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Items: 1 to 50 of 68

1.

Whole Genome Next-Generation Sequencing Mutation Identification in Pseudomonas aeruginosa.

Cetinbas M, Yu S, Sadreyev RI.

Curr Protoc Mol Biol. 2018 Oct;124(1):e69. doi: 10.1002/cpmb.69. Epub 2018 Sep 21.

PMID:
30239153
2.

RNA-seq: Basic Bioinformatics Analysis.

Ji F, Sadreyev RI.

Curr Protoc Mol Biol. 2018 Oct;124(1):e68. doi: 10.1002/cpmb.68. Epub 2018 Sep 17.

PMID:
30222249
3.

Robust interferon signature and suppressed tissue repair gene expression in synovial tissue from patients with postinfectious, Borrelia burgdorferi-induced Lyme arthritis.

Lochhead RB, Arvikar SL, Aversa JM, Sadreyev RI, Strle K, Steere AC.

Cell Microbiol. 2018 Sep 14:e12954. doi: 10.1111/cmi.12954. [Epub ahead of print]

PMID:
30218476
4.

Prospective Isolation of Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming.

Schwarz BA, Cetinbas M, Clement K, Walsh RM, Cheloufi S, Gu H, Langkabel J, Kamiya A, Schorle H, Meissner A, Sadreyev RI, Hochedlinger K.

Cell Stem Cell. 2018 Aug 2;23(2):289-305.e5. doi: 10.1016/j.stem.2018.06.013. Epub 2018 Jul 12.

PMID:
30017590
5.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE.

Mol Cell. 2018 Jul 5;71(1):191. doi: 10.1016/j.molcel.2018.06.022. No abstract available.

PMID:
29979966
6.

Mutant GNAS drives pancreatic tumourigenesis by inducing PKA-mediated SIK suppression and reprogramming lipid metabolism.

Patra KC, Kato Y, Mizukami Y, Widholz S, Boukhali M, Revenco I, Grossman EA, Ji F, Sadreyev RI, Liss AS, Screaton RA, Sakamoto K, Ryan DP, Mino-Kenudson M, Castillo CF, Nomura DK, Haas W, Bardeesy N.

Nat Cell Biol. 2018 Jul;20(7):811-822. doi: 10.1038/s41556-018-0122-3. Epub 2018 Jun 25.

PMID:
29941929
7.

Cell of origin dictates aggression and stem cell number in acute lymphoblastic leukemia.

Garcia EG, Iyer S, Garcia SP, Loontiens S, Sadreyev RI, Speleman F, Langenau DM.

Leukemia. 2018 Aug;32(8):1860-1865. doi: 10.1038/s41375-018-0130-0. Epub 2018 Apr 18. No abstract available.

PMID:
29749398
8.

Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors.

Bar-Nur O, Gerli MFM, Di Stefano B, Almada AE, Galvin A, Coffey A, Huebner AJ, Feige P, Verheul C, Cheung P, Payzin-Dogru D, Paisant S, Anselmo A, Sadreyev RI, Ott HC, Tajbakhsh S, Rudnicki MA, Wagers AJ, Hochedlinger K.

Stem Cell Reports. 2018 May 8;10(5):1505-1521. doi: 10.1016/j.stemcr.2018.04.009.

9.

The surveillance of pre-mRNA splicing is an early step in C. elegans RNAi of endogenous genes.

Newman MA, Ji F, Fischer SEJ, Anselmo A, Sadreyev RI, Ruvkun G.

Genes Dev. 2018 May 1;32(9-10):670-681. doi: 10.1101/gad.311514.118. Epub 2018 May 8.

10.

An inactivating mutation in the histone deacetylase SIRT6 causes human perinatal lethality.

Ferrer CM, Alders M, Postma AV, Park S, Klein MA, Cetinbas M, Pajkrt E, Glas A, van Koningsbruggen S, Christoffels VM, Mannens MMAM, Knegt L, Etchegaray JP, Sadreyev RI, Denu JM, Mostoslavsky G, van Maarle MC, Mostoslavsky R.

Genes Dev. 2018 Mar 1;32(5-6):373-388. doi: 10.1101/gad.307330.117. Epub 2018 Mar 19.

11.

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K.

Cell. 2018 Jan 25;172(3):629-631. doi: 10.1016/j.cell.2017.12.035. No abstract available.

12.

Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling.

Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K.

Cell. 2018 Jan 11;172(1-2):106-120.e21. doi: 10.1016/j.cell.2017.11.023. Epub 2017 Dec 14. Erratum in: Cell. 2018 Jan 25;172(3):629-631.

PMID:
29249356
13.

Polycomb Repressive Complex 2 Methylates Elongin A to Regulate Transcription.

Ardehali MB, Anselmo A, Cochrane JC, Kundu S, Sadreyev RI, Kingston RE.

Mol Cell. 2017 Dec 7;68(5):872-884.e6. doi: 10.1016/j.molcel.2017.10.025. Epub 2017 Nov 16.

PMID:
29153392
14.

Genetic Intersection of Tsix and Hedgehog Signaling during the Initiation of X-Chromosome Inactivation.

Del Rosario BC, Del Rosario AM, Anselmo A, Wang PI, Sadreyev RI, Lee JT.

Dev Cell. 2017 Nov 6;43(3):359-371.e6. doi: 10.1016/j.devcel.2017.09.027. Epub 2017 Oct 26.

15.

IRF3 and type I interferons fuel a fatal response to myocardial infarction.

King KR, Aguirre AD, Ye YX, Sun Y, Roh JD, Ng RP Jr, Kohler RH, Arlauckas SP, Iwamoto Y, Savol A, Sadreyev RI, Kelly M, Fitzgibbons TP, Fitzgerald KA, Mitchison T, Libby P, Nahrendorf M, Weissleder R.

Nat Med. 2017 Dec;23(12):1481-1487. doi: 10.1038/nm.4428. Epub 2017 Nov 6.

PMID:
29106401
16.

TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia.

Lobbardi R, Pinder J, Martinez-Pastor B, Theodorou M, Blackburn JS, Abraham BJ, Namiki Y, Mansour M, Abdelfattah NS, Molodtsov A, Alexe G, Toiber D, de Waard M, Jain E, Boukhali M, Lion M, Bhere D, Shah K, Gutierrez A, Stegmaier K, Silverman LB, Sadreyev RI, Asara JM, Oettinger MA, Haas W, Look AT, Young RA, Mostoslavsky R, Dellaire G, Langenau DM.

Cancer Discov. 2017 Nov;7(11):1336-1353. doi: 10.1158/2159-8290.CD-17-0267. Epub 2017 Oct 3.

17.

Genome-wide identification of autosomal genes with allelic imbalance of chromatin state.

Savol AJ, Wang PI, Jeon Y, Colognori D, Yildirim E, Pinter SF, Payer B, Lee JT, Sadreyev RI.

PLoS One. 2017 Aug 10;12(8):e0182568. doi: 10.1371/journal.pone.0182568. eCollection 2017.

18.

Synergistic activity and heterogeneous acquired resistance of combined MDM2 and MEK inhibition in KRAS mutant cancers.

Hata AN, Rowley S, Archibald HL, Gomez-Caraballo M, Siddiqui FM, Ji F, Jung J, Light M, Lee JS, Debussche L, Sidhu S, Sadreyev RI, Watters J, Engelman JA.

Oncogene. 2017 Nov 23;36(47):6581-6591. doi: 10.1038/onc.2017.258. Epub 2017 Aug 7.

19.

Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells.

Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K.

Nature. 2017 Aug 10;548(7666):219-223. doi: 10.1038/nature23274. Epub 2017 Jul 26.

20.

Macrophages Facilitate Electrical Conduction in the Heart.

Hulsmans M, Clauss S, Xiao L, Aguirre AD, King KR, Hanley A, Hucker WJ, Wülfers EM, Seemann G, Courties G, Iwamoto Y, Sun Y, Savol AJ, Sager HB, Lavine KJ, Fishbein GA, Capen DE, Da Silva N, Miquerol L, Wakimoto H, Seidman CE, Seidman JG, Sadreyev RI, Naxerova K, Mitchell RN, Brown D, Libby P, Weissleder R, Swirski FK, Kohl P, Vinegoni C, Milan DJ, Ellinor PT, Nahrendorf M.

Cell. 2017 Apr 20;169(3):510-522.e20. doi: 10.1016/j.cell.2017.03.050.

21.

Mutation of a nucleosome compaction region disrupts Polycomb-mediated axial patterning.

Lau MS, Schwartz MG, Kundu S, Savol AJ, Wang PI, Marr SK, Grau DJ, Schorderet P, Sadreyev RI, Tabin CJ, Kingston RE.

Science. 2017 Mar 10;355(6329):1081-1084. doi: 10.1126/science.aah5403. Epub 2017 Mar 9.

22.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.

Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE.

Mol Cell. 2017 Feb 2;65(3):432-446.e5. doi: 10.1016/j.molcel.2017.01.009. Erratum in: Mol Cell. 2018 Jul 5;71(1):191.

23.

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants.

Gregory KE, Samuel BS, Houghteling P, Shan G, Ausubel FM, Sadreyev RI, Walker WA.

Microbiome. 2016 Dec 30;4(1):68. doi: 10.1186/s40168-016-0214-x.

24.

Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.

Joh RI, Khanduja JS, Calvo IA, Mistry M, Palmieri CM, Savol AJ, Ho Sui SJ, Sadreyev RI, Aryee MJ, Motamedi M.

Mol Cell. 2016 Dec 15;64(6):1088-1101. doi: 10.1016/j.molcel.2016.11.020.

25.

Single-cell imaging of normal and malignant cell engraftment into optically clear prkdc-null SCID zebrafish.

Moore JC, Tang Q, Yordán NT, Moore FE, Garcia EG, Lobbardi R, Ramakrishnan A, Marvin DL, Anselmo A, Sadreyev RI, Langenau DM.

J Exp Med. 2016 Nov 14;213(12):2575-2589. Epub 2016 Oct 24.

26.

Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia.

Sykes DB, Kfoury YS, Mercier FE, Wawer MJ, Law JM, Haynes MK, Lewis TA, Schajnovitz A, Jain E, Lee D, Meyer H, Pierce KA, Tolliday NJ, Waller A, Ferrara SJ, Eheim AL, Stoeckigt D, Maxcy KL, Cobert JM, Bachand J, Szekely BA, Mukherjee S, Sklar LA, Kotz JD, Clish CB, Sadreyev RI, Clemons PA, Janzer A, Schreiber SL, Scadden DT.

Cell. 2016 Sep 22;167(1):171-186.e15. doi: 10.1016/j.cell.2016.08.057. Epub 2016 Sep 15.

27.

T cell immune deficiency in zap70 mutant zebrafish.

Moore JC, Mulligan TS, Torres Yordán N, Castranova D, Pham VN, Tang Q, Lobbardi R, Anselmo A, Liwski RS, Berman JN, Sadreyev RI, Weinstein BM, Langenau DM.

Mol Cell Biol. 2016 Sep 6. pii: MCB.00281-16. [Epub ahead of print]

28.

Enhancer regions show high histone H3.3 turnover that changes during differentiation.

Deaton AM, Gómez-Rodríguez M, Mieczkowski J, Tolstorukov MY, Kundu S, Sadreyev RI, Jansen LE, Kingston RE.

Elife. 2016 Jun 15;5. pii: e15316. doi: 10.7554/eLife.15316.

29.

SIRT6 Suppresses Pancreatic Cancer through Control of Lin28b.

Kugel S, Sebastián C, Fitamant J, Ross KN, Saha SK, Jain E, Gladden A, Arora KS, Kato Y, Rivera MN, Ramaswamy S, Sadreyev RI, Goren A, Deshpande V, Bardeesy N, Mostoslavsky R.

Cell. 2016 Jun 2;165(6):1401-1415. doi: 10.1016/j.cell.2016.04.033. Epub 2016 May 12.

30.

Single-cell transcriptional analysis of normal, aberrant, and malignant hematopoiesis in zebrafish.

Moore FE, Garcia EG, Lobbardi R, Jain E, Tang Q, Moore JC, Cortes M, Molodtsov A, Kasheta M, Luo CC, Garcia AJ, Mylvaganam R, Yoder JA, Blackburn JS, Sadreyev RI, Ceol CJ, North TE, Langenau DM.

J Exp Med. 2016 May 30;213(6):979-92. doi: 10.1084/jem.20152013. Epub 2016 May 2.

31.

A Specialized Mechanism of Translation Mediated by FXR1a-Associated MicroRNP in Cellular Quiescence.

Bukhari SIA, Truesdell SS, Lee S, Kollu S, Classon A, Boukhali M, Jain E, Mortensen RD, Yanagiya A, Sadreyev RI, Haas W, Vasudevan S.

Mol Cell. 2016 Mar 3;61(5):760-773. doi: 10.1016/j.molcel.2016.02.013.

32.

Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction.

Nishikawa JL, Boeszoermenyi A, Vale-Silva LA, Torelli R, Posteraro B, Sohn YJ, Ji F, Gelev V, Sanglard D, Sanguinetti M, Sadreyev RI, Mukherjee G, Bhyravabhotla J, Buhrlage SJ, Gray NS, Wagner G, Näär AM, Arthanari H.

Nature. 2016 Feb 25;530(7591):485-9. doi: 10.1038/nature16963. Epub 2016 Feb 17.

33.

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition.

Hata AN, Niederst MJ, Archibald HL, Gomez-Caraballo M, Siddiqui FM, Mulvey HE, Maruvka YE, Ji F, Bhang HE, Krishnamurthy Radhakrishna V, Siravegna G, Hu H, Raoof S, Lockerman E, Kalsy A, Lee D, Keating CL, Ruddy DA, Damon LJ, Crystal AS, Costa C, Piotrowska Z, Bardelli A, Iafrate AJ, Sadreyev RI, Stegmeier F, Getz G, Sequist LV, Faber AC, Engelman JA.

Nat Med. 2016 Mar;22(3):262-9. doi: 10.1038/nm.4040. Epub 2016 Feb 1.

34.

Chromatin topology is coupled to Polycomb group protein subnuclear organization.

Wani AH, Boettiger AN, Schorderet P, Ergun A, Münger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ.

Nat Commun. 2016 Jan 13;7:10291. doi: 10.1038/ncomms10291.

35.

Genome-wide analysis of differentially expressed miRNA in PLX4720-resistant and parental human thyroid cancer cell lines.

Varmeh S, Vanden Borre P, Gunda V, Brauner E, Holm T, Wang Y, Sadreyev RI, Parangi S.

Surgery. 2016 Jan;159(1):152-62. doi: 10.1016/j.surg.2015.06.046. Epub 2015 Oct 9.

36.

Using homology relations within a database markedly boosts protein sequence similarity search.

Tong J, Sadreyev RI, Pei J, Kinch LN, Grishin NV.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):7003-8. doi: 10.1073/pnas.1424324112. Epub 2015 May 18.

37.

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT.

Genetics. 2015 Jun;200(2):537-49. doi: 10.1534/genetics.115.176263. Epub 2015 Apr 9.

38.

The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites.

West JA, Davis CP, Sunwoo H, Simon MD, Sadreyev RI, Wang PI, Tolstorukov MY, Kingston RE.

Mol Cell. 2014 Sep 4;55(5):791-802. doi: 10.1016/j.molcel.2014.07.012. Epub 2014 Aug 21.

39.

H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex.

Bowman SK, Deaton AM, Domingues H, Wang PI, Sadreyev RI, Kingston RE, Bender W.

Elife. 2014 Jul 31;3:e02833. doi: 10.7554/eLife.02833.

40.

BRCA1 establishes DNA damage signaling and pericentric heterochromatin of the X chromosome in male meiosis.

Broering TJ, Alavattam KG, Sadreyev RI, Ichijima Y, Kato Y, Hasegawa K, Camerini-Otero RD, Lee JT, Andreassen PR, Namekawa SH.

J Cell Biol. 2014 Jun 9;205(5):663-75. doi: 10.1083/jcb.201311050.

41.

Informatics for molecular biologists.

Sadreyev RI.

Curr Protoc Mol Biol. 2014 Apr 14;106:19.0.1-2. doi: 10.1002/0471142727.mb1900s106. Review. No abstract available.

PMID:
24733239
42.

Bimodal quantitative relationships between histone modifications for X-linked and autosomal loci.

Sadreyev RI, Yildirim E, Pinter SF, Lee JT.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6949-54. doi: 10.1073/pnas.1216449110. Epub 2013 Apr 5.

43.

Xist RNA is a potent suppressor of hematologic cancer in mice.

Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT.

Cell. 2013 Feb 14;152(4):727-42. doi: 10.1016/j.cell.2013.01.034.

44.

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT.

Genome Res. 2012 Oct;22(10):1864-76. doi: 10.1101/gr.133751.111. Epub 2012 Sep 4.

45.

X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription.

Yildirim E, Sadreyev RI, Pinter SF, Lee JT.

Nat Struct Mol Biol. 2011 Dec 4;19(1):56-61. doi: 10.1038/nsmb.2195.

46.

A boundary element between Tsix and Xist binds the chromatin insulator Ctcf and contributes to initiation of X-chromosome inactivation.

Spencer RJ, del Rosario BC, Pinter SF, Lessing D, Sadreyev RI, Lee JT.

Genetics. 2011 Oct;189(2):441-54. doi: 10.1534/genetics.111.132662. Epub 2011 Aug 11.

47.

Analysis of CASP8 targets, predictions and assessment methods.

Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim BH, Grishin NV.

Database (Oxford). 2009;2009:bap003. Epub 2009 Apr 14.

48.

Considering scores between unrelated proteins in the search database improves profile comparison.

Sadreyev RI, Wang Y, Grishin NV.

BMC Bioinformatics. 2009 Dec 4;10:399. doi: 10.1186/1471-2105-10-399.

49.

Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

Sadreyev RI, Feramisco JD, Tsao H, Grishin NV.

Bioinformatics. 2009 Nov 15;25(22):2891-6. doi: 10.1093/bioinformatics/btp538. Epub 2009 Sep 10.

50.

Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database.

Feramisco JD, Sadreyev RI, Murray ML, Grishin NV, Tsao H.

J Invest Dermatol. 2009 Nov;129(11):2628-36. doi: 10.1038/jid.2009.108. Epub 2009 Jun 18. Erratum in: J Invest Dermatol. 2010 Mar;130(3):909-10.

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