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Items: 1 to 50 of 85

1.

Dynamic genetic regulation of gene expression during cellular differentiation.

Strober BJ, Elorbany R, Rhodes K, Krishnan N, Tayeb K, Battle A, Gilad Y.

Science. 2019 Jun 28;364(6447):1287-1290. doi: 10.1126/science.aaw0040.

PMID:
31249060
2.

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

Frésard L, Smail C, Ferraro NM, Teran NA, Li X, Smith KS, Bonner D, Kernohan KD, Marwaha S, Zappala Z, Balliu B, Davis JR, Liu B, Prybol CJ, Kohler JN, Zastrow DB, Reuter CM, Fisk DG, Grove ME, Davidson JM, Hartley T, Joshi R, Strober BJ, Utiramerur S; Undiagnosed Diseases Network; Care4Rare Canada Consortium, Lind L, Ingelsson E, Battle A, Bejerano G, Bernstein JA, Ashley EA, Boycott KM, Merker JD, Wheeler MT, Montgomery SB.

Nat Med. 2019 Jun;25(6):911-919. doi: 10.1038/s41591-019-0457-8. Epub 2019 Jun 3.

PMID:
31160820
3.

Contextual Fear Conditioning Alter Microglia Number and Morphology in the Rat Dorsal Hippocampus.

Chaaya N, Jacques A, Belmer A, Beecher K, Ali SA, Chehrehasa F, Battle AR, Johnson LR, Bartlett SE.

Front Cell Neurosci. 2019 May 14;13:214. doi: 10.3389/fncel.2019.00214. eCollection 2019.

4.

Editorial: Special issue of Biophysical Reviews dedicated to the joint 10th Asian Biophysics Association Symposium and 42nd Australian Society for Biophysics Meeting, Melbourne, Australia, December 2-6, 2018.

Battle AR, Norton RS, Böcking T, Noji H, Kim KK, Nagayama K.

Biophys Rev. 2019 Jun;11(3):245-247. doi: 10.1007/s12551-019-00553-y. Epub 2019 May 21. No abstract available.

5.

Addressing confounding artifacts in reconstruction of gene co-expression networks.

Parsana P, Ruberman C, Jaffe AE, Schatz MC, Battle A, Leek JT.

Genome Biol. 2019 May 16;20(1):94. doi: 10.1186/s13059-019-1700-9.

6.

Author Correction: Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration.

Ratnapriya R, Sosina OA, Starostik MR, Kwicklis M, Kapphahn RJ, Fritsche LG, Walton A, Arvanitis M, Gieser L, Pietraszkiewicz A, Montezuma SR, Chew EY, Battle A, Abecasis GR, Ferrington DA, Chatterjee N, Swaroop A.

Nat Genet. 2019 Jun;51(6):1067. doi: 10.1038/s41588-019-0430-y.

PMID:
31068672
7.

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors.

Saha A, Battle A.

Version 2. F1000Res. 2018 Nov 28 [revised 2019 Jan 1];7:1860. doi: 10.12688/f1000research.17145.2. eCollection 2018.

8.

Imputed gene associations identify replicable trans-acting genes enriched in transcription pathways and complex traits.

Wheeler HE, Ploch S, Barbeira AN, Bonazzola R, Andaleon A, Fotuhi Siahpirani A, Saha A, Battle A, Roy S, Im HK.

Genet Epidemiol. 2019 Apr 4. doi: 10.1002/gepi.22205. [Epub ahead of print]

PMID:
30950127
9.

Unprecedented Microbial Conversion of Biliverdin into Bilirubin-10-sulfonate.

Shiels RG, Vidimce J, Pearson AG, Matthews B, Wagner KH, Battle AR, Sakellaris H, Bulmer AC.

Sci Rep. 2019 Feb 27;9(1):2988. doi: 10.1038/s41598-019-39548-w.

10.

Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration.

Ratnapriya R, Sosina OA, Starostik MR, Kwicklis M, Kapphahn RJ, Fritsche LG, Walton A, Arvanitis M, Gieser L, Pietraszkiewicz A, Montezuma SR, Chew EY, Battle A, Abecasis GR, Ferrington DA, Chatterjee N, Swaroop A.

Nat Genet. 2019 Apr;51(4):606-610. doi: 10.1038/s41588-019-0351-9. Epub 2019 Feb 11. Erratum in: Nat Genet. 2019 Jun;51(6):1067.

PMID:
30742112
11.

Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances.

Timmers PR, Mounier N, Lall K, Fischer K, Ning Z, Feng X, Bretherick AD, Clark DW; eQTLGen Consortium, Agbessi M, Ahsan H, Alves I, Andiappan A, Awadalla P, Battle A, Bonder MJ, Boomsma D, Christiansen M, Claringbould A, Deelen P, van Dongen J, Esko T, Favé M, Franke L, Frayling T, Gharib SA, Gibson G, Hemani G, Jansen R, Kalnapenkis A, Kasela S, Kettunen J, Kim Y, Kirsten H, Kovacs P, Krohn K, Kronberg-Guzman J, Kukushkina V, Kutalik Z, Kähönen M, Lee B, Lehtimäki T, Loeffler M, Marigorta U, Metspalu A, van Meurs J, Milani L, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Perola M, Pervjakova N, Pierce B, Powell J, Prokisch H, Psaty BM, Raitakari O, Ring S, Ripatti S, Rotzschke O, Ruëger S, Saha A, Scholz M, Schramm K, Seppälä I, Stumvoll M, Sullivan P, Teumer A, Thiery J, Tong L, Tönjes A, Verlouw J, Visscher PM, Võsa U, Völker U, Yaghootkar H, Yang J, Zeng B, Zhang F, Agbessi M, Ahsan H, Alves I, Andiappan A, Awadalla P, Battle A, Bonder MJ, Boomsma D, Christiansen M, Claringbould A, Deelen P, van Dongen J, Esko T, Favé M, Franke L, Frayling T, Gharib SA, Gibson G, Hemani G, Jansen R, Kalnapenkis A, Kasela S, Kettunen J, Kim Y, Kirsten H, Kovacs P, Krohn K, Kronberg-Guzman J, Kukushkina V, Kutalik Z, Kähönen M, Lee B, Lehtimäki T, Loeffler M, Marigorta U, Metspalu A, van Meurs J, Milani L, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Perola M, Pervjakova N, Pierce B, Powell J, Prokisch H, Psaty BM, Raitakari O, Ring S, Ripatti S, Rotzschke O, Ruëger S, Saha A, Scholz M, Schramm K, Seppälä I, Stumvoll M, Sullivan P, Teumer A, Thiery J, Tong L, Tönjes A, Verlouw J, Visscher PM, Võsa U, Völker U, Yaghootkar H, Yang J, Zeng B, Zhang F, Shen X, Esko T, Kutalik Z, Wilson JF, Joshi PK.

Elife. 2019 Jan 15;8. pii: e39856. doi: 10.7554/eLife.39856.

12.

Microtopography of fear memory consolidation and extinction retrieval within prefrontal cortex and amygdala.

Jacques A, Chaaya N, Hettiarachchi C, Carmody ML, Beecher K, Belmer A, Chehrehasa F, Bartlett S, Battle AR, Johnson LR.

Psychopharmacology (Berl). 2019 Jan;236(1):383-397. doi: 10.1007/s00213-018-5068-4. Epub 2019 Jan 4.

PMID:
30610350
13.

Localization of Contextual and Context Removed Auditory Fear Memory within the Basolateral Amygdala Complex.

Chaaya N, Jacques A, Belmer A, Richard DJ, Bartlett SE, Battle AR, Johnson LR.

Neuroscience. 2019 Feb 1;398:231-251. doi: 10.1016/j.neuroscience.2018.12.004. Epub 2018 Dec 13.

PMID:
30552931
14.

Functional Neuronal Topography: A Statistical Approach to Micro Mapping Neuronal Location.

Jacques A, Wright A, Chaaya N, Overell A, Bergstrom HC, McDonald C, Battle AR, Johnson LR.

Front Neural Circuits. 2018 Oct 16;12:84. doi: 10.3389/fncir.2018.00084. eCollection 2018.

15.

Xenon-inhibition of the MscL mechano-sensitive channel and the CopB copper ATPase under different conditions suggests direct effects on these proteins.

Petrov E, Menon G, Rohde PR, Battle AR, Martinac B, Solioz M.

PLoS One. 2018 Jun 4;13(6):e0198110. doi: 10.1371/journal.pone.0198110. eCollection 2018.

16.

An update on contextual fear memory mechanisms: Transition between Amygdala and Hippocampus.

Chaaya N, Battle AR, Johnson LR.

Neurosci Biobehav Rev. 2018 Sep;92:43-54. doi: 10.1016/j.neubiorev.2018.05.013. Epub 2018 May 9. Review.

PMID:
29752958
17.

"Force-from-lipids" gating of mechanosensitive channels modulated by PUFAs.

Ridone P, Grage SL, Patkunarajah A, Battle AR, Ulrich AS, Martinac B.

J Mech Behav Biomed Mater. 2018 Mar;79:158-167. doi: 10.1016/j.jmbbm.2017.12.026. Epub 2017 Dec 28.

PMID:
29304430
18.

Genetic effects on gene expression across human tissues.

GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Lead analysts:; Laboratory, Data Analysis &Coordinating Center (LDACC):; NIH program management:; Biospecimen collection:; Pathology:; eQTL manuscript working group:, Battle A, Brown CD, Engelhardt BE, Montgomery SB.

Nature. 2017 Oct 11;550(7675):204-213. doi: 10.1038/nature24277. Erratum in: Nature. 2017 Dec 20;:.

19.

The impact of rare variation on gene expression across tissues.

Li X, Kim Y, Tsang EK, Davis JR, Damani FN, Chiang C, Hess GT, Zappala Z, Strober BJ, Scott AJ, Li A, Ganna A, Bassik MC, Merker JD; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Hall IM, Battle A, Montgomery SB.

Nature. 2017 Oct 11;550(7675):239-243. doi: 10.1038/nature24267.

20.

Co-expression networks reveal the tissue-specific regulation of transcription and splicing.

Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC; GTEx Consortium, Engelhardt BE, Battle A.

Genome Res. 2017 Nov;27(11):1843-1858. doi: 10.1101/gr.216721.116. Epub 2017 Oct 11.

21.

Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions.

Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Thomas DC, Wei P, Montgomery SB.

Am J Epidemiol. 2017 Oct 1;186(7):771-777. doi: 10.1093/aje/kwx229.

22.

FIRE: functional inference of genetic variants that regulate gene expression.

Ioannidis NM, Davis JR, DeGorter MK, Larson NB, McDonnell SK, French AJ, Battle AJ, Hastie TJ, Thibodeau SN, Montgomery SB, Bustamante CD, Sieh W, Whittemore AS.

Bioinformatics. 2017 Dec 15;33(24):3895-3901. doi: 10.1093/bioinformatics/btx534.

23.

Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration.

Parsana P, Amend SR, Hernandez J, Pienta KJ, Battle A.

BMC Cancer. 2017 Jun 26;17(1):447. doi: 10.1186/s12885-017-3413-3.

24.

Allele-specific expression reveals interactions between genetic variation and environment.

Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A.

Nat Methods. 2017 Jul;14(7):699-702. doi: 10.1038/nmeth.4298. Epub 2017 May 22.

25.

Population- and individual-specific regulatory variation in Sardinia.

Pala M, Zappala Z, Marongiu M, Li X, Davis JR, Cusano R, Crobu F, Kukurba KR, Gloudemans MJ, Reinier F, Berutti R, Piras MG, Mulas A, Zoledziewska M, Marongiu M, Sorokin EP, Hess GT, Smith KS, Busonero F, Maschio A, Steri M, Sidore C, Sanna S, Fiorillo E, Bassik MC, Sawcer SJ, Battle A, Novembre J, Jones C, Angius A, Abecasis GR, Schlessinger D, Cucca F, Montgomery SB.

Nat Genet. 2017 May;49(5):700-707. doi: 10.1038/ng.3840. Epub 2017 Apr 10.

26.

The impact of structural variation on human gene expression.

Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L; GTEx Consortium, Montgomery SB, Battle A, Conrad DF, Hall IM.

Nat Genet. 2017 May;49(5):692-699. doi: 10.1038/ng.3834. Epub 2017 Apr 3.

27.

Genetic variation in MHC proteins is associated with T cell receptor expression biases.

Sharon E, Sibener LV, Battle A, Fraser HB, Garcia KC, Pritchard JK.

Nat Genet. 2016 Sep;48(9):995-1002. doi: 10.1038/ng.3625. Epub 2016 Aug 1.

28.

Membrane Associated Synaptic Mineralocorticoid and Glucocorticoid Receptors Are Rapid Regulators of Dendritic Spines.

Russo MF, Ah Loy SR, Battle AR, Johnson LR.

Front Cell Neurosci. 2016 Jun 21;10:161. doi: 10.3389/fncel.2016.00161. eCollection 2016. No abstract available.

29.

Impact of the X Chromosome and sex on regulatory variation.

Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, Awadalla P, Mostafavi S, Battle A, Montgomery SB.

Genome Res. 2016 Jun;26(6):768-77. doi: 10.1101/gr.197897.115. Epub 2016 Apr 21.

30.

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants.

Davis JR, Fresard L, Knowles DA, Pala M, Bustamante CD, Battle A, Montgomery SB.

Am J Hum Genet. 2016 Jan 7;98(1):216-24. doi: 10.1016/j.ajhg.2015.11.021. Epub 2015 Dec 31.

31.

Utilizing health ambassadors to improve type 2 diabetes and cardiovascular disease outcomes in Gadsden County, Florida.

Suther S, Battle AM, Battle-Jones F, Seaborn C.

Eval Program Plann. 2016 Apr;55:17-26. doi: 10.1016/j.evalprogplan.2015.11.001. Epub 2015 Dec 2.

PMID:
26702881
32.

Biophysics of Mechanotransduction.

Martinac B, Battle AR.

Eur Biophys J. 2015 Oct;44(7):499-501. doi: 10.1007/s00249-015-1070-5. No abstract available.

PMID:
26315755
33.

Inducible release of particulates from liposomes using the mechanosensitive channel of large conductance and L-α-lysophosphatidylcholine.

Foo A, Battle AR, Chi G, Hankamer B, Landsberg MJ, Martinac B.

Eur Biophys J. 2015 Oct;44(7):521-30. doi: 10.1007/s00249-015-1055-4. Epub 2015 Jul 5.

PMID:
26143502
34.

Sharing and Specificity of Co-expression Networks across 35 Human Tissues.

Pierson E; GTEx Consortium, Koller D, Battle A, Mostafavi S, Ardlie KG, Getz G, Wright FA, Kellis M, Volpi S, Dermitzakis ET.

PLoS Comput Biol. 2015 May 13;11(5):e1004220. doi: 10.1371/journal.pcbi.1004220. eCollection 2015 May.

35.

Lipid-protein interactions: Lessons learned from stress.

Battle AR, Ridone P, Bavi N, Nakayama Y, Nikolaev YA, Martinac B.

Biochim Biophys Acta. 2015 Sep;1848(9):1744-56. doi: 10.1016/j.bbamem.2015.04.012. Epub 2015 Apr 25. Review.

36.

Patch clamp characterization of the effect of cardiolipin on MscS of E. coli.

Ridone P, Nakayama Y, Martinac B, Battle AR.

Eur Biophys J. 2015 Oct;44(7):567-76. doi: 10.1007/s00249-015-1020-2. Epub 2015 Apr 5.

PMID:
25842033
37.

EIF3G is associated with narcolepsy across ethnicities.

Holm A, Lin L, Faraco J, Mostafavi S, Battle A, Zhu X, Levinson DF, Han F, Gammeltoft S, Jennum P, Mignot E, Kornum BR.

Eur J Hum Genet. 2015 Nov;23(11):1573-80. doi: 10.1038/ejhg.2015.4. Epub 2015 Feb 11.

38.

Genomic variation. Impact of regulatory variation from RNA to protein.

Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y.

Science. 2015 Feb 6;347(6222):664-7. doi: 10.1126/science.1260793. Epub 2014 Dec 18.

39.

High-resolution transcriptome analysis with long-read RNA sequencing.

Cho H, Davis J, Li X, Smith KS, Battle A, Montgomery SB.

PLoS One. 2014 Sep 24;9(9):e108095. doi: 10.1371/journal.pone.0108095. eCollection 2014.

40.

Transcriptome sequencing of a large human family identifies the impact of rare noncoding variants.

Li X, Battle A, Karczewski KJ, Zappala Z, Knowles DA, Smith KS, Kukurba KR, Wu E, Simon N, Montgomery SB.

Am J Hum Genet. 2014 Sep 4;95(3):245-56. doi: 10.1016/j.ajhg.2014.08.004.

41.

Transcriptome analysis reveals differential splicing events in IPF lung tissue.

Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB.

PLoS One. 2014 May 7;9(5):e97550. doi: 10.1371/journal.pone.0097550. eCollection 2014. Erratum in: PLoS One. 2014;9(5):e97392.

42.

Determining causality and consequence of expression quantitative trait loci.

Battle A, Montgomery SB.

Hum Genet. 2014 Jun;133(6):727-35. doi: 10.1007/s00439-014-1446-0. Epub 2014 Apr 26. Review.

43.

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder.

Davies MN, Krause L, Bell JT, Gao F, Ward KJ, Wu H, Lu H, Liu Y, Tsai PC, Collier DA, Murphy T, Dempster E, Mill J; UK Brain Expression Consortium, Battle A, Mostafavi S, Zhu X, Henders A, Byrne E, Wray NR, Martin NG, Spector TD, Wang J.

Genome Biol. 2014 Apr 2;15(4):R56. doi: 10.1186/gb-2014-15-4-r56.

44.

Reducing cardiovascular disease risk in mid-life and older African Americans: a church-based longitudinal intervention project at baseline.

Ralston PA, Lemacks JL, Wickrama KK, Young-Clark I, Coccia C, Ilich JZ, Harris CM, Hart CB, Battle AM, O'Neal CW.

Contemp Clin Trials. 2014 May;38(1):69-81. doi: 10.1016/j.cct.2014.03.003. Epub 2014 Mar 28.

45.

Transcriptome analysis reveals differential splicing events in IPF lung tissue.

Nance T, Smith KS, Anaya V, Richardson R, Ho L, Pala M, Mostafavi S, Battle A, Feghali-Bostwick C, Rosen G, Montgomery SB.

PLoS One. 2014 Mar 19;9(3):e92111. doi: 10.1371/journal.pone.0092111. eCollection 2014.

46.

Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing.

Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, MacKinnon DF, Notes L, Schweizer B, Furman D, Montgomery SB, Urban AE, Koller D, Levinson DF.

Mol Psychiatry. 2014 Dec;19(12):1267-74. doi: 10.1038/mp.2013.161. Epub 2013 Dec 3.

47.

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D.

Genome Res. 2014 Jan;24(1):14-24. doi: 10.1101/gr.155192.113. Epub 2013 Oct 3.

48.

Community perceptions of black infant mortality: a qualitative inquiry.

Close FT, Suther S, Foster A, El-Amin S, Battle AM.

J Health Care Poor Underserved. 2013 Aug;24(3):1089-101. doi: 10.1353/hpu.2013.0118.

PMID:
23974383
49.

Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge.

Mostafavi S, Battle A, Zhu X, Urban AE, Levinson D, Montgomery SB, Koller D.

PLoS One. 2013 Jul 18;8(7):e68141. doi: 10.1371/journal.pone.0068141. Print 2013.

50.

Bacterial mechanosensitive channels: models for studying mechanosensory transduction.

Martinac B, Nomura T, Chi G, Petrov E, Rohde PR, Battle AR, Foo A, Constantine M, Rothnagel R, Carne S, Deplazes E, Cornell B, Cranfield CG, Hankamer B, Landsberg MJ.

Antioxid Redox Signal. 2014 Feb 20;20(6):952-69. doi: 10.1089/ars.2013.5471. Epub 2013 Aug 15. Review.

PMID:
23834368

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