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Items: 1 to 50 of 82

1.

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.

PMID:
30188530
2.

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.

PMID:
30010675
3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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
18.

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.

19.

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.

20.

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
21.

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.

22.

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
23.

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.

24.

An integrative approach to inferring biologically meaningful gene modules.

Cho JH, Wang K, Galas DJ.

BMC Syst Biol. 2011 Jul 26;5:117. doi: 10.1186/1752-0509-5-117.

25.

MicroRNA as biomarkers and regulators in B-cell chronic lymphocytic leukemia.

Moussay E, Wang K, Cho JH, van Moer K, Pierson S, Paggetti J, Nazarov PV, Palissot V, Hood LE, Berchem G, Galas DJ.

Proc Natl Acad Sci U S A. 2011 Apr 19;108(16):6573-8. doi: 10.1073/pnas.1019557108. Epub 2011 Apr 1.

26.

Markov logic networks in the analysis of genetic data.

Sakhanenko NA, Galas DJ.

J Comput Biol. 2010 Nov;17(11):1491-508. doi: 10.1089/cmb.2010.0044. Epub 2010 Oct 20.

27.

Embryonal carcinoma cell induction of miRNA and mRNA changes in co-cultured prostate stromal fibromuscular cells.

Vêncio EF, Pascal LE, Page LS, Denyer G, Wang AJ, Ruohola-Baker H, Zhang S, Wang K, Galas DJ, Liu AY.

J Cell Physiol. 2011 Jun;226(6):1479-88. doi: 10.1002/jcp.22464.

28.

The microRNA spectrum in 12 body fluids.

Weber JA, Baxter DH, Zhang S, Huang DY, Huang KH, Lee MJ, Galas DJ, Wang K.

Clin Chem. 2010 Nov;56(11):1733-41. doi: 10.1373/clinchem.2010.147405. Epub 2010 Sep 16.

29.

Export of microRNAs and microRNA-protective protein by mammalian cells.

Wang K, Zhang S, Weber J, Baxter D, Galas DJ.

Nucleic Acids Res. 2010 Nov;38(20):7248-59. doi: 10.1093/nar/gkq601. Epub 2010 Jul 7.

30.

A systems-biology approach to modular genetic complexity.

Carter GW, Rush CG, Uygun F, Sakhanenko NA, Galas DJ, Galitski T.

Chaos. 2010 Jun;20(2):026102. doi: 10.1063/1.3455183. Review.

31.

Analysis of genetic inheritance in a family quartet by whole-genome sequencing.

Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ.

Science. 2010 Apr 30;328(5978):636-9. doi: 10.1126/science.1186802. Epub 2010 Mar 10.

32.

Biological Information as Set-Based Complexity.

Galas DJ, Nykter M, Carter GW, Price ND, Shmulevich I.

IEEE Trans Inf Theory. 2010 Feb;56(2):667-677. Epub 2010 Feb 25.

33.

Maximal extraction of biological information from genetic interaction data.

Carter GW, Galas DJ, Galitski T.

PLoS Comput Biol. 2009 Apr;5(4):e1000347. doi: 10.1371/journal.pcbi.1000347. Epub 2009 Apr 3.

34.

Circulating microRNAs, potential biomarkers for drug-induced liver injury.

Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ.

Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4402-7. doi: 10.1073/pnas.0813371106. Epub 2009 Feb 25.

35.

Systems biology at the Institute for Systems Biology.

Hood L, Rowen L, Galas DJ, Aitchison JD.

Brief Funct Genomic Proteomic. 2008 Jul;7(4):239-48. doi: 10.1093/bfgp/eln027. Epub 2008 Jun 25.

PMID:
18579616
36.

Isothermal DNA amplification coupled with DNA nanosphere-based colorimetric detection.

Tan E, Wong J, Nguyen D, Zhang Y, Erwin B, Van Ness LK, Baker SM, Galas DJ, Niemz A.

Anal Chem. 2005 Dec 15;77(24):7984-92.

PMID:
16351146
37.

Duplication models for biological networks.

Chung F, Lu L, Dewey TG, Galas DJ.

J Comput Biol. 2003;10(5):677-87.

PMID:
14633392
38.

An historical perspective on genomic technologies.

Galas DJ, McCormack SJ.

Curr Issues Mol Biol. 2003 Oct;5(4):123-7. Review.

39.

Global science and U.S. security.

Galas DJ, Riggs H.

Science. 2003 Jun 20;300(5627):1847. No abstract available.

40.

Isothermal reactions for the amplification of oligonucleotides.

Van Ness J, Van Ness LK, Galas DJ.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4504-9. Epub 2003 Apr 4.

41.

Defining the mandate of proteomics in the post-genomics era: workshop report.

Kenyon GL, DeMarini DM, Fuchs E, Galas DJ, Kirsch JF, Leyh TS, Moos WH, Petsko GA, Ringe D, Rubin GM, Sheahan LC; National Research Council Steering Committee.

Mol Cell Proteomics. 2002 Oct;1(10):763-80.

42.

A duplication growth model of gene expression networks.

Bhan A, Galas DJ, Dewey TG.

Bioinformatics. 2002 Nov;18(11):1486-93.

PMID:
12424120
43.

Dynamic models of gene expression and classification.

Dewey TG, Galas DJ.

Funct Integr Genomics. 2001 Mar;1(4):269-78.

PMID:
11793246
44.

The invention of footprinting.

Galas DJ.

Trends Biochem Sci. 2001 Nov;26(11):690-3. No abstract available.

PMID:
11701330
45.

Sequence interpretation. Making sense of the sequence.

Galas DJ.

Science. 2001 Feb 16;291(5507):1257-60. No abstract available.

PMID:
11233451
46.

DNA bending and twisting properties of integration host factor determined by DNA cyclization.

Teter B, Goodman SD, Galas DJ.

Plasmid. 2000 Jan;43(1):73-84.

PMID:
10610821
47.

Interaction of Fis protein with DNA: bending and specificity of binding.

Bétermier M, Galas DJ, Chandler M.

Biochimie. 1994;76(10-11):958-67.

PMID:
7748940
48.

Important unanswered questions concerning radiation risk estimates.

Galas DJ.

Radiat Res. 1993 Oct;136(1):139-43.

PMID:
8210331
49.

Functional organization of the ends of IS 1: specific binding site for an IS1-encoded protein.

Zerbib D, Prentki P, Gamas P, Freund E, Galas DJ, Chandler M.

Mol Microbiol. 1990 Sep;4(9):1477-1486. doi: 10.1111/j.1365-2958.1990.tb02058.x.

PMID:
28776821
50.

Functional organization of the ends of IS1: specific binding site for an IS 1-encoded protein.

Zerbib D, Prentki P, Gamas P, Freund E, Galas DJ, Chandler M.

Mol Microbiol. 1990 Sep;4(9):1477-86.

PMID:
1962838

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