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Items: 1 to 20 of 35


Efficient algorithms to discover alterations with complementary functional association in cancer.

Sarto Basso R, Hochbaum DS, Vandin F.

PLoS Comput Biol. 2019 May 23;15(5):e1006802. doi: 10.1371/journal.pcbi.1006802. eCollection 2019 May.


NoMAS: A Computational Approach to Find Mutated Subnetworks Associated With Survival in Genome-Wide Cancer Studies.

Altieri F, Hansen TV, Vandin F.

Front Genet. 2019 Apr 10;10:265. doi: 10.3389/fgene.2019.00265. eCollection 2019.


Differentially mutated subnetworks discovery.

Hajkarim MC, Upfal E, Vandin F.

Algorithms Mol Biol. 2019 Mar 30;14:10. doi: 10.1186/s13015-019-0146-7. eCollection 2019.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Computational pan-genomics: status, promises and challenges.

Computational Pan-Genomics Consortium.

Brief Bioinform. 2018 Jan 1;19(1):118-135. doi: 10.1093/bib/bbw089. Review.


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.


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.


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.


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.


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.


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.


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.

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