Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 95

1.

Exome-Based Rare-Variant Analyses in CKD.

Cameron-Christie S, Wolock CJ, Groopman E, Petrovski S, Kamalakaran S, Povysil G, Vitsios D, Zhang M, Fleckner J, March RE, Gelfman S, Marasa M, Li Y, Sanna-Cherchi S, Kiryluk K, Allen AS, Fellström BC, Haefliger C, Platt A, Goldstein DB, Gharavi AG.

J Am Soc Nephrol. 2019 Jun;30(6):1109-1122. doi: 10.1681/ASN.2018090909. Epub 2019 May 13.

PMID:
31085678
2.

Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance.

Hayeck TJ, Stong N, Wolock CJ, Copeland B, Kamalakaran S, Goldstein DB, Allen AS.

Am J Hum Genet. 2019 Feb 7;104(2):299-309. doi: 10.1016/j.ajhg.2018.12.020. Epub 2019 Jan 24.

PMID:
30686509
3.

Family-based association tests for rare variants with censored traits.

Qi W, Allen AS, Li YJ.

PLoS One. 2019 Jan 25;14(1):e0210870. doi: 10.1371/journal.pone.0210870. eCollection 2019.

4.

Human genome-wide measurement of drug-responsive regulatory activity.

Johnson GD, Barrera A, McDowell IC, D'Ippolito AM, Majoros WH, Vockley CM, Wang X, Allen AS, Reddy TE.

Nat Commun. 2018 Dec 21;9(1):5317. doi: 10.1038/s41467-018-07607-x.

5.

Loss of tubulin deglutamylase CCP1 causes infantile-onset neurodegeneration.

Shashi V, Magiera MM, Klein D, Zaki M, Schoch K, Rudnik-Schöneborn S, Norman A, Lopes Abath Neto O, Dusl M, Yuan X, Bartesaghi L, De Marco P, Alfares AA, Marom R, Arold ST, Guzmán-Vega FJ, Pena LD, Smith EC, Steinlin M, Babiker MO, Mohassel P, Foley AR, Donkervoort S, Kaur R, Ghosh PS, Stanley V, Musaev D, Nava C, Mignot C, Keren B, Scala M, Tassano E, Picco P, Doneda P, Fiorillo C, Issa MY, Alassiri A, Alahmad A, Gerard A, Liu P, Yang Y, Ertl-Wagner B, Kranz PG, Wentzensen IM, Stucka R, Stong N, Allen AS, Goldstein DB; Undiagnosed Diseases Network, Schoser B, Rösler KM, Alfadhel M, Capra V, Chrast R, Strom TM, Kamsteeg EJ, Bönnemann CG, Gleeson JG, Martini R, Janke C, Senderek J.

EMBO J. 2018 Dec 3;37(23). pii: e100540. doi: 10.15252/embj.2018100540. Epub 2018 Nov 12.

PMID:
30420557
6.

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.

Gelfman S, Wang Q, Lu YF, Hall D, Bostick CD, Dhindsa R, Halvorsen M, McSweeney KM, Cotterill E, Edinburgh T, Beaumont MA, Frankel WN, Petrovski S, Allen AS, Boland MJ, Goldstein DB, Eglen SJ.

PLoS Comput Biol. 2018 Oct 1;14(10):e1006506. doi: 10.1371/journal.pcbi.1006506. eCollection 2018 Oct.

7.

De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.

Heinzen EL, O'Neill AC, Zhu X, Allen AS, Bahlo M, Chelly J, Chen MH, Dobyns WB, Freytag S, Guerrini R, Leventer RJ, Poduri A, Robertson SP, Walsh CA, Zhang M; Epi4K Consortium; Epilepsy Phenome/Genome Project.

PLoS Genet. 2018 May 8;14(5):e1007281. doi: 10.1371/journal.pgen.1007281. eCollection 2018 May.

8.

Somatic SLC35A2 variants in the brain are associated with intractable neocortical epilepsy.

Winawer MR, Griffin NG, Samanamud J, Baugh EH, Rathakrishnan D, Ramalingam S, Zagzag D, Schevon CA, Dugan P, Hegde M, Sheth SA, McKhann GM, Doyle WK, Grant GA, Porter BE, Mikati MA, Muh CR, Malone CD, Bergin AMR, Peters JM, McBrian DK, Pack AM, Akman CI, LaCoursiere CM, Keever KM, Madsen JR, Yang E, Lidov HGW, Shain C, Allen AS, Canoll PD, Crino PB, Poduri AH, Heinzen EL.

Ann Neurol. 2018 Jun;83(6):1133-1146. doi: 10.1002/ana.25243. Epub 2018 May 16.

9.

The underwater acoustic environment at SGaan Kinghlas-Bowie Seamount Marine Protected Area: Characterizing vessel traffic and associated noise using satellite AIS and acoustic datasets.

Allen AS, Yurk H, Vagle S, Pilkington J, Canessa R.

Mar Pollut Bull. 2018 Mar;128:82-88. doi: 10.1016/j.marpolbul.2018.01.014. Epub 2018 Jan 12.

PMID:
29571416
10.

Genome-wide association study (GWAS) of human host factors influencing viral severity of herpes simplex virus type 2 (HSV-2).

Kleinstein SE, Shea PR, Allen AS, Koelle DM, Wald A, Goldstein DB.

Genes Immun. 2019 Feb;20(2):112-120. doi: 10.1038/s41435-018-0013-4. Epub 2018 Feb 28.

11.

Correction: Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.

Gussow AB, Copeland BR, Dhindsa RS, Wang Q, Petrovski S, Majoros WH, Allen AS, Goldstein DB.

PLoS One. 2018 Jan 11;13(1):e0191298. doi: 10.1371/journal.pone.0191298. eCollection 2018.

12.

A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations.

Zhu X, Padmanabhan R, Copeland B, Bridgers J, Ren Z, Kamalakaran S, O'Driscoll-Collins A, Berkovic SF, Scheffer IE, Poduri A, Mei D, Guerrini R, Lowenstein DH, Allen AS, Heinzen EL, Goldstein DB.

PLoS Genet. 2017 Nov 29;13(11):e1007104. doi: 10.1371/journal.pgen.1007104. eCollection 2017 Nov.

13.

Mapping eQTL by leveraging multiple tissues and DNA methylation.

Acharya CR, Owzar K, Allen AS.

BMC Bioinformatics. 2017 Oct 18;18(1):455. doi: 10.1186/s12859-017-1856-9.

14.
15.

Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly.

Griffin NG, Cronin KD, Walley NM, Hulette CM, Grant GA, Mikati MA, LaBreche HG, Rehder CW, Allen AS, Crino PB, Heinzen EL.

Cold Spring Harb Mol Case Stud. 2017 Sep 1;3(5). pii: a001735. doi: 10.1101/mcs.a001735. Print 2017 Sep.

16.

Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics.

Gussow AB, Copeland BR, Dhindsa RS, Wang Q, Petrovski S, Majoros WH, Allen AS, Goldstein DB.

PLoS One. 2017 Aug 10;12(8):e0181604. doi: 10.1371/journal.pone.0181604. eCollection 2017. Erratum in: PLoS One. 2018 Jan 11;13(1):e0191298.

17.

Chemoreception drives plastic consumption in a hard coral.

Allen AS, Seymour AC, Rittschof D.

Mar Pollut Bull. 2017 Nov 15;124(1):198-205. doi: 10.1016/j.marpolbul.2017.07.030. Epub 2017 Jul 22.

PMID:
28743368
18.

Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.

Zhao J, Li D, Seo J, Allen AS, Gordân R.

Res Comput Mol Biol. 2017 May;10229:336-352. doi: 10.1007/978-3-319-56970-3_21. Epub 2017 Apr 12.

19.

Transversions have larger regulatory effects than transitions.

Guo C, McDowell IC, Nodzenski M, Scholtens DM, Allen AS, Lowe WL, Reddy TE.

BMC Genomics. 2017 May 19;18(1):394. doi: 10.1186/s12864-017-3785-4.

20.

Evaluating genetic susceptibility to Staphylococcus aureus bacteremia in African Americans using admixture mapping.

Cyr DD, Allen AS, Du GJ, Ruffin F, Adams C, Thaden JT, Maskarinec SA, Souli M, Guo S, Dykxhoorn DM, Scott WK, Fowler VG Jr.

Genes Immun. 2017 Mar;18(2):95-99. doi: 10.1038/gene.2017.6. Epub 2017 Mar 23.

21.

An Exome Sequencing Study to Assess the Role of Rare Genetic Variation in Pulmonary Fibrosis.

Petrovski S, Todd JL, Durheim MT, Wang Q, Chien JW, Kelly FL, Frankel C, Mebane CM, Ren Z, Bridgers J, Urban TJ, Malone CD, Finlen Copeland A, Brinkley C, Allen AS, O'Riordan T, McHutchison JG, Palmer SM, Goldstein DB.

Am J Respir Crit Care Med. 2017 Jul 1;196(1):82-93. doi: 10.1164/rccm.201610-2088OC.

22.

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

Majoros WH, Campbell MS, Holt C, DeNardo EK, Ware D, Allen AS, Yandell M, Reddy TE.

Bioinformatics. 2017 May 15;33(10):1437-1446. doi: 10.1093/bioinformatics/btw799.

23.

Leveraging population information in family-based rare variant association analyses of quantitative traits.

Jiang Y, Ji Y, Sibley AB, Li YJ, Allen AS.

Genet Epidemiol. 2017 Feb;41(2):98-107. doi: 10.1002/gepi.22022. Epub 2016 Dec 5.

PMID:
27917519
24.

Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy.

Hildebrand MS, Griffin NG, Damiano JA, Cops EJ, Burgess R, Ozturk E, Jones NC, Leventer RJ, Freeman JL, Harvey AS, Sadleir LG, Scheffer IE, Major H, Darbro BW, Allen AS, Goldstein DB, Kerrigan JF, Berkovic SF, Heinzen EL.

Am J Hum Genet. 2016 Aug 4;99(2):423-9. doi: 10.1016/j.ajhg.2016.05.031. Epub 2016 Jul 21.

25.

An intraorganizational model for developing and spreading quality improvement innovations.

Kellogg KC, Gainer LA, Allen AS, OʼSullivan T, Singer SJ.

Health Care Manage Rev. 2017 Oct/Dec;42(4):292-302. doi: 10.1097/HMR.0000000000000122.

26.

Exploiting expression patterns across multiple tissues to map expression quantitative trait loci.

Acharya CR, McCarthy JM, Owzar K, Allen AS.

BMC Bioinformatics. 2016 Jun 24;17:257. doi: 10.1186/s12859-016-1123-5.

27.

Testing Rare-Variant Association without Calling Genotypes Allows for Systematic Differences in Sequencing between Cases and Controls.

Hu YJ, Liao P, Johnston HR, Allen AS, Satten GA.

PLoS Genet. 2016 May 6;12(5):e1006040. doi: 10.1371/journal.pgen.1006040. eCollection 2016 May.

28.

The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes.

Gussow AB, Petrovski S, Wang Q, Allen AS, Goldstein DB.

Genome Biol. 2016 Jan 18;17:9. doi: 10.1186/s13059-016-0869-4.

29.

Polymorphisms in HLA Class II Genes Are Associated With Susceptibility to Staphylococcus aureus Infection in a White Population.

DeLorenze GN, Nelson CL, Scott WK, Allen AS, Ray GT, Tsai AL, Quesenberry CP Jr, Fowler VG Jr.

J Infect Dis. 2016 Mar 1;213(5):816-23. doi: 10.1093/infdis/jiv483. Epub 2015 Oct 8.

30.

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity.

Petrovski S, Gussow AB, Wang Q, Halvorsen M, Han Y, Weir WH, Allen AS, Goldstein DB.

PLoS Genet. 2015 Sep 2;11(9):e1005492. doi: 10.1371/journal.pgen.1005492. eCollection 2015 Sep.

31.

Incorporating Functional Information in Tests of Excess De Novo Mutational Load.

Jiang Y, Han Y, Petrovski S, Owzar K, Goldstein DB, Allen AS.

Am J Hum Genet. 2015 Aug 6;97(2):272-83. doi: 10.1016/j.ajhg.2015.06.013. Epub 2015 Jul 30.

32.

The genetics of neuropsychiatric diseases: looking in and beyond the exome.

Heinzen EL, Neale BM, Traynelis SF, Allen AS, Goldstein DB.

Annu Rev Neurosci. 2015 Jul 8;38:47-68. doi: 10.1146/annurev-neuro-071714-034136. Epub 2015 Apr 2. Review.

PMID:
25840007
33.

Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways.

Cirulli ET, Lasseigne BN, Petrovski S, Sapp PC, Dion PA, Leblond CS, Couthouis J, Lu YF, Wang Q, Krueger BJ, Ren Z, Keebler J, Han Y, Levy SE, Boone BE, Wimbish JR, Waite LL, Jones AL, Carulli JP, Day-Williams AG, Staropoli JF, Xin WW, Chesi A, Raphael AR, McKenna-Yasek D, Cady J, Vianney de Jong JM, Kenna KP, Smith BN, Topp S, Miller J, Gkazi A; FALS Sequencing Consortium, Al-Chalabi A, van den Berg LH, Veldink J, Silani V, Ticozzi N, Shaw CE, Baloh RH, Appel S, Simpson E, Lagier-Tourenne C, Pulst SM, Gibson S, Trojanowski JQ, Elman L, McCluskey L, Grossman M, Shneider NA, Chung WK, Ravits JM, Glass JD, Sims KB, Van Deerlin VM, Maniatis T, Hayes SD, Ordureau A, Swarup S, Landers J, Baas F, Allen AS, Bedlack RS, Harper JW, Gitler AD, Rouleau GA, Brown R, Harms MB, Cooper GM, Harris T, Myers RM, Goldstein DB.

Science. 2015 Mar 27;347(6229):1436-41. doi: 10.1126/science.aaa3650. Epub 2015 Feb 19.

34.

Testing the effect of rare compound-heterozygous and recessive mutations in case--parent sequencing studies.

Jiang Y, McCarthy JM, Allen AS.

Genet Epidemiol. 2015 Mar;39(3):166-72. doi: 10.1002/gepi.21885. Epub 2015 Jan 28.

PMID:
25631493
35.

Testing for risk and protective trends in genetic analyses of HIV acquisition.

Mccarthy JM, Shea PR, Goldstein DB, Allen AS.

Biostatistics. 2015 Apr;16(2):268-80. doi: 10.1093/biostatistics/kxu044. Epub 2014 Sep 29.

36.

Utilizing population controls in rare-variant case-parent association tests.

Jiang Y, Satten GA, Han Y, Epstein MP, Heinzen EL, Goldstein DB, Allen AS.

Am J Hum Genet. 2014 Jun 5;94(6):845-53. doi: 10.1016/j.ajhg.2014.04.014. Epub 2014 May 15.

37.

An evaluation of copy number variation detection tools from whole-exome sequencing data.

Tan R, Wang Y, Kleinstein SE, Liu Y, Zhu X, Guo H, Jiang Q, Allen AS, Zhu M.

Hum Mutat. 2014 Jul;35(7):899-907. doi: 10.1002/humu.22537. Epub 2014 May 1.

PMID:
24599517
38.

A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.

Nelson CL, Pelak K, Podgoreanu MV, Ahn SH, Scott WK, Allen AS, Cowell LG, Rude TH, Zhang Y, Tong A, Ruffin F, Sharma-Kuinkel BK, Fowler VG Jr.

BMC Infect Dis. 2014 Feb 13;14:83. doi: 10.1186/1471-2334-14-83.

39.

Robust regression analysis of copy number variation data based on a univariate score.

Satten GA, Allen AS, Ikeda M, Mulle JG, Warren ST.

PLoS One. 2014 Feb 7;9(2):e86272. doi: 10.1371/journal.pone.0086272. eCollection 2014.

40.

Genic intolerance to functional variation and the interpretation of personal genomes.

Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB.

PLoS Genet. 2013;9(8):e1003709. doi: 10.1371/journal.pgen.1003709. Epub 2013 Aug 22.

41.

De novo mutations in epileptic encephalopathies.

Epi4K Consortium; Epilepsy Phenome/Genome Project, Allen AS, Berkovic SF, Cossette P, Delanty N, Dlugos D, Eichler EE, Epstein MP, Glauser T, Goldstein DB, Han Y, Heinzen EL, Hitomi Y, Howell KB, Johnson MR, Kuzniecky R, Lowenstein DH, Lu YF, Madou MR, Marson AG, Mefford HC, Esmaeeli Nieh S, O'Brien TJ, Ottman R, Petrovski S, Poduri A, Ruzzo EK, Scheffer IE, Sherr EH, Yuskaitis CJ, Abou-Khalil B, Alldredge BK, Bautista JF, Berkovic SF, Boro A, Cascino GD, Consalvo D, Crumrine P, Devinsky O, Dlugos D, Epstein MP, Fiol M, Fountain NB, French J, Friedman D, Geller EB, Glauser T, Glynn S, Haut SR, Hayward J, Helmers SL, Joshi S, Kanner A, Kirsch HE, Knowlton RC, Kossoff EH, Kuperman R, Kuzniecky R, Lowenstein DH, McGuire SM, Motika PV, Novotny EJ, Ottman R, Paolicchi JM, Parent JM, Park K, Poduri A, Scheffer IE, Shellhaas RA, Sherr EH, Shih JJ, Singh R, Sirven J, Smith MC, Sullivan J, Lin Thio L, Venkat A, Vining EP, Von Allmen GK, Weisenberg JL, Widdess-Walsh P, Winawer MR.

Nature. 2013 Sep 12;501(7466):217-21. doi: 10.1038/nature12439. Epub 2013 Aug 11.

42.

Leveraging prior information to detect causal variants via multi-variant regression.

Long N, Dickson SP, Maia JM, Kim HS, Zhu Q, Allen AS.

PLoS Comput Biol. 2013;9(6):e1003093. doi: 10.1371/journal.pcbi.1003093. Epub 2013 Jun 6.

43.

Dispensing of electronically discontinued medications.

Allen AS.

Ann Intern Med. 2013 Apr 2;158(7):571-2. doi: 10.7326/0003-4819-158-7-201304020-00021. No abstract available.

PMID:
23546580
44.

Pharmacy dispensing of electronically discontinued medications.

Allen AS, Sequist TD.

Ann Intern Med. 2012 Nov 20;157(10):700-5. doi: 10.7326/0003-4819-157-10-201211200-00006.

PMID:
23165661
45.

A permutation procedure to correct for confounders in case-control studies, including tests of rare variation.

Epstein MP, Duncan R, Jiang Y, Conneely KN, Allen AS, Satten GA.

Am J Hum Genet. 2012 Aug 10;91(2):215-23. doi: 10.1016/j.ajhg.2012.06.004. Epub 2012 Jul 19.

46.

Stratification-score matching improves correction for confounding by population stratification in case-control association studies.

Epstein MP, Duncan R, Broadaway KA, He M, Allen AS, Satten GA.

Genet Epidemiol. 2012 Apr;36(3):195-205. doi: 10.1002/gepi.21611.

47.

A weighted accumulation test for associating rare genetic variation with quantitative phenotypes.

Xing C, Satten GA, Allen AS.

BMC Proc. 2011 Nov 29;5 Suppl 9:S6. doi: 10.1186/1753-6561-5-S9-S6.

48.

Clinician personality and the evaluation of higher-risk patient symptoms.

Allen AS, Orav EJ, Lee TH, Sequist TD.

J Patient Saf. 2011 Sep;7(3):122-6. doi: 10.1097/PTS.0b013e318223cb41.

PMID:
21738072
49.

SVA: software for annotating and visualizing sequenced human genomes.

Ge D, Ruzzo EK, Shianna KV, He M, Pelak K, Heinzen EL, Need AC, Cirulli ET, Maia JM, Dickson SP, Zhu M, Singh A, Allen AS, Goldstein DB.

Bioinformatics. 2011 Jul 15;27(14):1998-2000. doi: 10.1093/bioinformatics/btr317. Epub 2011 May 29.

50.

Control for confounding in case-control studies using the stratification score, a retrospective balancing score.

Allen AS, Satten GA.

Am J Epidemiol. 2011 Apr 1;173(7):752-60. doi: 10.1093/aje/kwq406. Epub 2011 Mar 14.

Supplemental Content

Loading ...
Support Center