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Items: 1 to 50 of 158

1.

Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons.

Yuan Y, Xie S, Darnell JC, Darnell AJ, Saito Y, Phatnani H, Murphy EA, Zhang C, Maniatis T, Darnell RB.

Genome Biol. 2018 Aug 15;19(1):117. doi: 10.1186/s13059-018-1493-2.

2.

The Future of Cross-Linking and Immunoprecipitation (CLIP).

Ule J, Hwang HW, Darnell RB.

Cold Spring Harb Perspect Biol. 2018 Aug 1;10(8). pii: a032243. doi: 10.1101/cshperspect.a032243. Review.

PMID:
30068528
3.

ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity.

Moore MJ, Blachere NE, Fak JJ, Park CY, Sawicka K, Parveen S, Zucker-Scharff I, Moltedo B, Rudensky AY, Darnell RB.

Elife. 2018 May 31;7. pii: e33057. doi: 10.7554/eLife.33057.

4.

Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types.

Jereb S, Hwang HW, Van Otterloo E, Govek EE, Fak JJ, Yuan Y, Hatten ME, Darnell RB.

Elife. 2018 Mar 26;7. pii: e34042. doi: 10.7554/eLife.34042.

5.

Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

Mak ACY, White MJ, Eckalbar WL, Szpiech ZA, Oh SS, Pino-Yanes M, Hu D, Goddard P, Huntsman S, Galanter J, Wu AC, Himes BE, Germer S, Vogel JM, Bunting KL, Eng C, Salazar S, Keys KL, Liberto J, Nuckton TJ, Nguyen TA, Torgerson DG, Kwok PY, Levin AM, Celedón JC, Forno E, Hakonarson H, Sleiman PM, Dahlin A, Tantisira KG, Weiss ST, Serebrisky D, Brigino-Buenaventura E, Farber HJ, Meade K, Lenoir MA, Avila PC, Sen S, Thyne SM, Rodriguez-Cintron W, Winkler CA, Moreno-Estrada A, Sandoval K, Rodriguez-Santana JR, Kumar R, Williams LK, Ahituv N, Ziv E, Seibold MA, Darnell RB, Zaitlen N, Hernandez RD, Burchard EG; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium.

Am J Respir Crit Care Med. 2018 Jun 15;197(12):1552-1564. doi: 10.1164/rccm.201712-2529OC.

PMID:
29509491
6.

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.

Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R.

Nat Commun. 2018 Feb 23;9(1):791. doi: 10.1038/s41467-017-02659-x.

7.

Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data.

Orange DE, Agius P, DiCarlo EF, Robine N, Geiger H, Szymonifka J, McNamara M, Cummings R, Andersen KM, Mirza S, Figgie M, Ivashkiv LB, Pernis AB, Jiang CS, Frank MO, Darnell RB, Lingampali N, Robinson WH, Gravallese E; Accelerating Medicines Partnership in Rheumatoid Arthritis and Lupus Network, Bykerk VP, Goodman SM, Donlin LT.

Arthritis Rheumatol. 2018 May;70(5):690-701. doi: 10.1002/art.40428. Epub 2018 Apr 2.

PMID:
29468833
8.

Elavl3 is essential for the maintenance of Purkinje neuron axons.

Ogawa Y, Kakumoto K, Yoshida T, Kuwako KI, Miyazaki T, Yamaguchi J, Konno A, Hata J, Uchiyama Y, Hirai H, Watanabe M, Darnell RB, Okano H, Okano HJ.

Sci Rep. 2018 Feb 9;8(1):2722. doi: 10.1038/s41598-018-21130-5.

9.

Whole Genome Sequencing-Based Discovery of Structural Variants in Glioblastoma.

Wrzeszczynski KO, Felice V, Shah M, Rahman S, Emde AK, Jobanputra V, O Frank M, Darnell RB.

Methods Mol Biol. 2018;1741:1-29. doi: 10.1007/978-1-4939-7659-1_1.

PMID:
29392687
10.

Pre-mRNA processing includes N6 methylation of adenosine residues that are retained in mRNA exons and the fallacy of "RNA epigenetics".

Darnell RB, Ke S, Darnell JE Jr.

RNA. 2018 Mar;24(3):262-267. doi: 10.1261/rna.065219.117. Epub 2017 Dec 8.

11.

T cells presenting viral antigens or autoantigens induce cytotoxic T cell anergy.

Blachère NE, Orange DE, Gantman EC, Santomasso BD, Couture GC, Ramirez-Montagut T, Fak J, O'Donovan KJ, Ru Z, Parveen S, Frank MO, Moore MJ, Darnell RB.

JCI Insight. 2017 Nov 2;2(21). pii: 96173. doi: 10.1172/jci.insight.96173. [Epub ahead of print]

12.

Genomic Patterns of De Novo Mutation in Simplex Autism.

Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE.

Cell. 2017 Oct 19;171(3):710-722.e12. doi: 10.1016/j.cell.2017.08.047. Epub 2017 Sep 28.

13.

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation.

Hwang HW, Saito Y, Park CY, Blachère NE, Tajima Y, Fak JJ, Zucker-Scharff I, Darnell RB.

Neuron. 2017 Sep 13;95(6):1334-1349.e5. doi: 10.1016/j.neuron.2017.08.024.

PMID:
28910620
14.

Excess Translation of Epigenetic Regulators Contributes to Fragile X Syndrome and Is Alleviated by Brd4 Inhibition.

Korb E, Herre M, Zucker-Scharff I, Gresack J, Allis CD, Darnell RB.

Cell. 2017 Sep 7;170(6):1209-1223.e20. doi: 10.1016/j.cell.2017.07.033. Epub 2017 Aug 17.

15.

Global mapping of miRNA-target interactions in cattle (Bos taurus).

Scheel TKH, Moore MJ, Luna JM, Nishiuchi E, Fak J, Darnell RB, Rice CM.

Sci Rep. 2017 Aug 15;7(1):8190. doi: 10.1038/s41598-017-07880-8.

16.

Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP.

Hwang HW, Darnell RB.

Methods Mol Biol. 2017;1648:79-93. doi: 10.1007/978-1-4939-7204-3_7.

PMID:
28766291
17.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

Neurol Genet. 2017 Jul 11;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug.

18.

Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer.

Luna JM, Barajas JM, Teng KY, Sun HL, Moore MJ, Rice CM, Darnell RB, Ghoshal K.

Mol Cell. 2017 Aug 3;67(3):400-410.e7. doi: 10.1016/j.molcel.2017.06.025. Epub 2017 Jul 20.

19.

m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover.

Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE Jr, Darnell RB.

Genes Dev. 2017 May 15;31(10):990-1006. doi: 10.1101/gad.301036.117.

20.

Immune Escape via a Transient Gene Expression Program Enables Productive Replication of a Latent Pathogen.

Linderman JA, Kobayashi M, Rayannavar V, Fak JJ, Darnell RB, Chao MV, Wilson AC, Mohr I.

Cell Rep. 2017 Jan 31;18(5):1312-1323. doi: 10.1016/j.celrep.2017.01.017.

21.

Successful Targeted Therapy of Refractory Pediatric ETV6-NTRK3 Fusion-Positive Secretory Breast Carcinoma.

Shukla N, Roberts SS, Baki MO, Mushtaq Q, Goss PE, Park BH, Gundem G, Tian K, Geiger H, Redfield K, Behr G, Benayed R, Zehir A, Hechtman JF, Darnell RB, Papaemmanuil E, Ladanyi M, Ku N, Kung AL, Baselga J, Drilon A, Hyman DM.

JCO Precis Oncol. 2017;2017. doi: 10.1200/PO.17.00034. Epub 2017 Aug 18. No abstract available.

22.

Reply.

Roberts WK, Blachère NE, Frank MO, Dousmanis A, Ransohoff RM, Darnell RB.

Ann Neurol. 2016 Nov;80(5):793-794. doi: 10.1002/ana.24784. Epub 2016 Oct 19. No abstract available.

PMID:
27669487
23.

Differential burden of rare protein truncating variants in Alzheimer's disease patients compared to centenarians.

Freudenberg-Hua Y, Li W, Abhyankar A, Vacic V, Cortes V, Ben-Avraham D, Koppel J, Greenwald B, Germer S; T2D-GENES Consortium, Darnell RB, Barzilai N, Freudenberg J, Atzmon G, Davies P.

Hum Mol Genet. 2016 Jul 15;25(14):3096-3105. Epub 2016 Jun 3.

24.

Proteolytic degradation and potential role of onconeural protein cdr2 in neurodegeneration.

Hwang JY, Lee J, Oh CK, Kang HW, Hwang IY, Um JW, Park HC, Kim S, Shin JH, Park WY, Darnell RB, Um HD, Chung KC, Kim K, Oh YJ.

Cell Death Dis. 2016 Jun 2;7(6):e2240. doi: 10.1038/cddis.2016.151.

25.

NOVA regulates Dcc alternative splicing during neuronal migration and axon guidance in the spinal cord.

Leggere JC, Saito Y, Darnell RB, Tessier-Lavigne M, Junge HJ, Chen Z.

Elife. 2016 May 25;5. pii: e14264. doi: 10.7554/eLife.14264.

26.

NOVA2-mediated RNA regulation is required for axonal pathfinding during development.

Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB.

Elife. 2016 May 25;5. pii: e14371. doi: 10.7554/eLife.14371.

27.

PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage.

Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB.

Cell Rep. 2016 Apr 12;15(2):423-35. doi: 10.1016/j.celrep.2016.03.023. Epub 2016 Mar 31.

28.

A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration.

Scheel TK, Luna JM, Liniger M, Nishiuchi E, Rozen-Gagnon K, Shlomai A, Auray G, Gerber M, Fak J, Keller I, Bruggmann R, Darnell RB, Ruggli N, Rice CM.

Cell Host Microbe. 2016 Mar 9;19(3):409-23. doi: 10.1016/j.chom.2016.02.007.

29.

Erratum: Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.

Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB.

Nat Protoc. 2016 Mar;11(3):616. doi: 10.1038/nprot0316-616c. Epub 2016 Feb 25. No abstract available.

PMID:
26914319
30.

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain.

Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma'ayan A, Buxbaum JD, Darnell RB.

Elife. 2016 Feb 19;5. pii: e10421. doi: 10.7554/eLife.10421.

31.

miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity.

Moore MJ, Scheel TK, Luna JM, Park CY, Fak JJ, Nishiuchi E, Rice CM, Darnell RB.

Nat Commun. 2015 Nov 25;6:8864. doi: 10.1038/ncomms9864.

32.

A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation.

Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kusśnierczyk A, Klungland A, Darnell JE Jr, Darnell RB.

Genes Dev. 2015 Oct 1;29(19):2037-53. doi: 10.1101/gad.269415.115. Epub 2015 Sep 24.

33.

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP.

Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5391-400. doi: 10.1073/pnas.1515737112. Epub 2015 Sep 15.

34.

BET protein Brd4 activates transcription in neurons and BET inhibitor Jq1 blocks memory in mice.

Korb E, Herre M, Zucker-Scharff I, Darnell RB, Allis CD.

Nat Neurosci. 2015 Oct;18(10):1464-73. doi: 10.1038/nn.4095. Epub 2015 Aug 24.

35.

A destructive feedback loop mediated by CXCL10 in central nervous system inflammatory disease.

Roberts WK, Blachère NE, Frank MO, Dousmanis A, Ransohoff RM, Darnell RB.

Ann Neurol. 2015 Oct;78(4):619-29. doi: 10.1002/ana.24494. Epub 2015 Aug 21.

36.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A.

Nat Methods. 2015 Aug;12(8):780-6. doi: 10.1038/nmeth.3454. Epub 2015 Jun 29.

37.

Hepatitis C virus RNA functionally sequesters miR-122.

Luna JM, Scheel TK, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, Jacobson IM, Rice CM, Darnell RB.

Cell. 2015 Mar 12;160(6):1099-110. doi: 10.1016/j.cell.2015.02.025.

38.

Structural insights into mis-regulation of protein kinase A in human tumors.

Cheung J, Ginter C, Cassidy M, Franklin MC, Rudolph MJ, Robine N, Darnell RB, Hendrickson WA.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1374-9. doi: 10.1073/pnas.1424206112. Epub 2015 Jan 20.

39.

Microexons--tiny but mighty.

Scheckel C, Darnell RB.

EMBO J. 2015 Feb 3;34(3):273-4. doi: 10.15252/embj.201490651. Epub 2014 Dec 22. No abstract available.

40.

Dendritic cell vaccines containing lymphocytes produce improved immunogenicity in patients with cancer.

Frank MO, Kaufman J, Parveen S, Blachère NE, Orange DE, Darnell RB.

J Transl Med. 2014 Dec 5;12:338. doi: 10.1186/s12967-014-0338-3.

41.

Disease variants in genomes of 44 centenarians.

Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde AK, Ben-Avraham D, Barzilai N, Oschwald D, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P.

Mol Genet Genomic Med. 2014 Sep;2(5):438-50. doi: 10.1002/mgg3.86. Epub 2014 Jun 15.

42.

T cells targeting a neuronal paraneoplastic antigen mediate tumor rejection and trigger CNS autoimmunity with humoral activation.

Blachère NE, Orange DE, Santomasso BD, Doerner J, Foo PK, Herre M, Fak J, Monette S, Gantman EC, Frank MO, Darnell RB.

Eur J Immunol. 2014 Nov;44(11):3240-51. doi: 10.1002/eji.201444624.

43.

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer.

Vanharanta S, Marney CB, Shu W, Valiente M, Zou Y, Mele A, Darnell RB, Massagué J.

Elife. 2014 Jun 4;3. doi: 10.7554/eLife.02734.

44.

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism.

Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C.

Cell Rep. 2014 Mar 27;6(6):1139-1152. doi: 10.1016/j.celrep.2014.02.005. Epub 2014 Mar 6.

45.

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.

Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB.

Nat Protoc. 2014 Feb;9(2):263-93. doi: 10.1038/nprot.2014.012. Epub 2014 Jan 9. Erratum in: Nat Protoc. 2016 Mar;11(3):616.

46.

Turkey must end violent response to protests.

Altindis E, Alpar MA, Aksay E, Beckwith J, Bökel C, Curl RF, Darnell RB, Elledge SJ, Erman B, Frahm J, Goff SP, Greengard P, Hoffmann R, Ilhan B, Kaslin J, Lipkin SM, Poulopoulou C, Raz E, Rubin MA, Salturk M, Schrock RR, Trautmann A, Unutmaz D, Weinstein H, Kizil C.

Science. 2013 Jul 19;341(6143):236. doi: 10.1126/science.341.6143.236-a. No abstract available. Erratum in: Science. 2013 Aug 30;341(6149):959.

PMID:
23869001
47.

RNA protein interaction in neurons.

Darnell RB.

Annu Rev Neurosci. 2013 Jul 8;36:243-70. doi: 10.1146/annurev-neuro-062912-114322. Epub 2013 May 20. Review.

48.

Prediction of clustered RNA-binding protein motif sites in the mammalian genome.

Zhang C, Lee KY, Swanson MS, Darnell RB.

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.

49.

Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice.

Poulos MG, Batra R, Li M, Yuan Y, Zhang C, Darnell RB, Swanson MS.

Hum Mol Genet. 2013 Sep 1;22(17):3547-58. doi: 10.1093/hmg/ddt209. Epub 2013 May 8.

50.

Ri/Nova gene-associated paraneoplastic subacute motor neuronopathy.

Younger DS, Graber J, Hayakawa-Yano Y, Parveen S, Frank M, Darnell RB.

Muscle Nerve. 2013 Apr;47(4):617-8. doi: 10.1002/mus.23783. Epub 2013 Mar 5. No abstract available.

PMID:
23463350

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