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Items: 1 to 50 of 76

1.

Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies.

Guièze R, Liu VM, Rosebrock D, Jourdain AA, Hernández-Sánchez M, Martinez Zurita A, Sun J, Ten Hacken E, Baranowski K, Thompson PA, Heo JM, Cartun Z, Aygün O, Iorgulescu JB, Zhang W, Notarangelo G, Livitz D, Li S, Davids MS, Biran A, Fernandes SM, Brown JR, Lako A, Ciantra ZB, Lawlor MA, Keskin DB, Udeshi ND, Wierda WG, Livak KJ, Letai AG, Neuberg D, Harper JW, Carr SA, Piccioni F, Ott CJ, Leshchiner I, Johannessen CM, Doench J, Mootha VK, Getz G, Wu CJ.

Cancer Cell. 2019 Oct 14;36(4):369-384.e13. doi: 10.1016/j.ccell.2019.08.005. Epub 2019 Sep 19.

PMID:
31543463
2.

RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis.

Li S, Sun J, Allesøe R, Datta K, Bao Y, Oliveira G, Forman J, Jin R, Olsen LR, Keskin DB, Shukla SA, Wu CJ, Livak KJ.

Nat Protoc. 2019 Aug;14(8):2571-2594. doi: 10.1038/s41596-019-0195-x. Epub 2019 Jul 24.

PMID:
31341290
3.

SMARTer single cell total RNA sequencing.

Verboom K, Everaert C, Bolduc N, Livak KJ, Yigit N, Rombaut D, Anckaert J, Lee S, Venø MT, Kjems J, Speleman F, Mestdagh P, Vandesompele J.

Nucleic Acids Res. 2019 Sep 19;47(16):e93. doi: 10.1093/nar/gkz535.

PMID:
31216024
4.

Targeted TCR Amplification from Single-Cell cDNA Libraries.

Li S, Livak KJ.

Methods Mol Biol. 2019;1979:197-224. doi: 10.1007/978-1-4939-9240-9_13.

PMID:
31028640
5.

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesøe RL, Richman AR, Kowalczyk MS, Abdelrahman S, Geduldig JE, Charbonneau S, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon NJ, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suvà ML, Wucherpfennig KW, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA.

Nature. 2019 Jan;565(7738):234-239. doi: 10.1038/s41586-018-0792-9. Epub 2018 Dec 19.

6.

Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome.

Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C.

Cell Syst. 2018 Sep 26;7(3):258-268.e3. doi: 10.1016/j.cels.2018.07.006. Epub 2018 Sep 5.

7.

A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens.

Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ.

Blood. 2018 Nov 1;132(18):1911-1921. doi: 10.1182/blood-2018-04-843763. Epub 2018 Aug 27.

8.

A practical solution for preserving single cells for RNA sequencing.

Attar M, Sharma E, Li S, Bryer C, Cubitt L, Broxholme J, Lockstone H, Kinchen J, Simmons A, Piazza P, Buck D, Livak KJ, Bowden R.

Sci Rep. 2018 Feb 1;8(1):2151. doi: 10.1038/s41598-018-20372-7.

9.

High-dimension single-cell analysis applied to cancer.

Wang L, Livak KJ, Wu CJ.

Mol Aspects Med. 2018 Feb;59:70-84. doi: 10.1016/j.mam.2017.08.005. Epub 2017 Aug 30. Review.

10.

Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.

Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ.

Genome Res. 2017 Aug;27(8):1300-1311. doi: 10.1101/gr.217331.116. Epub 2017 Jul 5.

11.

Corrigendum: Fluidic Logic Used in a Systems Approach to Enable Integrated Single-Cell Functional Analysis.

Ramalingam N, Fowler B, Szpankowski L, Leyrat AA, Hukari K, Maung MT, Yorza W, Norris M, Cesar C, Shuga J, Gonzales ML, Sanada CD, Wang X, Yeung R, Hwang W, Axsom J, Devaraju NS, Angeles ND, Greene C, Zhou MF, Ong ES, Poh CC, Lam M, Choi H, Htoo Z, Lee L, Chin CS, Shen ZW, Lu CT, Holcomb I, Ooi A, Stolarczyk C, Shuga T, Livak KJ, Larsen C, Unger M, West JA.

Front Bioeng Biotechnol. 2017 Mar 14;5:11. doi: 10.3389/fbioe.2017.00011. eCollection 2017.

12.

Transcriptional Networks in Single Perivascular Cells Sorted from Human Adipose Tissue Reveal a Hierarchy of Mesenchymal Stem Cells.

Hardy WR, Moldovan NI, Moldovan L, Livak KJ, Datta K, Goswami C, Corselli M, Traktuev DO, Murray IR, Péault B, March K.

Stem Cells. 2017 May;35(5):1273-1289. doi: 10.1002/stem.2599. Epub 2017 Mar 19.

13.

Deformation-induced transitional myofibroblasts contribute to compensatory lung growth.

Bennett RD, Ysasi AB, Wagner WL, Valenzuela CD, Tsuda A, Pyne S, Li S, Grimsby J, Pokharel P, Livak KJ, Ackermann M, Blainey P, Mentzer SJ.

Am J Physiol Lung Cell Mol Physiol. 2017 Jan 1;312(1):L79-L88. doi: 10.1152/ajplung.00383.2016. Epub 2016 Nov 11.

14.

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia.

Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ.

Cancer Cell. 2016 Nov 14;30(5):750-763. doi: 10.1016/j.ccell.2016.10.005. Epub 2016 Nov 3.

15.

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma.

Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, Francis JM, Patel AA, Onozato ML, Riggi N, Livak KJ, Gennert D, Satija R, Nahed BV, Curry WT, Martuza RL, Mylvaganam R, Iafrate AJ, Frosch MP, Golub TR, Rivera MN, Getz G, Rozenblatt-Rosen O, Cahill DP, Monje M, Bernstein BE, Louis DN, Regev A, Suvà ML.

Nature. 2016 Nov 10;539(7628):309-313. doi: 10.1038/nature20123. Epub 2016 Nov 2.

16.

Fluidic Logic Used in a Systems Approach to Enable Integrated Single-Cell Functional Analysis.

Ramalingam N, Fowler B, Szpankowski L, Leyrat AA, Hukari K, Maung MT, Yorza W, Norris M, Cesar C, Shuga J, Gonzales ML, Sanada CD, Wang X, Yeung R, Hwang W, Axsom J, Devaraju NS, Angeles ND, Greene C, Zhou MF, Ong ES, Poh CC, Lam M, Choi H, Htoo Z, Lee L, Chin CS, Shen ZW, Lu CT, Holcomb I, Ooi A, Stolarczyk C, Shuga T, Livak KJ, Larsen C, Unger M, West JA.

Front Bioeng Biotechnol. 2016 Sep 21;4:70. eCollection 2016. Erratum in: Front Bioeng Biotechnol. 2017 Mar 14;5:11.

17.

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction.

Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, Lundberg M, Fredriksson S, Hong J, Regev A, Livak KJ, Landegren U, Shalek AK.

Genome Biol. 2016 Sep 19;17(1):188. doi: 10.1186/s13059-016-1045-6.

18.

Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition.

Burger JA, Landau DA, Taylor-Weiner A, Bozic I, Zhang H, Sarosiek K, Wang L, Stewart C, Fan J, Hoellenriegel J, Sivina M, Dubuc AM, Fraser C, Han Y, Li S, Livak KJ, Zou L, Wan Y, Konoplev S, Sougnez C, Brown JR, Abruzzo LV, Carter SL, Keating MJ, Davids MS, Wierda WG, Cibulskis K, Zenz T, Werner L, Dal Cin P, Kharchencko P, Neuberg D, Kantarjian H, Lander E, Gabriel S, O'Brien S, Letai A, Weitz DA, Nowak MA, Getz G, Wu CJ.

Nat Commun. 2016 May 20;7:11589. doi: 10.1038/ncomms11589.

19.

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq.

Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I.

Genome Biol. 2016 Apr 28;17:77. doi: 10.1186/s13059-016-0938-8.

20.

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ.

Cancer Cell. 2014 Dec 8;26(6):813-825. doi: 10.1016/j.ccell.2014.10.012.

21.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.

Nat Biotechnol. 2014 Apr;32(4):381-386. doi: 10.1038/nbt.2859. Epub 2014 Mar 23.

22.

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments.

Wills QF, Livak KJ, Tipping AJ, Enver T, Goldson AJ, Sexton DW, Holmes C.

Nat Biotechnol. 2013 Aug;31(8):748-52. doi: 10.1038/nbt.2642. Epub 2013 Jul 21.

PMID:
23873083
23.

Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells.

Livak KJ, Wills QF, Tipping AJ, Datta K, Mittal R, Goldson AJ, Sexton DW, Holmes CC.

Methods. 2013 Jan;59(1):71-9. doi: 10.1016/j.ymeth.2012.10.004. Epub 2012 Oct 16.

24.

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution.

Weaver S, Dube S, Mir A, Qin J, Sun G, Ramakrishnan R, Jones RC, Livak KJ.

Methods. 2010 Apr;50(4):271-6. doi: 10.1016/j.ymeth.2010.01.003. Epub 2010 Jan 15.

PMID:
20079846
25.

Synthesis of conformationally preorganized and cell-permeable guanidine-based gamma-peptide nucleic acids (gammaGPNAs).

Sahu B, Chenna V, Lathrop KL, Thomas SM, Zon G, Livak KJ, Ly DH.

J Org Chem. 2009 Feb 20;74(4):1509-16. doi: 10.1021/jo802211n.

26.

Analyzing real-time PCR data by the comparative C(T) method.

Schmittgen TD, Livak KJ.

Nat Protoc. 2008;3(6):1101-8.

PMID:
18546601
27.

Methylation-dependent fragment separation: novel analysis of 5-methyl cytosine by capillary electrophoresis of amplified DNA using PCR incorporation of chemically modified dCTP.

Boyd VL, Moody KI, Karger AE, Livak KJ, Zon G, Burns JW.

Nucleosides Nucleotides Nucleic Acids. 2007;26(6-7):629-34.

PMID:
18066869
28.

Quantitative PCR based expression analysis on a nanoliter scale using polymer nano-well chips.

Dahl A, Sultan M, Jung A, Schwartz R, Lange M, Steinwand M, Livak KJ, Lehrach H, Nyarsik L.

Biomed Microdevices. 2007 Jun;9(3):307-14.

PMID:
17203381
29.

Real time PCR profiling of 330 human micro-RNAs.

Lao K, Xu NL, Sun YA, Livak KJ, Straus NA.

Biotechnol J. 2007 Jan;2(1):33-5.

PMID:
17124719
30.

Molecular load of pathologically occult metastases in pelvic lymph nodes is an independent prognostic marker of biochemical failure after localized prostate cancer treatment.

Ferrari AC, Stone NN, Kurek R, Mulligan E, McGregor R, Stock R, Unger P, Tunn U, Kaisary A, Droller M, Hall S, Renneberg H, Livak KJ, Gallagher RE, Mandeli J.

J Clin Oncol. 2006 Jul 1;24(19):3081-8.

PMID:
16809733
31.

Methylation-dependent fragment separation: direct detection of DNA methylation by capillary electrophoresis of PCR products from bisulfite-converted genomic DNA.

Boyd VL, Moody KI, Karger AE, Livak KJ, Zon G, Burns JW.

Anal Biochem. 2006 Jul 15;354(2):266-73. Epub 2006 May 6.

PMID:
16725101
32.

Multiplexing RT-PCR for the detection of multiple miRNA species in small samples.

Lao K, Xu NL, Yeung V, Chen C, Livak KJ, Straus NA.

Biochem Biophys Res Commun. 2006 Apr 28;343(1):85-9. Epub 2006 Feb 28.

PMID:
16529715
33.

Relapse of acute promyelocytic leukemia with PML-RARalpha mutant subclones independent of proximate all-trans retinoic acid selection pressure.

Gallagher RE, Schachter-Tokarz EL, Zhou DC, Ding W, Kim SH, Sankoorikal BJ, Bi W, Livak KJ, Slack JL, Willman CL.

Leukemia. 2006 Apr;20(4):556-62.

34.

Real-time quantification of microRNAs by stem-loop RT-PCR.

Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ.

Nucleic Acids Res. 2005 Nov 27;33(20):e179.

35.

SNP genotyping by the 5'-nuclease reaction.

Livak KJ.

Methods Mol Biol. 2003;212:129-47. No abstract available.

PMID:
12491907
36.

Quantitative real-time RT-PCR analysis of PML-RAR alpha mRNA in acute promyelocytic leukemia: assessment of prognostic significance in adult patients from intergroup protocol 0129.

Gallagher RE, Yeap BY, Bi W, Livak KJ, Beaubier N, Rao S, Bloomfield CD, Appelbaum FR, Tallman MS, Slack JL, Willman CL.

Blood. 2003 Apr 1;101(7):2521-8. Epub 2002 Dec 5.

PMID:
12468436
37.

Factors affecting the performance of 5' nuclease PCR assays for Listeria monocytogenes detection.

Lunge VR, Miller BJ, Livak KJ, Batt CA.

J Microbiol Methods. 2002 Nov;51(3):361-8.

PMID:
12223296
38.
39.

Pre-clinical validation of a novel, highly sensitive assay to detect PML-RARalpha mRNA using real-time reverse-transcription polymerase chain reaction.

Slack JL, Bi W, Livak KJ, Beaubier N, Yu M, Clark M, Kim SH, Gallagher RE, Willman CL.

J Mol Diagn. 2001 Nov;3(4):141-9.

40.

Fluorescence polarization in homogeneous nucleic acid analysis II: 5'-nuclease assay.

Latif S, Bauer-Sardina I, Ranade K, Livak KJ, Kwok PY.

Genome Res. 2001 Mar;11(3):436-40.

41.

SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease.

Martin ER, Lai EH, Gilbert JR, Rogala AR, Afshari AJ, Riley J, Finch KL, Stevens JF, Livak KJ, Slotterbeck BD, Slifer SH, Warren LL, Conneally PM, Schmechel DE, Purvis I, Pericak-Vance MA, Roses AD, Vance JM.

Am J Hum Genet. 2000 Aug;67(2):383-94. Epub 2000 Jun 21.

42.

Seven-color, homogeneous detection of six PCR products.

Lee LG, Livak KJ, Mullah B, Graham RJ, Vinayak RS, Woudenberg TM.

Biotechniques. 1999 Aug;27(2):342-9.

43.

Allelic discrimination using fluorogenic probes and the 5' nuclease assay.

Livak KJ.

Genet Anal. 1999 Feb;14(5-6):143-9.

PMID:
10084106
44.

Polymorphisms in the human DNA ligase I gene (LIG1) including a complex GT repeat.

Livak KJ, Little WA, Stack SL, Patterson TA.

Mutat Res. 1998 Nov;406(1):1-8.

PMID:
9920050
46.

A homogeneous, ligase-mediated DNA diagnostic test.

Chen X, Livak KJ, Kwok PY.

Genome Res. 1998 May;8(5):549-56.

47.

Structural analogues of TaqMan probes for real-time quantitative PCR.

Kuimelis RG, Livak KJ, Mullah B, Andrus A.

Nucleic Acids Symp Ser. 1997;(37):255-6.

PMID:
9586096
48.

Real time quantitative PCR.

Heid CA, Stevens J, Livak KJ, Williams PM.

Genome Res. 1996 Oct;6(10):986-94.

49.

The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus.

Chang FM, Kidd JR, Livak KJ, Pakstis AJ, Kidd KK.

Hum Genet. 1996 Jul;98(1):91-101.

PMID:
8682515
50.

A PCR-based assay for the detection of Escherichia coli Shiga-like toxin genes in ground beef.

Witham PK, Yamashiro CT, Livak KJ, Batt CA.

Appl Environ Microbiol. 1996 Apr;62(4):1347-53.

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