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Items: 1 to 50 of 253

1.

Electronic acute medical take - small measures to improve transparency, management, flow and efficiency; a model for the future hospital.

Lux D, Darnell R, Kee K, Burke C.

Future Healthc J. 2019 Jun;6(Suppl 2):63. doi: 10.7861/futurehosp.6-2s-s63. No abstract available.

2.

Germline NPM1 mutations lead to altered rRNA 2'-O-methylation and cause dyskeratosis congenita.

Nachmani D, Bothmer AH, Grisendi S, Mele A, Bothmer D, Lee JD, Monteleone E, Cheng K, Zhang Y, Bester AC, Guzzetti A, Mitchell CA, Mendez LM, Pozdnyakova O, Sportoletti P, Martelli MP, Vulliamy TJ, Safra M, Schwartz S, Luzzatto L, Bluteau O, Soulier J, Darnell RB, Falini B, Dokal I, Ito K, Clohessy JG, Pandolfi PP.

Nat Genet. 2019 Sep 30. doi: 10.1038/s41588-019-0502-z. [Epub ahead of print]

PMID:
31570891
3.

Identification of targetable BRAF ΔN486_P490 variant by whole genome sequencing leading to dabrafenib-induced remission of a BRAF-mutant pancreatic adenocarcinoma.

Wrzeszczynski KO, Rahman S, Frank MO, Arora K, Shah M, Geiger H, Felice V, Manaa D, Dikoglu E, Khaira D, Chimpiri AR, Michelini VV, Jobanputra V, Darnell RB, Powers S, Choi M.

Cold Spring Harb Mol Case Stud. 2019 Sep 13. pii: mcs.a004424. doi: 10.1101/mcs.a004424. [Epub ahead of print]

4.

A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP β-CTFs, Not Aβ.

Kwart D, Gregg A, Scheckel C, Murphy E, Paquet D, Duffield M, Fak J, Olsen O, Darnell R, Tessier-Lavigne M.

Neuron. 2019 Aug 12. pii: S0896-6273(19)30636-1. doi: 10.1016/j.neuron.2019.07.010. [Epub ahead of print]

PMID:
31416668
5.

Black Sigatoka in bananas: Ecoclimatic suitability and disease pressure assessments.

Yonow T, Ramirez-Villegas J, Abadie C, Darnell RE, Ota N, Kriticos DJ.

PLoS One. 2019 Aug 14;14(8):e0220601. doi: 10.1371/journal.pone.0220601. eCollection 2019.

6.

Correction to: Sequencing and curation strategies for identifying candidate glioblastoma treatments.

Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang X, Vacic V, Bergmann EA, Moore Vogel JL, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB.

BMC Med Genomics. 2019 Aug 2;12(1):114. doi: 10.1186/s12920-019-0563-y.

7.

AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke.

Kobayashi M, Benakis C, Anderson C, Moore MJ, Poon C, Uekawa K, Dyke JP, Fak JJ, Mele A, Park CY, Zhou P, Anrather J, Iadecola C, Darnell RB.

Cell Rep. 2019 Jul 23;28(4):979-991.e6. doi: 10.1016/j.celrep.2019.06.075.

8.

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.

Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG.

Nat Genet. 2019 Jun;51(6):973-980. doi: 10.1038/s41588-019-0420-0. Epub 2019 May 27.

PMID:
31133750
9.

Genomewide Profiling of the Enterococcus faecalis Transcriptional Response to Teixobactin Reveals CroRS as an Essential Regulator of Antimicrobial Tolerance.

Darnell RL, Knottenbelt MK, Todd Rose FO, Monk IR, Stinear TP, Cook GM.

mSphere. 2019 May 8;4(3). pii: e00228-19. doi: 10.1128/mSphere.00228-19.

10.

Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand.

Rushton-Green R, Darnell RL, Taiaroa G, Carter GP, Cook GM, Morgan XC.

Appl Environ Microbiol. 2019 Jun 17;85(13). pii: e00137-19. doi: 10.1128/AEM.00137-19. Print 2019 Jul 1.

11.

Sequencing and curation strategies for identifying candidate glioblastoma treatments.

Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang A, Vacic V, Bergmann EA, Vogel JLM, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB.

BMC Med Genomics. 2019 Apr 25;12(1):56. doi: 10.1186/s12920-019-0500-0. Erratum in: BMC Med Genomics. 2019 Aug 2;12(1):114.

12.

Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-Driven Cancer.

Slotkin EK, Diolaiti D, Shukla NN, Dela Cruz FS, Clark JJ, Gundem G, Yellapantula VD, Levine MF, You D, Ma P, Pachhal S, Ibanez Sanchez G, Benayed R, Jungbluth AA, Smyth LM, Mauguen A, Gushterova I, Ding H, Spraggon L, Darnell R, Califano A, Ladanyi M, Papaemmanuil E, Kung AL, Hyman DM, Roberts SS.

Cancer Discov. 2019 May;9(5):605-616. doi: 10.1158/2159-8290.CD-18-0953. Epub 2019 Mar 15.

PMID:
30877085
13.

Functional characterization of BcrR: a one-component transmembrane signal transduction system for bacitracin resistance.

Darnell RL, Nakatani Y, Knottenbelt MK, Gebhard S, Cook GM.

Microbiology. 2019 Apr;165(4):475-487. doi: 10.1099/mic.0.000781. Epub 2019 Feb 19.

PMID:
30777814
14.

Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function.

Saito Y, Yuan Y, Zucker-Scharff I, Fak JJ, Jereb S, Tajima Y, Licatalosi DD, Darnell RB.

Neuron. 2019 Feb 20;101(4):707-720.e5. doi: 10.1016/j.neuron.2018.12.019. Epub 2019 Jan 9.

PMID:
30638744
15.

A recurrent novel MGA-NUTM1 fusion identifies a new subtype of high-grade spindle cell sarcoma.

Diolaiti D, Dela Cruz FS, Gundem G, Bouvier N, Boulad M, Zhang Y, Chou AJ, Dunkel IJ, Sanghvi R, Shah M, Geiger H, Rahman S, Felice V, Wrzeszczynski KO, Darnell RB, Antonescu CR, French CA, Papaemmanuil E, Kung AL, Shukla N.

Cold Spring Harb Mol Case Stud. 2018 Dec 17;4(6). pii: a003194. doi: 10.1101/mcs.a003194. Print 2018 Dec.

16.

Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP).

Darnell JC, Mele A, Hung KYS, Darnell RB.

Cold Spring Harb Protoc. 2018 Dec 3;2018(12). doi: 10.1101/pdb.top097931.

PMID:
30510132
17.

Isolation of the RNA Cross-Linking Immunoprecipitation (CLIP) Tags, 5'-Linker Ligation, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) Amplification, and Sequencing.

Darnell JC, Mele A, Hung KYS, Darnell RB.

Cold Spring Harb Protoc. 2018 Dec 3;2018(12). doi: 10.1101/pdb.prot097972.

PMID:
30510128
18.

3'-Linker Ligation and Size Selection by SDS-PAGE for Cross-Linking Immunoprecipitation (CLIP).

Darnell JC, Mele A, Hung KYS, Darnell RB.

Cold Spring Harb Protoc. 2018 Dec 3;2018(12). doi: 10.1101/pdb.prot097964.

PMID:
30510127
19.

Immunoprecipitation and SDS-PAGE for Cross-Linking Immunoprecipitation (CLIP).

Darnell JC, Mele A, Hung KYS, Darnell RB.

Cold Spring Harb Protoc. 2018 Dec 3;2018(12). doi: 10.1101/pdb.prot097956.

PMID:
30510126
20.

Ultraviolet (UV) Cross-Linking of Live Cells, Lysate Preparation, and RNase Titration for Cross-Linking Immunoprecipitation (CLIP).

Darnell JC, Mele A, Hung KYS, Darnell RB.

Cold Spring Harb Protoc. 2018 Dec 3;2018(12). doi: 10.1101/pdb.prot097949.

PMID:
30510125
21.

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.

22.

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.

23.

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.

24.

Metabolites Identified during Varied Doses of Aspergillus Species in Zea mays Grains, and Their Correlation with Aflatoxin Levels.

Falade TDO, Chrysanthopoulos PK, Hodson MP, Sultanbawa Y, Fletcher M, Darnell R, Korie S, Fox G.

Toxins (Basel). 2018 May 7;10(5). pii: E187. doi: 10.3390/toxins10050187.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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
31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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
38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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

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