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Items: 41

1.

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs.

Listgarten J, Weinstein M, Kleinstiver BP, Sousa AA, Joung JK, Crawford J, Gao K, Hoang L, Elibol M, Doench JG, Fusi N.

Nat Biomed Eng. 2018 Jan;2(1):38-47. doi: 10.1038/s41551-017-0178-6. Epub 2018 Jan 10.

2.

Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.

Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG.

Nat Biotechnol. 2018 Feb;36(2):179-189. doi: 10.1038/nbt.4048. Epub 2017 Dec 18.

3.

Flexible Modeling of Genetic Effects on Function-Valued Traits.

Fusi N, Listgarten J.

J Comput Biol. 2017 Jun;24(6):524-535. doi: 10.1089/cmb.2016.0174. Epub 2017 Jan 5.

PMID:
28056190
4.

Identifying gene expression modules that define human cell fates.

Germanguz I, Listgarten J, Cinkornpumin J, Solomon A, Gaeta X, Lowry WE.

Stem Cell Res. 2016 May;16(3):712-24. doi: 10.1016/j.scr.2016.04.008. Epub 2016 Apr 13.

5.

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.

Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C, Orchard R, Virgin HW, Listgarten J, Root DE.

Nat Biotechnol. 2016 Feb;34(2):184-191. doi: 10.1038/nbt.3437. Epub 2016 Jan 18.

6.

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L.

Pac Symp Biocomput. 2015:342-6.

7.

Further improvements to linear mixed models for genome-wide association studies.

Widmer C, Lippert C, Weissbrod O, Fusi N, Kadie C, Davidson R, Listgarten J, Heckerman D.

Sci Rep. 2014 Nov 12;4:6874. doi: 10.1038/srep06874.

8.

let-7 miRNAs can act through notch to regulate human gliogenesis.

Patterson M, Gaeta X, Loo K, Edwards M, Smale S, Cinkornpumin J, Xie Y, Listgarten J, Azghadi S, Douglass SM, Pellegrini M, Lowry WE.

Stem Cell Reports. 2014 Nov 11;3(5):758-73. doi: 10.1016/j.stemcr.2014.08.015. Epub 2014 Oct 3.

9.

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants.

Lippert C, Xiang J, Horta D, Widmer C, Kadie C, Heckerman D, Listgarten J.

Bioinformatics. 2014 Nov 15;30(22):3206-14. doi: 10.1093/bioinformatics/btu504. Epub 2014 Jul 29.

10.

Epigenome-wide association studies without the need for cell-type composition.

Zou J, Lippert C, Heckerman D, Aryee M, Listgarten J.

Nat Methods. 2014 Mar;11(3):309-11. doi: 10.1038/nmeth.2815. Epub 2014 Jan 26.

PMID:
24464286
11.

Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction.

Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L.

Pac Symp Biocomput. 2014;19:224-8. doi: 10.1142/9789814583220_0022. No abstract available.

12.

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.

Bartha I, Carlson JM, Brumme CJ, McLaren PJ, Brumme ZL, John M, Haas DW, Martinez-Picado J, Dalmau J, López-Galíndez C, Casado C, Rauch A, Günthard HF, Bernasconi E, Vernazza P, Klimkait T, Yerly S, O'Brien SJ, Listgarten J, Pfeifer N, Lippert C, Fusi N, Kutalik Z, Allen TM, Müller V, Harrigan PR, Heckerman D, Telenti A, Fellay J.

Elife. 2013 Oct 29;2:e01123. doi: 10.7554/eLife.01123.

13.

The benefits of selecting phenotype-specific variants for applications of mixed models in genomics.

Lippert C, Quon G, Kang EY, Kadie CM, Listgarten J, Heckerman D.

Sci Rep. 2013;3:1815. doi: 10.1038/srep01815.

14.

FaST-LMM-Select for addressing confounding from spatial structure and rare variants.

Listgarten J, Lippert C, Heckerman D.

Nat Genet. 2013 May;45(5):470-1. doi: 10.1038/ng.2620. No abstract available.

PMID:
23619783
15.

A powerful and efficient set test for genetic markers that handles confounders.

Listgarten J, Lippert C, Kang EY, Xiang J, Kadie CM, Heckerman D.

Bioinformatics. 2013 Jun 15;29(12):1526-33. doi: 10.1093/bioinformatics/btt177. Epub 2013 Apr 18.

16.

The future of genome-based medicine.

Morris Q, Brenner SE, Listgarten J, Stegle O.

Pac Symp Biocomput. 2013:456-8. No abstract available.

17.

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.

Stegle O, Brenner SE, Morris Q, Listgarten J.

Pac Symp Biocomput. 2013;18:171-174. No abstract available.

18.

An exhaustive epistatic SNP association analysis on expanded Wellcome Trust data.

Lippert C, Listgarten J, Davidson RI, Baxter S, Poon H, Kadie CM, Heckerman D.

Sci Rep. 2013;3:1099. doi: 10.1038/srep01099. Epub 2013 Jan 22. Erratum in: Sci Rep. 2013 Feb 18;3:1321. Poong, Hoifung [corrected to Poon, Hoifung].

19.

Patterns of methylation heritability in a genome-wide analysis of four brain regions.

Quon G, Lippert C, Heckerman D, Listgarten J.

Nucleic Acids Res. 2013 Feb 1;41(4):2095-104. doi: 10.1093/nar/gks1449. Epub 2013 Jan 8.

20.

Co-operative additive effects between HLA alleles in control of HIV-1.

Matthews PC, Listgarten J, Carlson JM, Payne R, Huang KH, Frater J, Goedhals D, Steyn D, van Vuuren C, Paioni P, Jooste P, Ogwu A, Shapiro R, Mncube Z, Ndung'u T, Walker BD, Heckerman D, Goulder PJ.

PLoS One. 2012;7(10):e47799. doi: 10.1371/journal.pone.0047799. Epub 2012 Oct 19.

21.

Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1.

Carlson JM, Brumme CJ, Martin E, Listgarten J, Brockman MA, Le AQ, Chui CK, Cotton LA, Knapp DJ, Riddler SA, Haubrich R, Nelson G, Pfeifer N, Deziel CE, Heckerman D, Apps R, Carrington M, Mallal S, Harrigan PR, John M, Brumme ZL; International HIV Adaptation Collaborative.

J Virol. 2012 Dec;86(24):13202-16. doi: 10.1128/JVI.01998-12. Epub 2012 Oct 10.

22.

Improved linear mixed models for genome-wide association studies.

Listgarten J, Lippert C, Kadie CM, Davidson RI, Eskin E, Heckerman D.

Nat Methods. 2012 May 30;9(6):525-6. doi: 10.1038/nmeth.2037. No abstract available.

23.

Learning transcriptional regulatory relationships using sparse graphical models.

Zhang X, Cheng W, Listgarten J, Kadie C, Huang S, Wang W, Heckerman D.

PLoS One. 2012;7(5):e35762. doi: 10.1371/journal.pone.0035762. Epub 2012 May 7.

24.

Widespread impact of HLA restriction on immune control and escape pathways of HIV-1.

Carlson JM, Listgarten J, Pfeifer N, Tan V, Kadie C, Walker BD, Ndung'u T, Shapiro R, Frater J, Brumme ZL, Goulder PJ, Heckerman D.

J Virol. 2012 May;86(9):5230-43. doi: 10.1128/JVI.06728-11. Epub 2012 Feb 29.

25.

FaST linear mixed models for genome-wide association studies.

Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D.

Nat Methods. 2011 Sep 4;8(10):833-5. doi: 10.1038/nmeth.1681.

PMID:
21892150
26.

HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703.

Matthews PC, Adland E, Listgarten J, Leslie A, Mkhwanazi N, Carlson JM, Harndahl M, Stryhn A, Payne RP, Ogwu A, Huang KH, Frater J, Paioni P, Kloverpris H, Jooste P, Goedhals D, van Vuuren C, Steyn D, Riddell L, Chen F, Luzzi G, Balachandran T, Ndung'u T, Buus S, Carrington M, Shapiro R, Heckerman D, Goulder PJ.

J Immunol. 2011 May 15;186(10):5675-86. doi: 10.4049/jimmunol.1003711. Epub 2011 Apr 15.

27.

Correction for hidden confounders in the genetic analysis of gene expression.

Listgarten J, Kadie C, Schadt EE, Heckerman D.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16465-70. doi: 10.1073/pnas.1002425107. Epub 2010 Sep 1.

28.

Additive contribution of HLA class I alleles in the immune control of HIV-1 infection.

Leslie A, Matthews PC, Listgarten J, Carlson JM, Kadie C, Ndung'u T, Brander C, Coovadia H, Walker BD, Heckerman D, Goulder PJ.

J Virol. 2010 Oct;84(19):9879-88. doi: 10.1128/JVI.00320-10. Epub 2010 Jul 21.

29.

Rare HLA drive additional HIV evolution compared to more frequent alleles.

Rousseau CM, Lockhart DW, Listgarten J, Maley SN, Kadie C, Learn GH, Nickle DC, Heckerman DE, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder PJ, Korber BT, Walker BD, Mullins JI.

AIDS Res Hum Retroviruses. 2009 Mar;25(3):297-303. doi: 10.1089/aid.2008.0208.

30.

Statistical resolution of ambiguous HLA typing data.

Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000016. doi: 10.1371/journal.pcbi.1000016.

31.

Evidence that dysregulated DNA mismatch repair characterizes human nonmelanoma skin cancer.

Young LC, Listgarten J, Trotter MJ, Andrew SE, Tron VA.

Br J Dermatol. 2008 Jan;158(1):59-69. Epub 2007 Oct 26.

PMID:
17970804
32.

A statistical framework for modeling HLA-dependent T cell response data.

Listgarten J, Frahm N, Kadie C, Brander C, Heckerman D.

PLoS Comput Biol. 2007 Oct;3(10):1879-86.

33.

Extensive HLA class I allele promiscuity among viral CTL epitopes.

Frahm N, Yusim K, Suscovich TJ, Adams S, Sidney J, Hraber P, Hewitt HS, Linde CH, Kavanagh DG, Woodberry T, Henry LM, Faircloth K, Listgarten J, Kadie C, Jojic N, Sango K, Brown NV, Pae E, Zaman MT, Bihl F, Khatri A, John M, Mallal S, Marincola FM, Walker BD, Sette A, Heckerman D, Korber BT, Brander C.

Eur J Immunol. 2007 Sep;37(9):2419-33.

34.

Leveraging information across HLA alleles/supertypes improves epitope prediction.

Heckerman D, Kadie C, Listgarten J.

J Comput Biol. 2007 Jul-Aug;14(6):736-46.

PMID:
17691891
35.

Difference detection in LC-MS data for protein biomarker discovery.

Listgarten J, Neal RM, Roweis ST, Wong P, Emili A.

Bioinformatics. 2007 Jan 15;23(2):e198-204.

PMID:
17237092
36.

Practical proteomic biomarker discovery: taking a step back to leap forward.

Listgarten J, Emili A.

Drug Discov Today. 2005 Dec;10(23-24):1697-702.

PMID:
16376831
37.

Lymphovascular invasion is associated with poor survival in gastric cancer: an application of gene-expression and tissue array techniques.

Dicken BJ, Graham K, Hamilton SM, Andrews S, Lai R, Listgarten J, Jhangri GS, Saunders LD, Damaraju S, Cass C.

Ann Surg. 2006 Jan;243(1):64-73.

38.

Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry.

Listgarten J, Emili A.

Mol Cell Proteomics. 2005 Apr;4(4):419-34. Epub 2005 Mar 1. Review.

39.

Clinically validated benchmarking of normalisation techniques for two-colour oligonucleotide spotted microarray slides.

Listgarten J, Graham K, Damaraju S, Cass C, Mackey J, Zanke B.

Appl Bioinformatics. 2003;2(4):219-28.

PMID:
15130793
40.

Predictive models for breast cancer susceptibility from multiple single nucleotide polymorphisms.

Listgarten J, Damaraju S, Poulin B, Cook L, Dufour J, Driga A, Mackey J, Wishart D, Greiner R, Zanke B.

Clin Cancer Res. 2004 Apr 15;10(8):2725-37.

41.

Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 A resolution.

Listgarten JN, Maes D, Wyns L, Aguilar CF, Palmer RA.

Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):767-71.

PMID:
15299807

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