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Items: 27

1.

Enriched power of disease-concordant twin-case-only design in detecting interactions in genome-wide association studies.

Li W, Baumbach J, Mohammadnejad A, Brasch-Andersen C, Vandin F, Korbel JO, Tan Q.

Eur J Hum Genet. 2019 Apr;27(4):631-636. doi: 10.1038/s41431-018-0320-2. Epub 2019 Jan 18.

PMID:
30659261
2.

CoExpresso: assess the quantitative behavior of protein complexes in human cells.

Chalabi MH, Tsiamis V, Käll L, Vandin F, Schwämmle V.

BMC Bioinformatics. 2019 Jan 9;20(1):17. doi: 10.1186/s12859-018-2573-8.

3.

Principles of Systems Biology, No. 31.

Cho H, Berger B, Peng J, Galitzine C, Vitek O, Beltran PMJ, Cristea IM, Görtler F, Solbrig S, Wettig T, Oefner PJ, Spang R, Altenbuchinger M, Basso RS, Hochbaum D, Vandin F, Silverbush D, Cristea S, Yanovich G, Geiger T, Beerenwinkel N, Sharan R, Zhou Z, Luhmann N, Alikhan NF, Achtman M.

Cell Syst. 2018 Aug 22;7(2):133-135. doi: 10.1016/j.cels.2018.08.005.

PMID:
30138580
4.

De novo pathway-based biomarker identification.

Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J.

Nucleic Acids Res. 2017 Sep 19;45(16):e151. doi: 10.1093/nar/gkx642.

5.

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology.

Shrestha R, Hodzic E, Sauerwald T, Dao P, Wang K, Yeung J, Anderson S, Vandin F, Haffari G, Collins CC, Sahinalp SC.

Genome Res. 2017 Sep;27(9):1573-1588. doi: 10.1101/gr.221218.117. Epub 2017 Jul 18.

6.

Computational Methods for Characterizing Cancer Mutational Heterogeneity.

Vandin F.

Front Genet. 2017 Jun 14;8:83. doi: 10.3389/fgene.2017.00083. eCollection 2017. Review.

7.

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing.

Almeida D, Skov I, Lund J, Mohammadnejad A, Silva A, Vandin F, Tan Q, Baumbach J, Röttger R.

J Integr Bioinform. 2016 Dec 18;13(4):294. doi: 10.2390/biecoll-jib-2016-294.

PMID:
28187410
8.

Disease-Concordant Twins Empower Genetic Association Studies.

Tan Q, Li W, Vandin F.

Ann Hum Genet. 2017 Jan;81(1):20-26. doi: 10.1111/ahg.12181. Epub 2016 Dec 23.

9.

Efficient detection of differentially methylated regions using DiMmeR.

Almeida D, Skov I, Silva A, Vandin F, Tan Q, Röttger R, Baumbach J.

Bioinformatics. 2017 Feb 15;33(4):549-551. doi: 10.1093/bioinformatics/btw657.

PMID:
27794558
10.

Erratum to: CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.

Leiserson MD, Wu HT, Vandin F, Raphael BJ.

Genome Biol. 2016 Aug 2;17(1):168. No abstract available.

11.

Differentially Methylated Genomic Regions in Birth-Weight Discordant Twin Pairs.

Chen M, Baumbach J, Vandin F, Röttger R, Barbosa E, Dong M, Frost M, Christiansen L, Tan Q.

Ann Hum Genet. 2016 Mar;80(2):81-7. doi: 10.1111/ahg.12146. Epub 2016 Feb 1.

12.

Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer.

Leiserson MD, Vandin F, Wu HT, Raphael BJ.

Nat Genet. 2016 Feb;48(2):106-8. doi: 10.1038/ng.3491. No abstract available.

PMID:
26813760
13.

On the Sample Complexity of Cancer Pathways Identification.

Vandin F, Raphael BJ, Upfal E.

J Comput Biol. 2016 Jan;23(1):30-41. doi: 10.1089/cmb.2015.0100. Epub 2015 Dec 8.

14.

CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer.

Leiserson MD, Wu HT, Vandin F, Raphael BJ.

Genome Biol. 2015 Aug 8;16:160. doi: 10.1186/s13059-015-0700-7. Erratum in: Genome Biol. 2016;17(1):168.

15.

Accurate computation of survival statistics in genome-wide studies.

Vandin F, Papoutsaki A, Raphael BJ, Upfal E.

PLoS Comput Biol. 2015 May 7;11(5):e1004071. doi: 10.1371/journal.pcbi.1004071. eCollection 2015 May.

16.

Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data.

Raphael BJ, Vandin F.

J Comput Biol. 2015 Jun;22(6):510-27. doi: 10.1089/cmb.2014.0161. Epub 2015 Mar 18.

17.

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.

Leiserson MD, Vandin F, Wu HT, Dobson JR, Eldridge JV, Thomas JL, Papoutsaki A, Kim Y, Niu B, McLellan M, Lawrence MS, Gonzalez-Perez A, Tamborero D, Cheng Y, Ryslik GA, Lopez-Bigas N, Getz G, Ding L, Raphael BJ.

Nat Genet. 2015 Feb;47(2):106-14. doi: 10.1038/ng.3168. Epub 2014 Dec 15.

18.

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.

Raphael BJ, Dobson JR, Oesper L, Vandin F.

Genome Med. 2014 Jan 30;6(1):5. doi: 10.1186/gm524. eCollection 2014. Review.

19.

Mutational landscape and significance across 12 major cancer types.

Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MDM, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L.

Nature. 2013 Oct 17;502(7471):333-339. doi: 10.1038/nature12634.

20.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

Cancer Genome Atlas Research Network, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ Jr, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G.

N Engl J Med. 2013 May 30;368(22):2059-74. doi: 10.1056/NEJMoa1301689. Epub 2013 May 1. Erratum in: N Engl J Med. 2013 Jul 4;369(1):98.

21.

Ballast: a ball-based algorithm for structural motifs.

He L, Vandin F, Pandurangan G, Bailey-Kellogg C.

J Comput Biol. 2013 Feb;20(2):137-51. doi: 10.1089/cmb.2012.0246.

22.

Finding driver pathways in cancer: models and algorithms.

Vandin F, Upfal E, Raphael BJ.

Algorithms Mol Biol. 2012 Sep 6;7(1):23. doi: 10.1186/1748-7188-7-23.

23.

The mutational landscape of lethal castration-resistant prostate cancer.

Grasso CS, Wu YM, Robinson DR, Cao X, Dhanasekaran SM, Khan AP, Quist MJ, Jing X, Lonigro RJ, Brenner JC, Asangani IA, Ateeq B, Chun SY, Siddiqui J, Sam L, Anstett M, Mehra R, Prensner JR, Palanisamy N, Ryslik GA, Vandin F, Raphael BJ, Kunju LP, Rhodes DR, Pienta KJ, Chinnaiyan AM, Tomlins SA.

Nature. 2012 Jul 12;487(7406):239-43. doi: 10.1038/nature11125.

24.

Discovery of mutated subnetworks associated with clinical data in cancer.

Vandin F, Clay P, Upfal E, Raphael BJ.

Pac Symp Biocomput. 2012:55-66.

25.

De novo discovery of mutated driver pathways in cancer.

Vandin F, Upfal E, Raphael BJ.

Genome Res. 2012 Feb;22(2):375-85. doi: 10.1101/gr.120477.111. Epub 2011 Jun 7.

26.

MADMX: a strategy for maximal dense motif extraction.

Grossi R, Pietracaprina A, Pisanti N, Pucci G, Upfal E, Vandin F.

J Comput Biol. 2011 Apr;18(4):535-45. doi: 10.1089/cmb.2010.0177. Epub 2011 Mar 21.

PMID:
21417937
27.

Algorithms for detecting significantly mutated pathways in cancer.

Vandin F, Upfal E, Raphael BJ.

J Comput Biol. 2011 Mar;18(3):507-22. doi: 10.1089/cmb.2010.0265.

PMID:
21385051

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