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Items: 35

1.

Genome-wide somatic variant calling using localized colored de Bruijn graphs.

Narzisi G, Corvelo A, Arora K, Bergmann EA, Shah M, Musunuri R, Emde AK, Robine N, Vacic V, Zody MC.

Commun Biol. 2018 Mar 22;1:20. doi: 10.1038/s42003-018-0023-9. eCollection 2018.

2.

Placenta and appetite genes GDF15 and IGFBP7 are associated with hyperemesis gravidarum.

Fejzo MS, Sazonova OV, Sathirapongsasuti JF, Hallgrímsdóttir IB, Vacic V, MacGibbon KW, Schoenberg FP, Mancuso N, Slamon DJ, Mullin PM; 23andMe Research Team.

Nat Commun. 2018 Mar 21;9(1):1178. doi: 10.1038/s41467-018-03258-0.

3.

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.

Neurol Genet. 2017 Jul 11;3(4):e164. doi: 10.1212/NXG.0000000000000164. eCollection 2017 Aug.

4.

Indel variant analysis of short-read sequencing data with Scalpel.

Fang H, Bergmann EA, Arora K, Vacic V, Zody MC, Iossifov I, O'Rawe JA, Wu Y, Jimenez Barron LT, Rosenbaum J, Ronemus M, Lee YH, Wang Z, Dikoglu E, Jobanputra V, Lyon GJ, Wigler M, Schatz MC, Narzisi G.

Nat Protoc. 2016 Dec;11(12):2529-2548. doi: 10.1038/nprot.2016.150. Epub 2016 Nov 17.

5.

Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors.

Bagrodia A, Lee BH, Lee W, Cha EK, Sfakianos JP, Iyer G, Pietzak EJ, Gao SP, Zabor EC, Ostrovnaya I, Kaffenberger SD, Syed A, Arcila ME, Chaganti RS, Kundra R, Eng J, Hreiki J, Vacic V, Arora K, Oschwald DM, Berger MF, Bajorin DF, Bains MS, Schultz N, Reuter VE, Sheinfeld J, Bosl GJ, Al-Ahmadie HA, Solit DB, Feldman DR.

J Clin Oncol. 2016 Nov 20;34(33):4000-4007. doi: 10.1200/JCO.2016.68.7798. Epub 2016 Sep 30.

6.

Conpair: concordance and contamination estimator for matched tumor-normal pairs.

Bergmann EA, Chen BJ, Arora K, Vacic V, Zody MC.

Bioinformatics. 2016 Oct 15;32(20):3196-3198. Epub 2016 Jun 26.

7.

Differential burden of rare protein truncating variants in Alzheimer's disease patients compared to centenarians.

Freudenberg-Hua Y, Li W, Abhyankar A, Vacic V, Cortes V, Ben-Avraham D, Koppel J, Greenwald B, Germer S; T2D-GENES Consortium, Darnell RB, Barzilai N, Freudenberg J, Atzmon G, Davies P.

Hum Mol Genet. 2016 Jul 15;25(14):3096-3105. Epub 2016 Jun 3.

8.

Integrative genetic analysis of mouse and human AML identifies cooperating disease alleles.

Hatlen MA, Arora K, Vacic V, Grabowska EA, Liao W, Riley-Gillis B, Oschwald DM, Wang L, Joergens JE, Shih AH, Rapaport F, Gu S, Voza F, Asai T, Neel BG, Kharas MG, Gonen M, Levine RL, Nimer SD.

J Exp Med. 2016 Jan 11;213(1):25-34. doi: 10.1084/jem.20150524. Epub 2015 Dec 14.

9.

The Influence of Microdeletions and Microduplications of 16p11.2 on Global Transcription Profiles.

Kusenda M, Vacic V, Malhotra D, Rodgers L, Pavon K, Meth J, Kumar RA, Christian SL, Peeters H, Cho SS, Addington A, Rapoport JL, Sebat J.

J Child Neurol. 2015 Dec;30(14):1947-53. doi: 10.1177/0883073815602066. Epub 2015 Sep 20.

10.

Genome-wide association study of schizophrenia in Ashkenazi Jews.

Goes FS, McGrath J, Avramopoulos D, Wolyniec P, Pirooznia M, Ruczinski I, Nestadt G, Kenny EE, Vacic V, Peters I, Lencz T, Darvasi A, Mulle JG, Warren ST, Pulver AE.

Am J Med Genet B Neuropsychiatr Genet. 2015 Dec;168(8):649-59. doi: 10.1002/ajmg.b.32349. Epub 2015 Jul 21.

PMID:
26198764
11.

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response.

Beltran H, Eng K, Mosquera JM, Sigaras A, Romanel A, Rennert H, Kossai M, Pauli C, Faltas B, Fontugne J, Park K, Banfelder J, Prandi D, Madhukar N, Zhang T, Padilla J, Greco N, McNary TJ, Herrscher E, Wilkes D, MacDonald TY, Xue H, Vacic V, Emde AK, Oschwald D, Tan AY, Chen Z, Collins C, Gleave ME, Wang Y, Chakravarty D, Schiffman M, Kim R, Campagne F, Robinson BD, Nanus DM, Tagawa ST, Xiang JZ, Smogorzewska A, Demichelis F, Rickman DS, Sboner A, Elemento O, Rubin MA.

JAMA Oncol. 2015 Jul;1(4):466-74. doi: 10.1001/jamaoncol.2015.1313.

12.

Disease variants in genomes of 44 centenarians.

Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde AK, Ben-Avraham D, Barzilai N, Oschwald D, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P.

Mol Genet Genomic Med. 2014 Sep;2(5):438-50. doi: 10.1002/mgg3.86. Epub 2014 Jun 15.

13.

Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions.

Brannon AR, Vakiani E, Sylvester BE, Scott SN, McDermott G, Shah RH, Kania K, Viale A, Oschwald DM, Vacic V, Emde AK, Cercek A, Yaeger R, Kemeny NE, Saltz LB, Shia J, D'Angelica MI, Weiser MR, Solit DB, Berger MF.

Genome Biol. 2014 Aug 28;15(8):454. doi: 10.1186/s13059-014-0454-7.

14.

Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes.

Vacic V, Ozelius LJ, Clark LN, Bar-Shira A, Gana-Weisz M, Gurevich T, Gusev A, Kedmi M, Kenny EE, Liu X, Mejia-Santana H, Mirelman A, Raymond D, Saunders-Pullman R, Desnick RJ, Atzmon G, Burns ER, Ostrer H, Hakonarson H, Bergman A, Barzilai N, Darvasi A, Peter I, Guha S, Lencz T, Giladi N, Marder K, Pe'er I, Bressman SB, Orr-Urtreger A.

Hum Mol Genet. 2014 Sep 1;23(17):4693-702. doi: 10.1093/hmg/ddu158. Epub 2014 May 19.

15.

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM.

Nat Commun. 2014 Apr 11;5:3650. doi: 10.1038/ncomms4650.

16.

Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma.

Honeyman JN, Simon EP, Robine N, Chiaroni-Clarke R, Darcy DG, Lim II, Gleason CE, Murphy JM, Rosenberg BR, Teegan L, Takacs CN, Botero S, Belote R, Germer S, Emde AK, Vacic V, Bhanot U, LaQuaglia MP, Simon SM.

Science. 2014 Feb 28;343(6174):1010-4. doi: 10.1126/science.1249484.

17.

The variance of identity-by-descent sharing in the Wright-Fisher model.

Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I.

Genetics. 2013 Mar;193(3):911-28. doi: 10.1534/genetics.112.147215. Epub 2012 Dec 24.

18.

Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder.

Vacic V, Markwick PR, Oldfield CJ, Zhao X, Haynes C, Uversky VN, Iakoucheva LM.

PLoS Comput Biol. 2012;8(10):e1002709. doi: 10.1371/journal.pcbi.1002709. Epub 2012 Oct 4.

19.

High frequencies of de novo CNVs in bipolar disorder and schizophrenia.

Malhotra D, McCarthy S, Michaelson JJ, Vacic V, Burdick KE, Yoon S, Cichon S, Corvin A, Gary S, Gershon ES, Gill M, Karayiorgou M, Kelsoe JR, Krastoshevsky O, Krause V, Leibenluft E, Levy DL, Makarov V, Bhandari A, Malhotra AK, McMahon FJ, Nöthen MM, Potash JB, Rietschel M, Schulze TG, Sebat J.

Neuron. 2011 Dec 22;72(6):951-63. doi: 10.1016/j.neuron.2011.11.007.

20.

Disease mutations in disordered regions--exception to the rule?

Vacic V, Iakoucheva LM.

Mol Biosyst. 2012 Jan;8(1):27-32. doi: 10.1039/c1mb05251a. Epub 2011 Nov 14. Review.

21.

Duplications of the neuropeptide receptor gene VIPR2 confer significant risk for schizophrenia.

Vacic V, McCarthy S, Malhotra D, Murray F, Chou HH, Peoples A, Makarov V, Yoon S, Bhandari A, Corominas R, Iakoucheva LM, Krastoshevsky O, Krause V, Larach-Walters V, Welsh DK, Craig D, Kelsoe JR, Gershon ES, Leal SM, Dell Aquila M, Morris DW, Gill M, Corvin A, Insel PA, McClellan J, King MC, Karayiorgou M, Levy DL, DeLisi LE, Sebat J.

Nature. 2011 Mar 24;471(7339):499-503. doi: 10.1038/nature09884. Epub 2011 Feb 23. Erratum in: Nature. 2011 Jun 2;474(7349):114.

22.

Graphlet kernels for prediction of functional residues in protein structures.

Vacic V, Iakoucheva LM, Lonardi S, Radivojac P.

J Comput Biol. 2010 Jan;17(1):55-72. doi: 10.1089/cmb.2009.0029.

23.

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

Bogunovic D, O'Neill DW, Belitskaya-Levy I, Vacic V, Yu YL, Adams S, Darvishian F, Berman R, Shapiro R, Pavlick AC, Lonardi S, Zavadil J, Osman I, Bhardwaj N.

Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20429-34. doi: 10.1073/pnas.0905139106. Epub 2009 Nov 13.

24.

Microduplications of 16p11.2 are associated with schizophrenia.

McCarthy SE, Makarov V, Kirov G, Addington AM, McClellan J, Yoon S, Perkins DO, Dickel DE, Kusenda M, Krastoshevsky O, Krause V, Kumar RA, Grozeva D, Malhotra D, Walsh T, Zackai EH, Kaplan P, Ganesh J, Krantz ID, Spinner NB, Roccanova P, Bhandari A, Pavon K, Lakshmi B, Leotta A, Kendall J, Lee YH, Vacic V, Gary S, Iakoucheva LM, Crow TJ, Christian SL, Lieberman JA, Stroup TS, Lehtimäki T, Puura K, Haldeman-Englert C, Pearl J, Goodell M, Willour VL, Derosse P, Steele J, Kassem L, Wolff J, Chitkara N, McMahon FJ, Malhotra AK, Potash JB, Schulze TG, Nöthen MM, Cichon S, Rietschel M, Leibenluft E, Kustanovich V, Lajonchere CM, Sutcliffe JS, Skuse D, Gill M, Gallagher L, Mendell NR; Wellcome Trust Case Control Consortium, Craddock N, Owen MJ, O'Donovan MC, Shaikh TH, Susser E, Delisi LE, Sullivan PF, Deutsch CK, Rapoport J, Levy DL, King MC, Sebat J.

Nat Genet. 2009 Nov;41(11):1223-7. doi: 10.1038/ng.474. Epub 2009 Oct 25.

25.

Identification, analysis, and prediction of protein ubiquitination sites.

Radivojac P, Vacic V, Haynes C, Cocklin RR, Mohan A, Heyen JW, Goebl MG, Iakoucheva LM.

Proteins. 2010 Feb 1;78(2):365-80. doi: 10.1002/prot.22555.

26.

The unfoldomics decade: an update on intrinsically disordered proteins.

Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S1. doi: 10.1186/1471-2164-9-S2-S1.

27.

A probabilistic method for small RNA flowgram matching.

Vacic V, Jin H, Zhu JK, Lonardi S.

Pac Symp Biocomput. 2008:75-86.

28.

Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis.

Jin H, Vacic V, Girke T, Lonardi S, Zhu JK.

BMC Mol Biol. 2008 Jan 14;9:6. doi: 10.1186/1471-2199-9-6.

29.

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T.

J Comput Biol. 2007 Nov;14(9):1160-75.

PMID:
17990975
30.

Composition Profiler: a tool for discovery and visualization of amino acid composition differences.

Vacic V, Uversky VN, Dunker AK, Lonardi S.

BMC Bioinformatics. 2007 Jun 19;8:211.

31.

Characterization of molecular recognition features, MoRFs, and their binding partners.

Vacic V, Oldfield CJ, Mohan A, Radivojac P, Cortese MS, Uversky VN, Dunker AK.

J Proteome Res. 2007 Jun;6(6):2351-66. Epub 2007 May 9.

32.

DisProt: the Database of Disordered Proteins.

Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, Tantos A, Szabo B, Tompa P, Chen J, Uversky VN, Obradovic Z, Dunker AK.

Nucleic Acids Res. 2007 Jan;35(Database issue):D786-93. Epub 2006 Dec 1.

33.

Analysis of molecular recognition features (MoRFs).

Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, Dunker AK, Uversky VN.

J Mol Biol. 2006 Oct 6;362(5):1043-59. Epub 2006 Aug 4.

PMID:
16935303
34.

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.

Vacic V, Iakoucheva LM, Radivojac P.

Bioinformatics. 2006 Jun 15;22(12):1536-7. Epub 2006 Apr 21.

PMID:
16632492
35.

DisProt: a database of protein disorder.

Vucetic S, Obradovic Z, Vacic V, Radivojac P, Peng K, Iakoucheva LM, Cortese MS, Lawson JD, Brown CJ, Sikes JG, Newton CD, Dunker AK.

Bioinformatics. 2005 Jan 1;21(1):137-40. Epub 2004 Aug 13.

PMID:
15310560

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