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Items: 28

1.

The evolutionary history of 2,658 cancers.

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD; PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P; PCAWG Consortium.

Nature. 2020 Feb;578(7793):122-128. doi: 10.1038/s41586-019-1907-7. Epub 2020 Feb 6.

PMID:
32025013
2.

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.

Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar A; PCAWG Evolution and Heterogeneity Working Group, Morris Q; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):731. doi: 10.1038/s41467-020-14352-7.

3.

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
4.

The selector genes midline and H15 control ventral leg pattern by both inhibiting Dpp signaling and specifying ventral fate.

Svendsen PC, Phillips LA, Deshwar AR, Ryu JR, Najand N, Brook WJ.

Dev Biol. 2019 Nov 1;455(1):19-31. doi: 10.1016/j.ydbio.2019.05.012. Epub 2019 Jul 9.

PMID:
31299230
5.

Disruption of the PTHLH regulatory landscape results in features consistent with hyperparathyroid disease.

Deshwar AR, Spielmann M, Vi L, Mendoza-Londono R, Dupuis L, Stimec J, Howard A, Harrington J, Kannu P.

Am J Med Genet A. 2019 Apr;179(4):663-667. doi: 10.1002/ajmg.a.61071. Epub 2019 Feb 25.

PMID:
30803154
6.

Hey2 regulates the size of the cardiac progenitor pool during vertebrate heart development.

Gibb N, Lazic S, Yuan X, Deshwar AR, Leslie M, Wilson MD, Scott IC.

Development. 2018 Nov 21;145(22). pii: dev167510. doi: 10.1242/dev.167510.

7.

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.

8.

Double KRAS and BRAF Mutations in Surgically Treated Colorectal Cancer Liver Metastases: An International, Multi-institutional Case Series.

Deshwar A, Margonis GA, Andreatos N, Barbon C, Wang J, Buettner S, Wagner D, Sasaki K, Beer A, Løes IM, Pikoulis E, Damaskos C, Garmpis N, Kamphues K, He J, Kaczirek K, Poultsides G, Lønning PE, Mischinger HJ, Aucejo FN, Kreis ME, Wolfgang CL, Weiss MJ.

Anticancer Res. 2018 May;38(5):2891-2895.

PMID:
29715113
9.

Genetic And Morphological Evaluation (GAME) score for patients with colorectal liver metastases.

Margonis GA, Sasaki K, Gholami S, Kim Y, Andreatos N, Rezaee N, Deshwar A, Buettner S, Allen PJ, Kingham TP, Pawlik TM, He J, Cameron JL, Jarnagin WR, Wolfgang CL, D'Angelica MI, Weiss MJ.

Br J Surg. 2018 Aug;105(9):1210-1220. doi: 10.1002/bjs.10838. Epub 2018 Apr 25.

PMID:
29691844
10.

Diagnostic intervals and pancreatic ductal adenocarcinoma (PDAC) resectability: a single-center retrospective analysis.

Deshwar AB, Sugar E, Torto D, De Jesus-Acosta A, Weiss MJ, Wolfgang CL, Le D, He J, Burkhart R, Zheng L, Laheru D, Yarchoan M.

Ann Pancreat Cancer. 2018;1. pii: 13. doi: 10.21037/apc.2018.02.01. Epub 2018 Feb 27.

11.

The Prognostic Value of Varying Definitions of Positive Resection Margin in Patients with Colorectal Cancer Liver Metastases.

Wang J, Margonis GA, Amini N, Andreatos N, Yuan C, Damaskos C, Antoniou E, Garmpis N, Buettner S, Barbon C, Deshwar A, He J, Burkhart R, Pawlik TM, Wolfgang CL, Weiss MJ.

J Gastrointest Surg. 2018 Aug;22(8):1350-1357. doi: 10.1007/s11605-018-3748-3. Epub 2018 Apr 9.

PMID:
29633114
12.

Systemic treatment and primary tumor location in patients with metastatic colorectal cancer.

Antoniou E, Andreatos N, Margonis GA, Papalois A, Wang J, Damaskos C, Garmpis N, Buettner S, Deshwar A, Pappas V, Weiss MJ, Pawlik TM, Pikoulis E.

J BUON. 2017 Nov-Dec;22(6):1447-1456.

13.

Severe rhizomelic shortening in a child with a complex duplication/deletion rearrangement of chromosome X.

Deshwar AR, Dupuis L, Bergmann C, Stavropoulos J, Mendoza-Londono R.

Am J Med Genet A. 2018 Feb;176(2):450-454. doi: 10.1002/ajmg.a.38570. Epub 2017 Dec 22.

PMID:
29271572
14.

Preoperative bevacizumab and volumetric recovery after resection of colorectal liver metastases.

Margonis GA, Buettner S, Andreatos N, Sasaki K, Pour MZ, Deshwar A, Wang J, Ghasebeh MA, Damaskos C, Rezaee N, Pawlik TM, Wolfgang CL, Kamel IR, Weiss MJ.

J Surg Oncol. 2017 Dec;116(8):1150-1158. doi: 10.1002/jso.24769. Epub 2017 Jul 25.

PMID:
28743167
15.

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
16.

The prognostic utility of the "Tumor Burden Score" based on preoperative radiographic features of colorectal liver metastases.

Sasaki K, Margonis GA, Andreatos N, Zhang XF, Buettner S, Wang J, Deshwar A, He J, Wolfgang CL, Weiss M, Pawlik TM.

J Surg Oncol. 2017 Sep;116(4):515-523. doi: 10.1002/jso.24678. Epub 2017 May 25.

PMID:
28543544
17.

Mespaa can potently induce cardiac fates in zebrafish.

Deshwar AR, Onderisin JC, Aleksandrova A, Yuan X, Burrows JTA, Scott IC.

Dev Biol. 2016 Oct 1;418(1):17-27. doi: 10.1016/j.ydbio.2016.08.022. Epub 2016 Aug 20.

18.

The Apelin receptor enhances Nodal/TGFβ signaling to ensure proper cardiac development.

Deshwar AR, Chng SC, Ho L, Reversade B, Scott IC.

Elife. 2016 Apr 14;5. pii: e13758. doi: 10.7554/eLife.13758.

19.

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.

20.

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.

21.

Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

Deshwar AG, Vembu S, Morris Q.

Pac Symp Biocomput. 2015:20-31.

22.

The PPFIA1-PP2A protein complex promotes trafficking of Kif7 to the ciliary tip and Hedgehog signaling.

Liu YC, Couzens AL, Deshwar AR, B McBroom-Cerajewski LD, Zhang X, Puviindran V, Scott IC, Gingras AC, Hui CC, Angers S.

Sci Signal. 2014 Dec 9;7(355):ra117. doi: 10.1126/scisignal.2005608.

PMID:
25492966
23.

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.

24.

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
25.

Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression.

Mezlini AM, Wang B, Deshwar A, Morris Q, Goldenberg A.

PLoS One. 2013 Oct 2;8(10):e73168. doi: 10.1371/journal.pone.0073168. eCollection 2013.

26.

ENU-induced mutation in the DNA-binding domain of KLF3 reveals important roles for KLF3 in cardiovascular development and function in mice.

Kelsey L, Flenniken AM, Qu D, Funnell AP, Pearson R, Zhou YQ, Voronina I, Berberovic Z, Wood G, Newbigging S, Weiss ES, Wong M, Quach I, Yeh SY, Deshwar AR, Scott IC, McKerlie C, Henkelman M, Backx P, Simpson J, Osborne L, Rossant J, Crossley M, Bruneau B, Adamson SL.

PLoS Genet. 2013;9(7):e1003612. doi: 10.1371/journal.pgen.1003612. Epub 2013 Jul 11.

27.

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.

28.

Smarcd3b and Gata5 promote a cardiac progenitor fate in the zebrafish embryo.

Lou X, Deshwar AR, Crump JG, Scott IC.

Development. 2011 Aug;138(15):3113-23. doi: 10.1242/dev.064279. Epub 2011 Jun 29.

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