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Cited In for PubMed (Select 11382362)


Inferring tree causal models of cancer progression with probability raising.

Loohuis LO, Caravagna G, Graudenzi A, Ramazzotti D, Mauri G, Antoniotti M, Mishra B.

PLoS One. 2014 Oct 9;9(10):e108358. doi: 10.1371/journal.pone.0108358. eCollection 2014.


Cancer evolution: mathematical models and computational inference.

Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.

Syst Biol. 2015 Jan;64(1):e1-25. doi: 10.1093/sysbio/syu081. Epub 2014 Oct 7.


Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics.

Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schäffer AA, Schwartz R.

PLoS Comput Biol. 2014 Jul 31;10(7):e1003740. doi: 10.1371/journal.pcbi.1003740. eCollection 2014 Jul.


Methods and challenges in timing chromosomal abnormalities within cancer samples.

Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P.

Bioinformatics. 2013 Dec 15;29(24):3113-20. doi: 10.1093/bioinformatics/btt546. Epub 2013 Sep 23.


TrAp: a tree approach for fingerprinting subclonal tumor composition.

Strino F, Parisi F, Micsinai M, Kluger Y.

Nucleic Acids Res. 2013 Sep;41(17):e165. doi: 10.1093/nar/gkt641. Epub 2013 Jul 27.


Temporal ordering of cancer microarray data through a reinforcement learning based approach.

Czibula G, Bocicor IM, Czibula IG.

PLoS One. 2013;8(4):e60883. doi: 10.1371/journal.pone.0060883. Epub 2013 Apr 2.


A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis.

Cheng YK, Beroukhim R, Levine RL, Mellinghoff IK, Holland EC, Michor F.

PLoS Comput Biol. 2012 Jan;8(1):e1002337. doi: 10.1371/journal.pcbi.1002337. Epub 2012 Jan 5.


The temporal order of genetic and pathway alterations in tumorigenesis.

Gerstung M, Eriksson N, Lin J, Vogelstein B, Beerenwinkel N.

PLoS One. 2011;6(11):e27136. doi: 10.1371/journal.pone.0027136. Epub 2011 Nov 1.


Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy.

Ozery-Flato M, Linhart C, Trakhtenbrot L, Izraeli S, Shamir R.

Genome Biol. 2011 Jun 29;12(6):R61. doi: 10.1186/gb-2011-12-6-r61.


Accurate reconstruction of the temporal order of mutations in neoplastic progression.

Sprouffske K, Pepper JW, Maley CC.

Cancer Prev Res (Phila). 2011 Jul;4(7):1135-44. doi: 10.1158/1940-6207.CAPR-10-0374. Epub 2011 Apr 13.


CDCOCA: a statistical method to define complexity dependence of co-occuring chromosomal aberrations.

Kumar N, Rehrauer H, Cai H, Baudis M.

BMC Med Genomics. 2011 Mar 3;4:21. doi: 10.1186/1755-8794-4-21.


Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis.

Letouzé E, Allory Y, Bollet MA, Radvanyi F, Guyon F.

Genome Biol. 2010;11(7):R76. doi: 10.1186/gb-2010-11-7-r76. Epub 2010 Jul 22.


The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias.

Lilljebjörn H, Soneson C, Andersson A, Heldrup J, Behrendtz M, Kawamata N, Ogawa S, Koeffler HP, Mitelman F, Johansson B, Fontes M, Fioretos T.

Hum Mol Genet. 2010 Aug 15;19(16):3150-8. doi: 10.1093/hmg/ddq224. Epub 2010 May 31.


A differentiation-based phylogeny of cancer subtypes.

Riester M, Stephan-Otto Attolini C, Downey RJ, Singer S, Michor F.

PLoS Comput Biol. 2010 May 6;6(5):e1000777. doi: 10.1371/journal.pcbi.1000777.


Applying unmixing to gene expression data for tumor phylogeny inference.

Schwartz R, Shackney SE.

BMC Bioinformatics. 2010 Jan 20;11:42. doi: 10.1186/1471-2105-11-42.


Quantifying cancer progression with conjunctive Bayesian networks.

Gerstung M, Baudis M, Moch H, Beerenwinkel N.

Bioinformatics. 2009 Nov 1;25(21):2809-15. doi: 10.1093/bioinformatics/btp505. Epub 2009 Aug 19.


A comparison of colon and rectal somatic DNA alterations.

Slattery ML, Curtin K, Wolff RK, Boucher KM, Sweeney C, Edwards S, Caan BJ, Samowitz W.

Dis Colon Rectum. 2009 Jul;52(7):1304-11. doi: 10.1007/DCR.0b013e3181a0e5df.


Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression.

Pathare S, Schäffer AA, Beerenwinkel N, Mahimkar M.

Int J Cancer. 2009 Jun 15;124(12):2864-71. doi: 10.1002/ijc.24267.


Oncogenetic tree model of somatic mutations and DNA methylation in colon tumors.

Sweeney C, Boucher KM, Samowitz WS, Wolff RK, Albertsen H, Curtin K, Caan BJ, Slattery ML.

Genes Chromosomes Cancer. 2009 Jan;48(1):1-9. doi: 10.1002/gcc.20614.

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