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Items: 9

1.

A community effort to create standards for evaluating tumor subclonal reconstruction.

Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W; DREAM SMC-Het Participants, Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC.

Nat Biotechnol. 2020 Jan;38(1):97-107. doi: 10.1038/s41587-019-0364-z. Epub 2020 Jan 9.

PMID:
31919445
2.

COSSMO: predicting competitive alternative splice site selection using deep learning.

Bretschneider H, Gandhi S, Deshwar AG, Zuberi K, Frey BJ.

Bioinformatics. 2018 Jul 1;34(13):i429-i437. doi: 10.1093/bioinformatics/bty244.

3.

Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism.

Kemaladewi DU, Maino E, Hyatt E, Hou H, Ding M, Place KM, Zhu X, Bassi P, Baghestani Z, Deshwar AG, Merico D, Xiong HY, Frey BJ, Wilson MD, Ivakine EA, Cohn RD.

Nat Med. 2017 Aug;23(8):984-989. doi: 10.1038/nm.4367. Epub 2017 Jul 17.

PMID:
28714989
4.

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC.

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.

5.

PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.

Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q.

Genome Biol. 2015 Feb 13;16:35. doi: 10.1186/s13059-015-0602-8.

6.

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

Deshwar AG, Vembu S, Morris Q.

Pac Symp Biocomput. 2015:20-31.

7.

Inferring clonal evolution of tumors from single nucleotide somatic mutations.

Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q.

BMC Bioinformatics. 2014 Feb 1;15:35. doi: 10.1186/1471-2105-15-35.

8.

PLIDA: cross-platform gene expression normalization using perturbed topic models.

Deshwar AG, Morris Q.

Bioinformatics. 2014 Apr 1;30(7):956-61. doi: 10.1093/bioinformatics/btt574. Epub 2013 Oct 11.

PMID:
24123674
9.

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.

Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q.

Genome Med. 2013 Mar 28;5(3):29. doi: 10.1186/gm433.

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