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De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM; NISC Comparative Sequencing Program, Mullikin JC, Burgess SM.

Sci Adv. 2019 Jun 26;5(6):eaav0547. doi: 10.1126/sciadv.aav0547. eCollection 2019 Jun.


Multiple non-catalytic ADAMs are novel integrin α4 ligands.

Wang L, Hoggard JA, Korleski ED, Long GV, Ree BC, Hensley K, Bond SR, Wolfsberg TG, Chen J, Zeczycki TN, Bridges LC.

Mol Cell Biochem. 2018 May;442(1-2):29-38. doi: 10.1007/s11010-017-3190-y. Epub 2017 Sep 14.


Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer.

Winter JM, Gildea DE, Andreas JP, Gatti DM, Williams KA, Lee M, Hu Y, Zhang S; NISC Comparative Sequencing Program, Mullikin JC, Wolfsberg TG, McDonnell SK, Fogarty ZC, Larson MC, French AJ, Schaid DJ, Thibodeau SN, Churchill GA, Crawford NP.

Cell Syst. 2017 Jan 25;4(1):31-45.e6. doi: 10.1016/j.cels.2016.10.018. Epub 2016 Dec 1.


A 2.5-year snapshot of Mendelian discovery.

Solomon BD, Lee T, Nguyen AD, Wolfsberg TG.

Mol Genet Genomic Med. 2016 Apr 3;4(4):392-4. doi: 10.1002/mgg3.221. eCollection 2016 Jul. No abstract available.


Mutational analysis of the tyrosine kinome in serous and clear cell endometrial cancer uncovers rare somatic mutations in TNK2 and DDR1.

Rudd ML, Mohamed H, Price JC, O'Hara AJ, Le Gallo M, Urick ME; NISC Comparative Sequencing Program, Cruz P, Zhang S, Hansen NF, Godwin AK, Sgroi DC, Wolfsberg TG, Mullikin JC, Merino MJ, Bell DW.

BMC Cancer. 2014 Nov 26;14:884. doi: 10.1186/1471-2407-14-884.


trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.

Renaud G, LaFave MC, Liang J, Wolfsberg TG, Burgess SM.

BMC Bioinformatics. 2014 Oct 13;15:329. doi: 10.1186/1471-2105-15-329.


A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi.

Moreland RT, Nguyen AD, Ryan JF, Schnitzler CE, Koch BJ, Siewert K, Wolfsberg TG, Baxevanis AD.

BMC Genomics. 2014 Apr 28;15:316. doi: 10.1186/1471-2164-15-316.


MLV integration site selection is driven by strong enhancers and active promoters.

LaFave MC, Varshney GK, Gildea DE, Wolfsberg TG, Baxevanis AD, Burgess SM.

Nucleic Acids Res. 2014 Apr;42(7):4257-69. doi: 10.1093/nar/gkt1399. Epub 2014 Jan 23.


The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution.

Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P; NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD.

Science. 2013 Dec 13;342(6164):1242592. doi: 10.1126/science.1242592.


Clinical genomic database.

Solomon BD, Nguyen AD, Bear KA, Wolfsberg TG.

Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9851-5. doi: 10.1073/pnas.1302575110. Epub 2013 May 21.


A multicenter study of glucocerebrosidase mutations in dementia with Lewy bodies.

Nalls MA, Duran R, Lopez G, Kurzawa-Akanbi M, McKeith IG, Chinnery PF, Morris CM, Theuns J, Crosiers D, Cras P, Engelborghs S, De Deyn PP, Van Broeckhoven C, Mann DM, Snowden J, Pickering-Brown S, Halliwell N, Davidson Y, Gibbons L, Harris J, Sheerin UM, Bras J, Hardy J, Clark L, Marder K, Honig LS, Berg D, Maetzler W, Brockmann K, Gasser T, Novellino F, Quattrone A, Annesi G, De Marco EV, Rogaeva E, Masellis M, Black SE, Bilbao JM, Foroud T, Ghetti B, Nichols WC, Pankratz N, Halliday G, Lesage S, Klebe S, Durr A, Duyckaerts C, Brice A, Giasson BI, Trojanowski JQ, Hurtig HI, Tayebi N, Landazabal C, Knight MA, Keller M, Singleton AB, Wolfsberg TG, Sidransky E.

JAMA Neurol. 2013 Jun;70(6):727-35. doi: 10.1001/jamaneurol.2013.1925.


A large-scale zebrafish gene knockout resource for the genome-wide study of gene function.

Varshney GK, Lu J, Gildea DE, Huang H, Pei W, Yang Z, Huang SC, Schoenfeld D, Pho NH, Casero D, Hirase T, Mosbrook-Davis D, Zhang S, Jao LE, Zhang B, Woods IG, Zimmerman S, Schier AF, Wolfsberg TG, Pellegrini M, Burgess SM, Lin S.

Genome Res. 2013 Apr;23(4):727-35. doi: 10.1101/gr.151464.112. Epub 2013 Feb 4.


The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion.

Varshney GK, Huang H, Zhang S, Lu J, Gildea DE, Yang Z, Wolfsberg TG, Lin S, Burgess SM.

Nucleic Acids Res. 2013 Jan;41(Database issue):D861-4. doi: 10.1093/nar/gks946. Epub 2012 Nov 24.


High-efficiency transduction of rhesus hematopoietic repopulating cells by a modified HIV1-based lentiviral vector.

Uchida N, Hargrove PW, Lap CJ, Evans ME, Phang O, Bonifacino AC, Krouse AE, Metzger ME, Nguyen AD, Hsieh MM, Wolfsberg TG, Donahue RE, Persons DA, Tisdale JF.

Mol Ther. 2012 Oct;20(10):1882-92. doi: 10.1038/mt.2012.159. Epub 2012 Aug 7.


The stat3/socs3a pathway is a key regulator of hair cell regeneration in zebrafish. [corrected].

Liang J, Wang D, Renaud G, Wolfsberg TG, Wilson AF, Burgess SM.

J Neurosci. 2012 Aug 1;32(31):10662-73. doi: 10.1523/JNEUROSCI.5785-10.2012. Erratum in: J Neurosci. 2012 Oct 3;32(40):14052.


Predisposition to cancer caused by genetic and functional defects of mammalian Atad5.

Bell DW, Sikdar N, Lee KY, Price JC, Chatterjee R, Park HD, Fox J, Ishiai M, Rudd ML, Pollock LM, Fogoros SK, Mohamed H, Hanigan CL; NISC Comparative Sequencing Program, Zhang S, Cruz P, Renaud G, Hansen NF, Cherukuri PF, Borate B, McManus KJ, Stoepel J, Sipahimalani P, Godwin AK, Sgroi DC, Merino MJ, Elliot G, Elkahloun A, Vinson C, Takata M, Mullikin JC, Wolfsberg TG, Hieter P, Lim DS, Myung K.

PLoS Genet. 2011 Aug;7(8):e1002245. doi: 10.1371/journal.pgen.1002245. Epub 2011 Aug 25.


Using the NCBI Map Viewer to browse genomic sequence data.

Wolfsberg TG.

Curr Protoc Hum Genet. 2011 Apr;Chapter 18:Unit18.5. doi: 10.1002/0471142905.hg1805s69.


A curated online resource for SOX10 and pigment cell molecular genetic pathways.

Baxter LL, Moreland RT, Nguyen AD, Wolfsberg TG, Pavan WJ.

Database (Oxford). 2010 Oct 25;2010:baq025. doi: 10.1093/database/baq025.


Feline leukemia virus integrase and capsid packaging functions do not change the insertion profile of standard Moloney retroviral vectors.

Métais JY, Topp S, Doty RT, Borate B, Nguyen AD, Wolfsberg TG, Abkowitz JL, Dunbar CE.

Gene Ther. 2010 Jun;17(6):799-804. doi: 10.1038/gt.2010.24. Epub 2010 Mar 18.


Using the NCBI map viewer to browse genomic sequence data.

Wolfsberg TG.

Curr Protoc Bioinformatics. 2010 Mar;Chapter 1:Unit 1.5.1-25. doi: 10.1002/0471250953.bi0105s29.


No evidence for clonal selection due to lentiviral integration sites in human induced pluripotent stem cells.

Winkler T, Cantilena A, Métais JY, Xu X, Nguyen AD, Borate B, Antosiewicz-Bourget JE, Wolfsberg TG, Thomson JA, Dunbar CE.

Stem Cells. 2010 Apr;28(4):687-94. doi: 10.1002/stem.322.


Multicenter analysis of glucocerebrosidase mutations in Parkinson's disease.

Sidransky E, Nalls MA, Aasly JO, Aharon-Peretz J, Annesi G, Barbosa ER, Bar-Shira A, Berg D, Bras J, Brice A, Chen CM, Clark LN, Condroyer C, De Marco EV, Dürr A, Eblan MJ, Fahn S, Farrer MJ, Fung HC, Gan-Or Z, Gasser T, Gershoni-Baruch R, Giladi N, Griffith A, Gurevich T, Januario C, Kropp P, Lang AE, Lee-Chen GJ, Lesage S, Marder K, Mata IF, Mirelman A, Mitsui J, Mizuta I, Nicoletti G, Oliveira C, Ottman R, Orr-Urtreger A, Pereira LV, Quattrone A, Rogaeva E, Rolfs A, Rosenbaum H, Rozenberg R, Samii A, Samaddar T, Schulte C, Sharma M, Singleton A, Spitz M, Tan EK, Tayebi N, Toda T, Troiano AR, Tsuji S, Wittstock M, Wolfsberg TG, Wu YR, Zabetian CP, Zhao Y, Ziegler SG.

N Engl J Med. 2009 Oct 22;361(17):1651-61. doi: 10.1056/NEJMoa0901281.


Identifying putative promoter regions of Hermansky-Pudlak syndrome genes by means of phylogenetic footprinting.

Stanescu H, Wolfsberg TG, Moreland RT, Ayub MH, Erickson E, Westbroek W, Huizing M, Gahl WA, Helip-Wooley A.

Ann Hum Genet. 2009 Jul;73(Pt 4):422-8. doi: 10.1111/j.1469-1809.2009.00525.x.


Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota.

Scharschmidt TC, List K, Grice EA, Szabo R; NISC Comparative Sequencing Program, Renaud G, Lee CC, Wolfsberg TG, Bugge TH, Segre JA.

J Invest Dermatol. 2009 Oct;129(10):2435-42. doi: 10.1038/jid.2009.104. Epub 2009 Apr 23.


Sustained high-level polyclonal hematopoietic marking and transgene expression 4 years after autologous transplantation of rhesus macaques with SIV lentiviral vector-transduced CD34+ cells.

Kim YJ, Kim YS, Larochelle A, Renaud G, Wolfsberg TG, Adler R, Donahue RE, Hematti P, Hong BK, Roayaei J, Akagi K, Riberdy JM, Nienhuis AW, Dunbar CE, Persons DA.

Blood. 2009 May 28;113(22):5434-43. doi: 10.1182/blood-2008-10-185199. Epub 2009 Apr 1.


Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.

Toleno DM, Renaud G, Wolfsberg TG, Islam M, Wildman DE, Siegmund KD, Hacia JG.

BMC Bioinformatics. 2009 Mar 5;10:77. doi: 10.1186/1471-2105-10-77.


Gpnmb is a melanoblast-expressed, MITF-dependent gene.

Loftus SK, Antonellis A, Matera I, Renaud G, Baxter LL, Reid D, Wolfsberg TG, Chen Y, Wang C; NISC Comparative Sequencing Program, Prasad MK, Bessling SL, McCallion AS, Green ED, Bennett DC, Pavan WJ.

Pigment Cell Melanoma Res. 2009 Feb;22(1):99-110. doi: 10.1111/j.1755-148X.2008.00518.x. Epub 2008 Nov 1.


Identification of neural crest and glial enhancers at the mouse Sox10 locus through transgenesis in zebrafish.

Antonellis A, Huynh JL, Lee-Lin SQ, Vinton RM, Renaud G, Loftus SK, Elliot G, Wolfsberg TG, Green ED, McCallion AS, Pavan WJ.

PLoS Genet. 2008 Sep 5;4(9):e1000174. doi: 10.1371/journal.pgen.1000174.


Reduced genotoxicity of avian sarcoma leukosis virus vectors in rhesus long-term repopulating cells compared to standard murine retrovirus vectors.

Hu J, Renaud G, Gomes TJ, Ferris A, Hendrie PC, Donahue RE, Hughes SH, Wolfsberg TG, Russell DW, Dunbar CE.

Mol Ther. 2008 Sep;16(9):1617-23. doi: 10.1038/mt.2008.135. Epub 2008 Jun 24. Erratum in: Mol Ther. 2008 Oct;16(10):1770.. Golmes, Theotonius [corrected to Gomes, Theotonius J].


A diversity profile of the human skin microbiota.

Grice EA, Kong HH, Renaud G, Young AC; NISC Comparative Sequencing Program, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA.

Genome Res. 2008 Jul;18(7):1043-50. doi: 10.1101/gr.075549.107. Epub 2008 May 23.


Sequence similarity searching using the BLAST family of programs.

Wolfsberg TG, Madden TL.

Curr Protoc Protein Sci. 2001 May;Chapter 2:Unit2.5. doi: 10.1002/0471140864.ps0205s15.


Using the NCBI Map Viewer to browse genomic sequence data.

Wolfsberg TG.

Curr Protoc Bioinformatics. 2007 Jan;Chapter 1:Unit 1.5. doi: 10.1002/0471250953.bi0105s16.


DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status.

Pike BL, Greiner TC, Wang X, Weisenburger DD, Hsu YH, Renaud G, Wolfsberg TG, Kim M, Weisenberger DJ, Siegmund KD, Ye W, Groshen S, Mehrian-Shai R, Delabie J, Chan WC, Laird PW, Hacia JG.

Leukemia. 2008 May;22(5):1035-43. doi: 10.1038/leu.2008.18. Epub 2008 Feb 21.


Sequence similarity searching using the BLAST family of programs.

Wolfsberg TG, Madden TL.

Curr Protoc Mol Biol. 2001 May;Chapter 19:Unit 19.3. doi: 10.1002/0471142727.mb1903s46.


Identification of motifs in protein sequences.

Sonnhammer EL, Wolfsberg TG.

Curr Protoc Cell Biol. 2001 May;Appendix 1:Appendix 1C. doi: 10.1002/0471143030.cba01cs00. Review.


The ENCODEdb portal: simplified access to ENCODE Consortium data.

Elnitski LL, Shah P, Moreland RT, Umayam L, Wolfsberg TG, Baxevanis AD.

Genome Res. 2007 Jun;17(6):954-9.


Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function.

Baxter LL, Hsu BJ, Umayam L, Wolfsberg TG, Larson DM, Frith MC, Kawai J, Hayashizaki Y, Carninci P, Pavan WJ.

Pigment Cell Res. 2007 Jun;20(3):201-9.


DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays.

Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS.

Nat Methods. 2006 Jul;3(7):503-9.


Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS).

Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, Zhou D, Luo S, Vasicek TJ, Daly MJ, Wolfsberg TG, Collins FS.

Genome Res. 2006 Jan;16(1):123-31. Epub 2005 Dec 12.


Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements.

Eriksson PR, Mendiratta G, McLaughlin NB, Wolfsberg TG, Mariño-Ramírez L, Pompa TA, Jainerin M, Landsman D, Shen CH, Clark DJ.

Mol Cell Biol. 2005 Oct;25(20):9127-37.


Distinct genomic integration of MLV and SIV vectors in primate hematopoietic stem and progenitor cells.

Hematti P, Hong BK, Ferguson C, Adler R, Hanawa H, Sellers S, Holt IE, Eckfeldt CE, Sharma Y, Schmidt M, von Kalle C, Persons DA, Billings EM, Verfaillie CM, Nienhuis AW, Wolfsberg TG, Dunbar CE, Calmels B.

PLoS Biol. 2004 Dec;2(12):e423. Epub 2004 Nov 23.


GeneLink: a database to facilitate genetic studies of complex traits.

Gillanders EM, Masiello A, Gildea D, Umayam L, Duggal P, Jones MP, Klein AP, Freas-Lutz D, Ibay G, Trout K, Wolfsberg TG, Trent JM, Bailey-Wilson JE, Baxevanis AD.

BMC Genomics. 2004 Oct 18;5:81.


Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells.

Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS.

Proc Natl Acad Sci U S A. 2004 Feb 17;101(7):1892-7. Epub 2004 Feb 9.


Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites.

Crawford GE, Holt IE, Mullikin JC, Tai D, Blakesley R, Bouffard G, Young A, Masiello C, Green ED, Wolfsberg TG, Collins FS; National Institutes Of Health Intramural Sequencing Center.

Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):992-7. Epub 2004 Jan 19.


A user's guide to the human genome.

Wolfsberg TG, Wetterstrand KA, Guyer MS, Collins FS, Baxevanis AD.

Nat Genet. 2002 Sep;32 Suppl:1-79. No abstract available. Erratum in: Nat Genet 2002 Oct;32(2):332.


Web alert. Differentiation and gene regulation.

Wolfsberg TG.

Curr Opin Genet Dev. 2001 Oct;11(5):491. No abstract available.


Expressed sequence tags (ESTs).

Wolfsberg TG, Landsman D.

Methods Biochem Anal. 2001;43:283-301. No abstract available.


Web alert. Genetics of disease.

Wolfsberg TG, Makalowska I, Makalowski W.

Curr Opin Genet Dev. 2001 Jun;11(3):237-8.


Organelle genome resource at NCBI.

Wolfsberg TG, Schafer S, Tatusov RL, Tatusov TA.

Trends Biochem Sci. 2001 Mar;26(3):199-203. No abstract available.


Guide to the draft human genome.

Wolfsberg TG, McEntyre J, Schuler GD.

Nature. 2001 Feb 15;409(6822):824-6.


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