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Shared and organism-specific host responses to childhood diarrheal diseases revealed by whole blood transcript profiling.

DeBerg HA, Zaidi MB, Altman MC, Khaenam P, Gersuk VH, Campos FD, Perez-Martinez I, Meza-Segura M, Chaussabel D, Banchereau J, Estrada-Garcia T, Linsley PS.

PLoS One. 2018 Jan 29;13(1):e0192082. doi: 10.1371/journal.pone.0192082. eCollection 2018.


Remodeling T cell compartments during anti-CD3 immunotherapy of type 1 diabetes.

Long SA, Thorpe J, Herold KC, Ehlers M, Sanda S, Lim N, Linsley PS, Nepom GT, Harris KM.

Cell Immunol. 2017 Sep;319:3-9. doi: 10.1016/j.cellimm.2017.07.007. Epub 2017 Aug 18.


A phenotypically and functionally distinct human TH2 cell subpopulation is associated with allergic disorders.

Wambre E, Bajzik V, DeLong JH, O'Brien K, Nguyen QA, Speake C, Gersuk VH, DeBerg HA, Whalen E, Ni C, Farrington M, Jeong D, Robinson D, Linsley PS, Vickery BP, Kwok WW.

Sci Transl Med. 2017 Aug 2;9(401). pii: eaam9171. doi: 10.1126/scitranslmed.aam9171.


Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes.

Long SA, Thorpe J, DeBerg HA, Gersuk V, Eddy J, Harris KM, Ehlers M, Herold KC, Nepom GT, Linsley PS.

Sci Immunol. 2016 Nov;1(5). pii: eaai7793. doi: 10.1126/sciimmunol.aai7793. Epub 2016 Nov 18.


Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations.

Mpina M, Maurice NJ, Yajima M, Slichter CK, Miller HW, Dutta M, McElrath MJ, Stuart KD, De Rosa SC, McNevin JP, Linsley PS, Abdulla S, Tanner M, Hoffman SL, Gottardo R, Daubenberger CA, Prlic M.

J Immunol. 2017 Jul 1;199(1):107-118. doi: 10.4049/jimmunol.1601989. Epub 2017 Jun 2.


Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.

Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS.

J Immunol. 2017 Jul 1;199(1):323-335. doi: 10.4049/jimmunol.1700172. Epub 2017 May 31.


MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R.

Genome Biol. 2015 Dec 10;16:278. doi: 10.1186/s13059-015-0844-5.


The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types.

Linsley PS, Chaussabel D, Speake C.

PLoS One. 2015 Sep 23;10(9):e0138726. doi: 10.1371/journal.pone.0138726. eCollection 2015.


Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis.

Linsley PS, Speake C, Whalen E, Chaussabel D.

PLoS One. 2014 Oct 14;9(10):e109760. doi: 10.1371/journal.pone.0109760. eCollection 2014.


A transcriptomic reporter assay employing neutrophils to measure immunogenic activity of septic patients' plasma.

Khaenam P, Rinchai D, Altman MC, Chiche L, Buddhisa S, Kewcharoenwong C, Suwannasaen D, Mason M, Whalen E, Presnell S, Susaengrat W, O'Brien K, Nguyen QA, Gersuk V, Linsley PS, Lertmemongkolchai G, Chaussabel D.

J Transl Med. 2014 Mar 11;12:65. doi: 10.1186/1479-5876-12-65.


A multiplexed siRNA screening strategy to identify genes in the PARP pathway.

Stec E, Locco L, Szymanski S, Bartz SR, Toniatti C, Needham RH, Palmieri A, Carleton M, Cleary MA, Jackson AL, Linsley PS, Strulovici B, Ferrer M, Santini F.

J Biomol Screen. 2012 Dec;17(10):1316-28. doi: 10.1177/1087057112453071. Epub 2012 Jul 10.


Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver.

Androsavich JR, Chau BN, Bhat B, Linsley PS, Walter NG.

RNA. 2012 Aug;18(8):1510-26. doi: 10.1261/rna.033308.112. Epub 2012 Jun 27.


Functional genomics identifies therapeutic targets for MYC-driven cancer.

Toyoshima M, Howie HL, Imakura M, Walsh RM, Annis JE, Chang AN, Frazier J, Chau BN, Loboda A, Linsley PS, Cleary MA, Park JR, Grandori C.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9545-50. doi: 10.1073/pnas.1121119109. Epub 2012 May 23.


Synthetic lethality of PARP inhibition in BRCA-network disrupted tumor cells is associated with interferon pathway activation and enhanced by interferon-γ.

Warrener P, Kim S, Williams SM, Biery M, Gordon M, Toniatti C, Cleary MA, Linsley PS, Carleton M.

Apoptosis. 2012 Jul;17(7):691-701. doi: 10.1007/s10495-012-0707-4.


Pillars article: CTLA-4 can function as a negative regulator of T cell activation. Immunity. 1994. 1: 405-413.

Walunas TL, Lenschow DJ, Bakker CY, Linsley PS, Freeman GJ, Green JM, Thompson CB, Bluestone JA.

J Immunol. 2011 Oct 1;187(7):3466-74. No abstract available.


miR-146a is a significant brake on autoimmunity, myeloproliferation, and cancer in mice.

Boldin MP, Taganov KD, Rao DS, Yang L, Zhao JL, Kalwani M, Garcia-Flores Y, Luong M, Devrekanli A, Xu J, Sun G, Tay J, Linsley PS, Baltimore D.

J Exp Med. 2011 Jun 6;208(6):1189-201. doi: 10.1084/jem.20101823. Epub 2011 May 9.


Effect of Xpcl1 activation and p27(Kip1) loss on gene expression in murine lymphoma.

Kuppers DA, Hwang HC, Jackson AL, Linsley PS, Clurman BE, Fero ML.

PLoS One. 2011 Mar 11;6(3):e14758. doi: 10.1371/journal.pone.0014758.


Pillars article: long-term acceptance of skin and cardiac allografts after blocking CD40 and CD28 pathways. Nature. 1996. 381: 434-438. 1996.

Larsen CP, Elwood ET, Alexander DZ, Ritchie SC, Hendrix R, Tucker-Burden C, Cho HR, Aruffo A, Hollenbaugh D, Linsley PS, Winn KJ, Pearson TC.

J Immunol. 2011 Mar 1;186(5):2693-7. No abstract available.


Comparison of different miR-21 inhibitor chemistries in a cardiac disease model.

Thum T, Chau N, Bhat B, Gupta SK, Linsley PS, Bauersachs J, Engelhardt S.

J Clin Invest. 2011 Feb;121(2):461-2; author reply 462-3. doi: 10.1172/JCI45938. Epub 2011 Feb 1. No abstract available.


Hidden reach of the micromanagers.

Linsley PS, Jackson AL.

BMC Biol. 2010 May 11;8:53. doi: 10.1186/1741-7007-8-53. Review.


The therapeutic potential of microRNA modulation.

Jackson A, Linsley PS.

Discov Med. 2010 Apr;9(47):311-8. Review.


Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application.

Jackson AL, Linsley PS.

Nat Rev Drug Discov. 2010 Jan;9(1):57-67. doi: 10.1038/nrd3010. Review.


Off-target and a portion of target-specific siRNA mediated mRNA degradation is Ago2 'Slicer' independent and can be mediated by Ago1.

Vickers TA, Lima WF, Wu H, Nichols JG, Linsley PS, Crooke ST.

Nucleic Acids Res. 2009 Nov;37(20):6927-41. doi: 10.1093/nar/gkp735. Epub 2009 Sep 18.


Myc-regulated microRNAs attenuate embryonic stem cell differentiation.

Lin CH, Jackson AL, Guo J, Linsley PS, Eisenman RN.

EMBO J. 2009 Oct 21;28(20):3157-70. doi: 10.1038/emboj.2009.254. Epub 2009 Sep 10.


MicroRNA miR-210 modulates cellular response to hypoxia through the MYC antagonist MNT.

Zhang Z, Sun H, Dai H, Walsh RM, Imakura M, Schelter J, Burchard J, Dai X, Chang AN, Diaz RL, Marszalek JR, Bartz SR, Carleton M, Cleary MA, Linsley PS, Grandori C.

Cell Cycle. 2009 Sep 1;8(17):2756-68. Epub 2009 Sep 29.


The clinical utility of inhibiting CD28-mediated costimulation.

Linsley PS, Nadler SG.

Immunol Rev. 2009 May;229(1):307-21. doi: 10.1111/j.1600-065X.2009.00780.x. Review.


Identification of SULF2 as a novel transcriptional target of p53 by use of integrated genomic analyses.

Chau BN, Diaz RL, Saunders MA, Cheng C, Chang AN, Warrener P, Bradshaw J, Linsley PS, Cleary MA.

Cancer Res. 2009 Feb 15;69(4):1368-74. doi: 10.1158/0008-5472.CAN-08-2742. Epub 2009 Feb 3.


MicroRNA-like off-target transcript regulation by siRNAs is species specific.

Burchard J, Jackson AL, Malkov V, Needham RH, Tan Y, Bartz SR, Dai H, Sachs AB, Linsley PS.

RNA. 2009 Feb;15(2):308-15. doi: 10.1261/rna.1326809.


Coordinated regulation of cell cycle transcripts by p53-Inducible microRNAs, miR-192 and miR-215.

Georges SA, Biery MC, Kim SY, Schelter JM, Guo J, Chang AN, Jackson AL, Carleton MO, Linsley PS, Cleary MA, Chau BN.

Cancer Res. 2008 Dec 15;68(24):10105-12. doi: 10.1158/0008-5472.CAN-08-1846.


MicroRNA 21 promotes glioma invasion by targeting matrix metalloproteinase regulators.

Gabriely G, Wurdinger T, Kesari S, Esau CC, Burchard J, Linsley PS, Krichevsky AM.

Mol Cell Biol. 2008 Sep;28(17):5369-80. doi: 10.1128/MCB.00479-08. Epub 2008 Jun 30.


Median absolute deviation to improve hit selection for genome-scale RNAi screens.

Chung N, Zhang XD, Kreamer A, Locco L, Kuan PF, Bartz S, Linsley PS, Ferrer M, Strulovici B.

J Biomol Screen. 2008 Feb;13(2):149-58. doi: 10.1177/1087057107312035. Epub 2008 Jan 23.


An efficient and fully automated high-throughput transfection method for genome-scale siRNA screens.

Chung N, Locco L, Huff KW, Bartz S, Linsley PS, Ferrer M, Strulovici B.

J Biomol Screen. 2008 Feb;13(2):142-8. doi: 10.1177/1087057107312032. Epub 2008 Jan 23.


MicroRNAs in the miR-106b family regulate p21/CDKN1A and promote cell cycle progression.

Ivanovska I, Ball AS, Diaz RL, Magnus JF, Kibukawa M, Schelter JM, Kobayashi SV, Lim L, Burchard J, Jackson AL, Linsley PS, Cleary MA.

Mol Cell Biol. 2008 Apr;28(7):2167-74. doi: 10.1128/MCB.01977-07. Epub 2008 Jan 22.


An optimized lentivirus-mediated RNAi screen reveals kinase modulators of kinesin-5 inhibitor sensitivity.

Klinghoffer RA, Roberts B, Annis J, Frazier J, Lewis P, Linsley PS, Cleary MA.

Assay Drug Dev Technol. 2008 Feb;6(1):105-19. doi: 10.1089/adt.2007.106.


Chromosome 20q amplification regulates in vitro response to Kinesin-5 inhibitor.

Jackson AL, Mao M, Kobayashi S, Ward T, Biery M, Dai H, Bartz SR, Linsley PS.

Cancer Inform. 2008;6:147-64. Epub 2008 Mar 26.


Mustering the micromanagers.

Lim LP, Linsley PS.

Nat Biotechnol. 2007 Sep;25(9):996-7. No abstract available.


MicroRNAs and cell cycle regulation.

Carleton M, Cleary MA, Linsley PS.

Cell Cycle. 2007 Sep 1;6(17):2127-32. Epub 2007 Jun 26. Review.


A microRNA component of the p53 tumour suppressor network.

He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, Hannon GJ.

Nature. 2007 Jun 28;447(7148):1130-4. Epub 2007 Jun 6.


Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies.

Kittler R, Surendranath V, Heninger AK, Slabicki M, Theis M, Putz G, Franke K, Caldarelli A, Grabner H, Kozak K, Wagner J, Rees E, Korn B, Frenzel C, Sachse C, Sönnichsen B, Guo J, Schelter J, Burchard J, Linsley PS, Jackson AL, Habermann B, Buchholz F.

Nat Methods. 2007 Apr;4(4):337-44. Epub 2007 Mar 11.


PPARalpha siRNA-treated expression profiles uncover the causal sufficiency network for compound-induced liver hypertrophy.

Dai X, De Souza AT, Dai H, Lewis DL, Lee CK, Spencer AG, Herweijer H, Hagstrom JE, Linsley PS, Bassett DE, Ulrich RG, He YD.

PLoS Comput Biol. 2007 Mar 2;3(3):e30. Epub 2007 Jan 2.


Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression.

Linsley PS, Schelter J, Burchard J, Kibukawa M, Martin MM, Bartz SR, Johnson JM, Cummins JM, Raymond CK, Dai H, Chau N, Cleary M, Jackson AL, Carleton M, Lim L.

Mol Cell Biol. 2007 Mar;27(6):2240-52. Epub 2007 Jan 22.


Small interfering RNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 disruptions.

Bartz SR, Zhang Z, Burchard J, Imakura M, Martin M, Palmieri A, Needham R, Guo J, Gordon M, Chung N, Warrener P, Jackson AL, Carleton M, Oatley M, Locco L, Santini F, Smith T, Kunapuli P, Ferrer M, Strulovici B, Friend SH, Linsley PS.

Mol Cell Biol. 2006 Dec;26(24):9377-86. Epub 2006 Sep 25.


Minimizing the risk of reporting false positives in large-scale RNAi screens.

Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prévôt B, Root DE, Sabatini DM, Taipale J, Perrimon N, Bernards R.

Nat Methods. 2006 Oct;3(10):777-9.


Designing siRNA that distinguish between genes that differ by a single nucleotide.

Schwarz DS, Ding H, Kennington L, Moore JT, Schelter J, Burchard J, Linsley PS, Aronin N, Xu Z, Zamore PD.

PLoS Genet. 2006 Sep 8;2(9):e140. Epub 2006 Jul 24.


Transcriptional and phenotypic comparisons of Ppara knockout and siRNA knockdown mice.

De Souza AT, Dai X, Spencer AG, Reppen T, Menzie A, Roesch PL, He Y, Caguyong MJ, Bloomer S, Herweijer H, Wolff JA, Hagstrom JE, Lewis DL, Linsley PS, Ulrich RG.

Nucleic Acids Res. 2006;34(16):4486-94. Epub 2006 Aug 31.


Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing.

Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Khvorova A, Linsley PS.

RNA. 2006 Jul;12(7):1197-205. Epub 2006 May 8.


Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity.

Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, Linsley PS.

RNA. 2006 Jul;12(7):1179-87. Epub 2006 May 8.


RNA interference-mediated silencing of mitotic kinesin KIF14 disrupts cell cycle progression and induces cytokinesis failure.

Carleton M, Mao M, Biery M, Warrener P, Kim S, Buser C, Marshall CG, Fernandes C, Annis J, Linsley PS.

Mol Cell Biol. 2006 May;26(10):3853-63.


Gene expression changes associated with progression and response in chronic myeloid leukemia.

Radich JP, Dai H, Mao M, Oehler V, Schelter J, Druker B, Sawyers C, Shah N, Stock W, Willman CL, Friend S, Linsley PS.

Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2794-9. Epub 2006 Feb 13.

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