach to personalized cancer therapy.

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.

Genome Med. 2016 Jun 1;8(1):62. doi: 10.1186/s13073-016-0313-0.

11.

Exome sequencing of extreme clopidogrel response phenotypes identifies B4GALT2 as a determinant of on-treatment platelet reactivity.

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.

Clin Pharmacol Ther. 2016 Sep;100(3):287-94. doi: 10.1002/cpt.401. Epub 2016 Jun 20.

12.

Personal Genome Sequencing in Ostensibly Healthy Individuals and the PeopleSeq Consortium.

Linderman MD, Nielsen DE, Green RC.

J Pers Med. 2016 Mar 25;6(2). pii: E14. doi: 10.3390/jpm6020014. Review.

13.

Impact of Genomic Counseling on Informed Decision-Making among ostensibly Healthy Individuals Seeking Personal Genome Sequencing: the HealthSeq Project.

Suckiel SA, Linderman MD, Sanderson SC, Diaz GA, Wasserstein M, Kasarskis A, Schadt EE, Zinberg RE.

J Genet Couns. 2016 Oct;25(5):1044-53. doi: 10.1007/s10897-016-9935-z. Epub 2016 Feb 22.

PMID:
26898680
14.

Toward clinical genomics in everyday medicine: perspectives and recommendations.

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.

Expert Rev Mol Diagn. 2016;16(5):521-32. doi: 10.1586/14737159.2016.1146593. Epub 2016 Feb 24.

15.

A dynamical model improves reconstruction of handwriting from multichannel electromyographic recordings.

Okorokova E, Lebedev M, Linderman M, Ossadtchi A.

Front Neurosci. 2015 Oct 29;9:389. doi: 10.3389/fnins.2015.00389. eCollection 2015. Erratum in: Front Neurosci. 2015;9:517.

16.

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

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; DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.

Nat Genet. 2015 Dec;47(12):1415-25. doi: 10.1038/ng.3437. Epub 2015 Nov 9.

17.

Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project.

Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, Wasserstein M, Kasarskis A, Schadt EE.

Eur J Hum Genet. 2016 Jan;24(1):153. doi: 10.1038/ejhg.2015.179. Epub 2015 Oct 28. No abstract available.

18.

Preparing the next generation of genomicists: a laboratory-style course in medical genomics.

Linderman MD, Bashir A, Diaz GA, Kasarskis A, Sanderson SC, Zinberg RE, Mahajan M, Shah H, Suckiel S, Zweig M, Schadt EE.

BMC Med Genomics. 2015 Aug 12;8:47. doi: 10.1186/s12920-015-0124-y.

19.

Motivations, concerns and preferences of personal genome sequencing research participants: Baseline findings from the HealthSeq project.

Sanderson SC, Linderman MD, Suckiel SA, Diaz GA, Zinberg RE, Ferryman K, Wasserstein M, Kasarskis A, Schadt EE.

Eur J Hum Genet. 2016 Jan;24(1):14-20. doi: 10.1038/ejhg.2015.118. Epub 2015 Jun 3. Erratum in: Eur J Hum Genet. 2016 Jan;24(1):153.

20.

Novel, compound heterozygous, single-nucleotide variants in MARS2 associated with developmental delay, poor growth, and sensorineural hearing loss.

Webb BD, Wheeler PG, Hagen JJ, Cohen N, Linderman MD, Diaz GA, Naidich TP, Rodenburg RJ, Houten SM, Schadt EE.

Hum Mutat. 2015 Jun;36(6):587-92. doi: 10.1002/humu.22781. Epub 2015 Apr 8.

21.

How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study.

Sanderson SC, Linderman MD, Zinberg R, Bashir A, Kasarskis A, Zweig M, Suckiel S, Shah H, Mahajan M, Diaz GA, Schadt EE.

Genet Med. 2015 Nov;17(11):866-74. doi: 10.1038/gim.2014.203. Epub 2015 Jan 29.

PMID:
25634025
22.

Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis.

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.

BMC Med Genomics. 2014 Aug 2;7:48. doi: 10.1186/1755-8794-7-48.

23.

Costs of telaprevir-based triple therapy for hepatitis C: $189,000 per sustained virological response.

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.

Hepatology. 2014 Oct;60(4):1187-95. doi: 10.1002/hep.27340. Epub 2014 Aug 25.

24.

Analytical validation of whole exome and whole genome sequencing for clinical applications.

Linderman MD, Brandt T, Edelmann L, Jabado O, Kasai Y, Kornreich R, Mahajan M, Shah H, Kasarskis A, Schadt EE.

BMC Med Genomics. 2014 Apr 23;7:20. doi: 10.1186/1755-8794-7-20.

25.

Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study.

Sanderson SC, Linderman MD, Kasarskis A, Bashir A, Diaz GA, Mahajan MC, Shah H, Wasserstein M, Zinberg RE, Zweig M, Schadt EE.

Genome Med. 2013 Dec 30;5(12):113. doi: 10.1186/gm518. eCollection 2013.

26.

A founder mutation in COL4A3 causes autosomal recessive Alport syndrome in the Ashkenazi Jewish population.

Webb BD, Brandt T, Liu L, Jalas C, Liao J, Fedick A, Linderman MD, Diaz GA, Kornreich R, Trachtman H, Mehta L, Edelmann L.

Clin Genet. 2014 Aug;86(2):155-60. doi: 10.1111/cge.12247. Epub 2013 Sep 2.

PMID:
23927549
27.

Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.

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; BioBank Japan Project; CHARGE Consortium, Thomson C, Ziv E, Singleton AB, Loos RJ, Sleiman PM, Ganesh S, McCarroll S, Becker DM, Wilson JG, Lettre G, Reiner AP.

Hum Mol Genet. 2013 Jun 15;22(12):2529-38. doi: 10.1093/hmg/ddt087. Epub 2013 Feb 26.

28.

Time-dependent statistical and correlation properties of neural signals during handwriting.

Rupasov VI, Lebedev MA, Erlichman JS, Lee SL, Leiter JC, Linderman M.

PLoS One. 2012;7(9):e43945. doi: 10.1371/journal.pone.0043945. Epub 2012 Sep 11.

29.

CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data.

Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP.

Bioinformatics. 2012 Sep 15;28(18):2400-1. doi: 10.1093/bioinformatics/bts425. Epub 2012 Jul 10.

30.

Feline exocrine pancreatic carcinoma: a retrospective study of 34 cases.

Linderman MJ, Brodsky EM, de Lorimier LP, Clifford CA, Post GS.

Vet Comp Oncol. 2013 Sep;11(3):208-18. doi: 10.1111/j.1476-5829.2012.00320.x. Epub 2012 May 21.

PMID:
22612638
31.

Neuronal variability during handwriting: lognormal distribution.

Rupasov VI, Lebedev MA, Erlichman JS, Linderman M.

PLoS One. 2012;7(4):e34759. doi: 10.1371/journal.pone.0034759. Epub 2012 Apr 13.

32.

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE.

Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK.

Nat Biotechnol. 2011 Oct 2;29(10):886-91. doi: 10.1038/nbt.1991.

33.

Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology.

Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP.

Nat Rev Genet. 2011 Mar;12(3):224. doi: 10.1038/nrg2857-c2. Epub 2011 Feb 8. No abstract available.

PMID:
21301474
34.

Computational solutions to large-scale data management and analysis.

Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP.

Nat Rev Genet. 2010 Sep;11(9):647-57. doi: 10.1038/nrg2857. Review.

35.

High-throughput Bayesian Network Learning using Heterogeneous Multicore Computers.

Linderman MD, Athalye V, Meng TH, Asadi NB, Bruggner R, Nolan GP.

ICS. 2010 Jun;2010:95-104. doi: 10.1145/1810085.1810101.

36.

Towards Program Optimization through Automated Analysis of Numerical Precision.

Linderman MD, Ho M, Dill DL, Meng TH, Nolan GP.

Proc CGO. 2010 Apr;2010:230-237. doi: 10.1145/1772954.1772987.

37.

Recognition of handwriting from electromyography.

Linderman M, Lebedev MA, Erlichman JS.

PLoS One. 2009 Aug 26;4(8):e6791. doi: 10.1371/journal.pone.0006791.

38.

Land use change: complexity and comparisons.

Rindfuss RR, Entwisle B, Walsh SJ, An L, Badenoch N, Brown DG, Deadman P, Evans TP, Fox J, Geoghegan J, Gutmann M, Kelly M, Linderman M, Liu J, Malanson GP, Mena CF, Messina JP, Moran EF, Parker DC, Parton W, Prasartkul P, Robinson DT, Sawangdee Y, Vanwey LK, Verburg PH.

J Land Use Sci. 2008 Jan 1;3(1):1-10. No abstract available.

39.

Case studies, cross-site comparisons, and the challenge of generalization: comparing agent-based models of land-use change in frontier regions.

Parker DC, Entwisle B, Rindfuss RR, Vanwey LK, Manson SM, Moran E, An L, Deadman P, Evans TP, Linderman M, Rizi SM, Malanson G.

J Land Use Sci. 2008 Jan 1;3(1):41-72.

40.

Increasing the performance of cortically-controlled prostheses.

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.

Conf Proc IEEE Eng Med Biol Soc. 2006;Suppl:6652-6. Review.

PMID:
17959477
41.

HermesB: a continuous neural recording system for freely behaving primates.

Santhanam G, Linderman MD, Gilja V, Afshar A, Ryu SI, Meng TH, Shenoy KV.

IEEE Trans Biomed Eng. 2007 Nov;54(11):2037-50.

PMID:
18018699
42.

Multiday electrophysiological recordings from freely behaving primates.

Gilja V, Linderman MD, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:5643-6.

PMID:
17947159
43.

Neural recording stability of chronic electrode arrays in freely behaving primates.

Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:4387-91.

PMID:
17946626
44.

An autonomous, broadband, multi-channel neural recording system for freely behaving primates.

Linderman MD, Gilja V, Santhanam G, Afshar A, Ryu S, Meng TH, Shenoy KV.

Conf Proc IEEE Eng Med Biol Soc. 2006;1:1212-5.

PMID:
17946450
45.

Temporal changes in giant panda habitat connectivity across boundaries of Wolong Nature Reserve, China.

Viña A, Bearer S, Chen X, He G, Linderman M, An L, Zhang H, Ouyang Z, Liu J.

Ecol Appl. 2007 Jun;17(4):1019-30.

PMID:
17555215
46.

Interactive effects of natural and human disturbances on vegetation dynamics across landscapes.

Linderman MA, An L, Bearer S, He G, Ouyang Z, Liu J.

Ecol Appl. 2006 Apr;16(2):452-63.

PMID:
16711036
47.

Ecological degradation in protected areas: the case of Wolong Nature Reserve for giant pandas.

Liu J, Linderman M, Ouyang Z, An L, Yang J, Zhang H.

Science. 2001 Apr 6;292(5514):98-101.

48.

Serum alanine aminotransferase levels and prevalence of hepatitis A, B, and delta in outpatients.

Jensen DM, Dickerson DD, Linderman MA, Kessler H.

Arch Intern Med. 1987 Oct;147(10):1734-7.

PMID:
2821943

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