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Items: 1 to 20 of 79

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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
8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

RCytoscape: tools for exploratory network analysis.

Shannon PT, Grimes M, Kutlu B, Bot JJ, Galas DJ.

BMC Bioinformatics. 2013 Jul 9;14:217. doi: 10.1186/1471-2105-14-217.

14.

The spectrum of circulating RNA: a window into systems toxicology.

Wang K, Yuan Y, Li H, Cho JH, Huang D, Gray L, Qin S, Galas DJ.

Toxicol Sci. 2013 Apr;132(2):478-92. doi: 10.1093/toxsci/kft014. Epub 2013 Jan 28.

PMID:
23358195
15.

Relations between the set-complexity and the structure of graphs and their sub-graphs.

Ignac TM, Sakhanenko NA, Galas DJ.

EURASIP J Bioinform Syst Biol. 2012 Sep 21;2012(1):13. doi: 10.1186/1687-4153-2012-13.

16.

Comparing the MicroRNA spectrum between serum and plasma.

Wang K, Yuan Y, Cho JH, McClarty S, Baxter D, Galas DJ.

PLoS One. 2012;7(7):e41561. doi: 10.1371/journal.pone.0041561. Epub 2012 Jul 31.

17.

Probabilistic logic methods and some applications to biology and medicine.

Sakhanenko NA, Galas DJ.

J Comput Biol. 2012 Mar;19(3):316-36. doi: 10.1089/cmb.2011.0234. Review.

PMID:
22401592
18.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.

Nucleic Acids Res. 2012 Mar;40(6):e42. doi: 10.1093/nar/gkr1248. Epub 2011 Dec 22.

19.

The systems biology of neurofibromatosis type 1--critical roles for microRNA.

Lee MJ, Cho JH, Galas DJ, Wang K.

Exp Neurol. 2012 Jun;235(2):464-8. doi: 10.1016/j.expneurol.2011.10.023. Epub 2011 Oct 31. Review.

PMID:
22075182
20.

Chromosomal haplotypes by genetic phasing of human families.

Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF.

Am J Hum Genet. 2011 Sep 9;89(3):382-97. doi: 10.1016/j.ajhg.2011.07.023.

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