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Items: 1 to 20 of 47

1.

Computational Inference Software for Tetrad Assembly from Randomly Arrayed Yeast Colonies.

Sakhanenko NA, Cromie GA, Dudley AM, Galas DJ.

G3 (Bethesda). 2019 Jul 9;9(7):2071-2088. doi: 10.1534/g3.119.400166.

2.

Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma.

Giraldez MD, Spengler RM, Etheridge A, Goicochea AJ, Tuck M, Choi SW, Galas DJ, Tewari M.

EMBO J. 2019 Jun 3;38(11). pii: e101695. doi: 10.15252/embj.2019101695. Epub 2019 May 3.

3.

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

Murillo OD, Thistlethwaite W, Rozowsky J, Subramanian SL, Lucero R, Shah N, Jackson AR, Srinivasan S, Chung A, Laurent CD, Kitchen RR, Galeev T, Warrell J, Diao JA, Welsh JA, Hanspers K, Riutta A, Burgstaller-Muehlbacher S, Shah RV, Yeri A, Jenkins LM, Ahsen ME, Cordon-Cardo C, Dogra N, Gifford SM, Smith JT, Stolovitzky G, Tewari AK, Wunsch BH, Yadav KK, Danielson KM, Filant J, Moeller C, Nejad P, Paul A, Simonson B, Wong DK, Zhang X, Balaj L, Gandhi R, Sood AK, Alexander RP, Wang L, Wu C, Wong DTW, Galas DJ, Van Keuren-Jensen K, Patel T, Jones JC, Das S, Cheung KH, Pico AR, Su AI, Raffai RL, Laurent LC, Roth ME, Gerstein MB, Milosavljevic A.

Cell. 2019 Apr 4;177(2):463-477.e15. doi: 10.1016/j.cell.2019.02.018.

4.

The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.

Das S; Extracellular RNA Communication Consortium, Ansel KM, Bitzer M, Breakefield XO, Charest A, Galas DJ, Gerstein MB, Gupta M, Milosavljevic A, McManus MT, Patel T, Raffai RL, Rozowsky J, Roth ME, Saugstad JA, Van Keuren-Jensen K, Weaver AM, Laurent LC.

Cell. 2019 Apr 4;177(2):231-242. doi: 10.1016/j.cell.2019.03.023. Review.

PMID:
30951667
5.

Multivariate Analysis of Data Sets with Missing Values: An Information Theory-Based Reliability Function.

Uechi L, Galas DJ, Sakhanenko NA.

J Comput Biol. 2019 Feb;26(2):152-171. doi: 10.1089/cmb.2018.0179. Epub 2018 Nov 29.

6.

Erratum: Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.

Giraldez MD, Spengler RM, Etheridge A, Godoy PM, Barczak AJ, Srinivasan S, Hoff PL, Tanriverdi K, Courtright A, Lu S, Khoory J, Rubio R, Baxter D, Driedonks TAP, Buermans HPJ, Hoen ENMN, Jiang H, Wang K, Ghiran I, Wang YE, Keuren-Jensen KV, Freedman JE, Woodruff PG, Laurent LC, Erle DJ, Galas DJ, Tewari M.

Nat Biotechnol. 2018 Sep 6;36(9):899. doi: 10.1038/nbt0918-899b. No abstract available.

7.

Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.

Giraldez MD, Spengler RM, Etheridge A, Godoy PM, Barczak AJ, Srinivasan S, De Hoff PL, Tanriverdi K, Courtright A, Lu S, Khoory J, Rubio R, Baxter D, Driedonks TAP, Buermans HPJ, Nolte-'t Hoen ENM, Jiang H, Wang K, Ghiran I, Wang YE, Van Keuren-Jensen K, Freedman JE, Woodruff PG, Laurent LC, Erle DJ, Galas DJ, Tewari M.

Nat Biotechnol. 2018 Sep;36(8):746-757. doi: 10.1038/nbt.4183. Epub 2018 Jul 16.

8.

Small RNA profiling of low biomass samples: identification and removal of contaminants.

Heintz-Buschart A, Yusuf D, Kaysen A, Etheridge A, Fritz JV, May P, de Beaufort C, Upadhyaya BB, Ghosal A, Galas DJ, Wilmes P.

BMC Biol. 2018 May 14;16(1):52. doi: 10.1186/s12915-018-0522-7.

9.

sRNAnalyzer-a flexible and customizable small RNA sequencing data analysis pipeline.

Wu X, Kim TK, Baxter D, Scherler K, Gordon A, Fong O, Etheridge A, Galas DJ, Wang K.

Nucleic Acids Res. 2017 Dec 1;45(21):12140-12151. doi: 10.1093/nar/gkx999.

10.

The Information Content of Discrete Functions and Their Application in Genetic Data Analysis.

Sakhanenko NA, Kunert-Graf J, Galas DJ.

J Comput Biol. 2017 Dec;24(12):1153-1178. doi: 10.1089/cmb.2017.0143. Epub 2017 Oct 13.

11.

Reprogramming progeria fibroblasts re-establishes a normal epigenetic landscape.

Chen Z, Chang WY, Etheridge A, Strickfaden H, Jin Z, Palidwor G, Cho JH, Wang K, Kwon SY, Doré C, Raymond A, Hotta A, Ellis J, Kandel RA, Dilworth FJ, Perkins TJ, Hendzel MJ, Galas DJ, Stanford WL.

Aging Cell. 2017 Aug;16(4):870-887. doi: 10.1111/acel.12621. Epub 2017 Jun 8.

12.

A genome wide dosage suppressor network reveals genomic robustness.

Patra B, Kon Y, Yadav G, Sevold AW, Frumkin JP, Vallabhajosyula RR, Hintze A, Østman B, Schossau J, Bhan A, Marzolf B, Tamashiro JK, Kaur A, Baliga NS, Grayhack EJ, Adami C, Galas DJ, Raval A, Phizicky EM, Ray A.

Nucleic Acids Res. 2017 Jan 9;45(1):255-270. doi: 10.1093/nar/gkw1148. Epub 2016 Nov 29.

13.

Biological data analysis as an information theory problem: multivariable dependence measures and the shadows algorithm.

Sakhanenko NA, Galas DJ.

J Comput Biol. 2015 Nov;22(11):1005-24. doi: 10.1089/cmb.2015.0051. Epub 2015 Sep 3.

14.

Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease.

Krishna A, Biryukov M, Trefois C, Antony PM, Hussong R, Lin J, Heinäniemi M, Glusman G, Köglsberger S, Boyd O, van den Berg BH, Linke D, Huang D, Wang K, Hood L, Tholey A, Schneider R, Galas DJ, Balling R, May P.

BMC Genomics. 2014 Dec 20;15:1154. doi: 10.1186/1471-2164-15-1154.

15.

Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes.

Schubert J, Siekierska A, Langlois M, May P, Huneau C, Becker F, Muhle H, Suls A, Lemke JR, de Kovel CG, Thiele H, Konrad K, Kawalia A, Toliat MR, Sander T, Rüschendorf F, Caliebe A, Nagel I, Kohl B, Kecskés A, Jacmin M, Hardies K, Weckhuysen S, Riesch E, Dorn T, Brilstra EH, Baulac S, Møller RS, Hjalgrim H, Koeleman BP; EuroEPINOMICS RES Consortium, Jurkat-Rott K, Lehman-Horn F, Roach JC, Glusman G, Hood L, Galas DJ, Martin B, de Witte PA, Biskup S, De Jonghe P, Helbig I, Balling R, Nürnberg P, Crawford AD, Esguerra CV, Weber YG, Lerche H.

Nat Genet. 2014 Dec;46(12):1327-32. doi: 10.1038/ng.3130. Epub 2014 Nov 2.

PMID:
25362483
16.

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD.

Nat Biotechnol. 2014 Jul;32(7):663-9. doi: 10.1038/nbt.2895. Epub 2014 May 18.

17.

Discovering pair-wise genetic interactions: an information theory-based approach.

Ignac TM, Skupin A, Sakhanenko NA, Galas DJ.

PLoS One. 2014 Mar 26;9(3):e92310. doi: 10.1371/journal.pone.0092310. eCollection 2014.

18.

Molecular evidence of stress-induced acute heart injury in a mouse model simulating posttraumatic stress disorder.

Cho JH, Lee I, Hammamieh R, Wang K, Baxter D, Scherler K, Etheridge A, Kulchenko A, Gautam A, Muhie S, Chakraborty N, Galas DJ, Jett M, Hood L.

Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3188-93. doi: 10.1073/pnas.1400113111. Epub 2014 Feb 10.

19.

Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

Galas DJ, Sakhanenko NA, Skupin A, Ignac T.

J Comput Biol. 2014 Feb;21(2):118-40. doi: 10.1089/cmb.2013.0039. Epub 2013 Dec 30.

20.

An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae.

Wilkening S, Lin G, Fritsch ES, Tekkedil MM, Anders S, Kuehn R, Nguyen M, Aiyar RS, Proctor M, Sakhanenko NA, Galas DJ, Gagneur J, Deutschbauer A, Steinmetz LM.

Genetics. 2014 Mar;196(3):853-65. doi: 10.1534/genetics.113.160291. Epub 2013 Dec 27.

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