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Items: 34

1.

Tools for annotation and comparison of structural variation.

Sedlazeck FJ, Dhroso A, Bodian DL, Paschall J, Hermes F, Zook JM.

F1000Res. 2017 Oct 3;6:1795. doi: 10.12688/f1000research.12516.1. eCollection 2017.

2.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

3.

International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases.

Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M Jr, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H.

Am J Hum Genet. 2017 May 4;100(5):695-705. doi: 10.1016/j.ajhg.2017.04.003.

4.

Open Targets: a platform for therapeutic target identification and validation.

Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.

Nucleic Acids Res. 2017 Jan 4;45(D1):D985-D994. doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29.

5.

Highly sensitive and ultrafast read mapping for RNA-seq analysis.

Medina I, Tárraga J, Martínez H, Barrachina S, Castillo MI, Paschall J, Salavert-Torres J, Blanquer-Espert I, Hernández-García V, Quintana-Ortí ES, Dopazo J.

DNA Res. 2016 Apr;23(2):93-100. doi: 10.1093/dnares/dsv039. Epub 2016 Jan 5.

6.

The Matchmaker Exchange: a platform for rare disease gene discovery.

Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL.

Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858.

7.

The European Genome-phenome Archive of human data consented for biomedical research.

Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P.

Nat Genet. 2015 Jul;47(7):692-5. doi: 10.1038/ng.3312. No abstract available.

8.

Truncation of the flash-lag effect by a fixed spatial landmark.

Paschall JD, Mazurek ME.

J Opt Soc Am A Opt Image Sci Vis. 2014 Sep 1;31(9):1993-2001. doi: 10.1364/JOSAA.31.001993.

PMID:
25401439
9.

RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research.

Thompson R, Johnston L, Taruscio D, Monaco L, Béroud C, Gut IG, Hansson MG, 't Hoen PB, Patrinos GP, Dawkins H, Ensini M, Zatloukal K, Koubi D, Heslop E, Paschall JE, Posada M, Robinson PN, Bushby K, Lochmüller H.

J Gen Intern Med. 2014 Aug;29 Suppl 3:S780-7. doi: 10.1007/s11606-014-2908-8. Review.

10.

Paraproteinemic maculopathy.

Mansour AM, Arevalo JF, Badal J, Moorthy RS, Shah GK, Zegarra H, Pulido JS, Charbaji A, Amselem L, Lavaque AJ, Casella A, Ahmad B, Paschall JG, Caimi A, Staurenghi G.

Ophthalmology. 2014 Oct;121(10):1925-32. doi: 10.1016/j.ophtha.2014.04.007. Epub 2014 Jun 18.

PMID:
24950591
11.

DbVar and DGVa: public archives for genomic structural variation.

Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, Chen C, Maguire M, Corbett M, Zhou G, Paschall J, Ananiev V, Flicek P, Church DM.

Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. doi: 10.1093/nar/gks1213. Epub 2012 Nov 27.

12.

Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality.

Zuvich RL, Armstrong LL, Bielinski SJ, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes MG, Jarvik GP, Jiang L, Kullo IJ, Li R, Ling H, Manolio TA, Matsumoto ME, McCarty CA, McDavid AN, Mirel DB, Olson LM, Paschall JE, Pugh EW, Rasmussen LV, Rasmussen-Torvik LJ, Turner SD, Wilke RA, Ritchie MD.

Genet Epidemiol. 2011 Dec;35(8):887-98. doi: 10.1002/gepi.20639.

13.

Assessing and managing risk when sharing aggregate genetic variant data.

Craig DW, Goor RM, Wang Z, Paschall J, Ostell J, Feolo M, Sherry ST, Manolio TA.

Nat Rev Genet. 2011 Sep 16;12(10):730-6. doi: 10.1038/nrg3067. Review. Erratum in: Nat Rev Genet. 2011 Nov;12(11):801.

14.

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, Shetty S, Rossi MR, Rudd MK, South ST, Brothman AR, Sanger WG, Iyer RK, Crolla JA, Thorland EC, Aradhya S, Ledbetter DH, Martin CL.

Genet Med. 2011 Sep;13(9):777-84. doi: 10.1097/GIM.0b013e31822c79f9.

15.

Acromioclavicular joint synovial chondromatosis.

Molloy JM, Paschall JC, Bui-Mansfield LT.

J Orthop Sports Phys Ther. 2011 Feb;41(2):118. doi: 10.2519/jospt.2011.0403. Epub 2011 Jan 31. No abstract available.

PMID:
21285526
16.

Quality control procedures for genome-wide association studies.

Turner S, Armstrong LL, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, de Andrade M, Doheny KF, Haines JL, Hayes G, Jarvik G, Jiang L, Kullo IJ, Li R, Ling H, Manolio TA, Matsumoto M, McCarty CA, McDavid AN, Mirel DB, Paschall JE, Pugh EW, Rasmussen LV, Wilke RA, Zuvich RL, Ritchie MD.

Curr Protoc Hum Genet. 2011 Jan;Chapter 1:Unit1.19. doi: 10.1002/0471142905.hg0119s68.

17.

Public data archives for genomic structural variation.

Church DM, Lappalainen I, Sneddon TP, Hinton J, Maguire M, Lopez J, Garner J, Paschall J, DiCuccio M, Yaschenko E, Scherer SW, Feuk L, Flicek P.

Nat Genet. 2010 Oct;42(10):813-4. doi: 10.1038/ng1010-813. No abstract available.

18.

Quality control and quality assurance in genotypic data for genome-wide association studies.

Laurie CC, Doheny KF, Mirel DB, Pugh EW, Bierut LJ, Bhangale T, Boehm F, Caporaso NE, Cornelis MC, Edenberg HJ, Gabriel SB, Harris EL, Hu FB, Jacobs KB, Kraft P, Landi MT, Lumley T, Manolio TA, McHugh C, Painter I, Paschall J, Rice JP, Rice KM, Zheng X, Weir BS; GENEVA Investigators.

Genet Epidemiol. 2010 Sep;34(6):591-602. doi: 10.1002/gepi.20516.

19.

Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease.

Hamza TH, Zabetian CP, Tenesa A, Laederach A, Montimurro J, Yearout D, Kay DM, Doheny KF, Paschall J, Pugh E, Kusel VI, Collura R, Roberts J, Griffith A, Samii A, Scott WK, Nutt J, Factor SA, Payami H.

Nat Genet. 2010 Sep;42(9):781-5. doi: 10.1038/ng.642. Epub 2010 Aug 15.

20.

Genome-wide association study of bone mineral density in premenopausal European-American women and replication in African-American women.

Koller DL, Ichikawa S, Lai D, Padgett LR, Doheny KF, Pugh E, Paschall J, Hui SL, Edenberg HJ, Xuei X, Peacock M, Econs MJ, Foroud T.

J Clin Endocrinol Metab. 2010 Apr;95(4):1802-9. doi: 10.1210/jc.2009-1903. Epub 2010 Feb 17.

21.

The Gene, Environment Association Studies consortium (GENEVA): maximizing the knowledge obtained from GWAS by collaboration across studies of multiple conditions.

Cornelis MC, Agrawal A, Cole JW, Hansel NN, Barnes KC, Beaty TH, Bennett SN, Bierut LJ, Boerwinkle E, Doheny KF, Feenstra B, Feingold E, Fornage M, Haiman CA, Harris EL, Hayes MG, Heit JA, Hu FB, Kang JH, Laurie CC, Ling H, Manolio TA, Marazita ML, Mathias RA, Mirel DB, Paschall J, Pasquale LR, Pugh EW, Rice JP, Udren J, van Dam RM, Wang X, Wiggs JL, Williams K, Yu K; GENEVA Consortium.

Genet Epidemiol. 2010 May;34(4):364-72. doi: 10.1002/gepi.20492.

22.

Genome-wide association study of bipolar disorder in European American and African American individuals.

Smith EN, Bloss CS, Badner JA, Barrett T, Belmonte PL, Berrettini W, Byerley W, Coryell W, Craig D, Edenberg HJ, Eskin E, Foroud T, Gershon E, Greenwood TA, Hipolito M, Koller DL, Lawson WB, Liu C, Lohoff F, McInnis MG, McMahon FJ, Mirel DB, Murray SS, Nievergelt C, Nurnberger J, Nwulia EA, Paschall J, Potash JB, Rice J, Schulze TG, Scheftner W, Panganiban C, Zaitlen N, Zandi PP, Zöllner S, Schork NJ, Kelsoe JR.

Mol Psychiatry. 2009 Aug;14(8):755-63. doi: 10.1038/mp.2009.43. Epub 2009 Jun 2.

23.
24.

CrossSearch, a user-friendly search engine for detecting chemically cross-linked peptides in conjugated proteins.

Nadeau OW, Wyckoff GJ, Paschall JE, Artigues A, Sage J, Villar MT, Carlson GM.

Mol Cell Proteomics. 2008 Apr;7(4):739-49. doi: 10.1074/mcp.M800020-MCP200. Epub 2008 Feb 16.

25.

The NCBI dbGaP database of genotypes and phenotypes.

Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L, Popova N, Pretel S, Ziyabari L, Lee M, Shao Y, Wang ZY, Sirotkin K, Ward M, Kholodov M, Zbicz K, Beck J, Kimelman M, Shevelev S, Preuss D, Yaschenko E, Graeff A, Ostell J, Sherry ST.

Nat Genet. 2007 Oct;39(10):1181-6.

26.

Evidence for the location of the allosteric activation switch in the multisubunit phosphorylase kinase complex from mass spectrometric identification of chemically crosslinked peptides.

Nadeau OW, Anderson DW, Yang Q, Artigues A, Paschall JE, Wyckoff GJ, McClintock JL, Carlson GM.

J Mol Biol. 2007 Feb 2;365(5):1429-45. Epub 2006 Oct 21.

27.

SPEED: a molecular-evolution-based database of mammalian orthologous groups.

Vallender EJ, Paschall JE, Malcom CM, Lahn BT, Wyckoff GJ.

Bioinformatics. 2006 Nov 15;22(22):2835-7. Epub 2006 Sep 11.

PMID:
16966361
28.

FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.

Paschall JE, Oleksiak MF, VanWye JD, Roach JL, Whitehead JA, Wyckoff GJ, Kolell KJ, Crawford DL.

BMC Genomics. 2004 Dec 20;5(1):96.

29.

Hemodynamic support in fluid-refractory pediatric septic shock.

Ceneviva G, Paschall JA, Maffei F, Carcillo JA.

Pediatrics. 1998 Aug;102(2):e19.

PMID:
9685464
30.

Overview of a general orthopedic practice.

Paschall J Jr.

Orthopedics. 1998 May;21(5):573-6; discussion 576-80.

PMID:
9606697
31.

Electromyographic activity of selected shoulder muscles in commonly used therapeutic exercises.

Ballantyne BT, O'Hare SJ, Paschall JL, Pavia-Smith MM, Pitz AM, Gillon JF, Soderberg GL.

Phys Ther. 1993 Oct;73(10):668-77; discussion 677-82.

PMID:
8378423
32.

Awake porcine model of intraperitoneal sepsis and altered oxygen utilization.

Hoban LD, Paschall JA, Eckstein J, Reusch D, Hermiller J, Rowe B, Nevola JJ, Carcillo JA.

Circ Shock. 1991 Jun;34(2):252-62.

PMID:
1934326
33.

Amrinone during porcine intraperitoneal sepsis.

Hermiller JB, Mehegan JP, Nadkarni VM, Paschall JA, Nevola JJ, Fletcher MA, Williams TJ.

Circ Shock. 1991 Jun;34(2):247-51.

PMID:
1934325
34.

Old united and ununited fractures of the patella.

PASCHALL J Jr, GHORMLEY RK, DOCKERTY MB.

Surgery. 1949 Nov;26(5):777-86, illust. No abstract available.

PMID:
15392739

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