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Items: 29

1.

Rapid and reversible suppression of ALT by DAXX in osteosarcoma cells.

Yost KE, Clatterbuck Soper SF, Walker RL, Pineda MA, Zhu YJ, Ester CD, Showman S, Roschke AV, Waterfall JJ, Meltzer PS.

Sci Rep. 2019 Mar 14;9(1):4544. doi: 10.1038/s41598-019-41058-8.

2.

Harnessing synthetic lethality to predict the response to cancer treatment.

Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, McGarry L, James D, Amzallag A, Park SG, Cheng K, Robinson W, Atias D, Stossel C, Buzhor E, Stein G, Waterfall JJ, Meltzer PS, Golan T, Hannenhalli S, Gottlieb E, Benes CH, Samuels Y, Shanks E, Ruppin E.

Nat Commun. 2018 Jun 29;9(1):2546. doi: 10.1038/s41467-018-04647-1.

3.

Does ATRX germline variation predispose to osteosarcoma? Three additional cases of osteosarcoma in two ATR-X syndrome patients.

Masliah-Planchon J, Lévy D, Héron D, Giuliano F, Badens C, Fréneaux P, Galmiche L, Guinebretierre JM, Cellier C, Waterfall JJ, Aït-Raïs K, Pierron G, Glorion C, Desguerre I, Soler C, Deville A, Delattre O, Michon J, Bourdeaut F.

Eur J Hum Genet. 2018 Aug;26(8):1217-1221. doi: 10.1038/s41431-018-0147-x. Epub 2018 Apr 30.

PMID:
29706636
4.

Analysis of the 9p21.3 sequence associated with coronary artery disease reveals a tendency for duplication in a CAD patient.

Kouprina N, Liskovykh M, Lee NCO, Noskov VN, Waterfall JJ, Walker RL, Meltzer PS, Topol EJ, Larionov V.

Oncotarget. 2018 Feb 26;9(20):15275-15291. doi: 10.18632/oncotarget.24567. eCollection 2018 Mar 16.

5.

A Non-canonical Polycomb Dependency in Synovial Sarcoma.

Waterfall JJ, Meltzer PS.

Cancer Cell. 2018 Mar 12;33(3):344-346. doi: 10.1016/j.ccell.2018.02.013.

6.

The epigenetic control of stemness in CD8+ T cell fate commitment.

Pace L, Goudot C, Zueva E, Gueguen P, Burgdorf N, Waterfall JJ, Quivy JP, Almouzni G, Amigorena S.

Science. 2018 Jan 12;359(6372):177-186. doi: 10.1126/science.aah6499.

PMID:
29326266
7.

Common Molecular Subtypes Among Asian Hepatocellular Carcinoma and Cholangiocarcinoma.

Chaisaingmongkol J, Budhu A, Dang H, Rabibhadana S, Pupacdi B, Kwon SM, Forgues M, Pomyen Y, Bhudhisawasdi V, Lertprasertsuke N, Chotirosniramit A, Pairojkul C, Auewarakul CU, Sricharunrat T, Phornphutkul K, Sangrajrang S, Cam M, He P, Hewitt SM, Ylaya K, Wu X, Andersen JB, Thorgeirsson SS, Waterfall JJ, Zhu YJ, Walling J, Stevenson HS, Edelman D, Meltzer PS, Loffredo CA, Hama N, Shibata T, Wiltrout RH, Harris CC, Mahidol C, Ruchirawat M, Wang XW; TIGER-LC Consortium.

Cancer Cell. 2017 Jul 10;32(1):57-70.e3. doi: 10.1016/j.ccell.2017.05.009. Epub 2017 Jun 22.

8.

Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors.

Killian JK, Dorssers LC, Trabert B, Gillis AJ, Cook MB, Wang Y, Waterfall JJ, Stevenson H, Smith WI Jr, Noyes N, Retnakumar P, Stoop JH, Oosterhuis JW, Meltzer PS, McGlynn KA, Looijenga LH.

Genome Res. 2016 Nov;26(11):1490-1504. Epub 2016 Oct 20.

9.

Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant.

Li J, Woods SL, Healey S, Beesley J, Chen X, Lee JS, Sivakumaran H, Wayte N, Nones K, Waterfall JJ, Pearson J, Patch AM, Senz J, Ferreira MA, Kaurah P, Mackenzie R, Heravi-Moussavi A, Hansford S, Lannagan TRM, Spurdle AB, Simpson PT, da Silva L, Lakhani SR, Clouston AD, Bettington M, Grimpen F, Busuttil RA, Di Costanzo N, Boussioutas A, Jeanjean M, Chong G, Fabre A, Olschwang S, Faulkner GJ, Bellos E, Coin L, Rioux K, Bathe OF, Wen X, Martin HC, Neklason DW, Davis SR, Walker RL, Calzone KA, Avital I, Heller T, Koh C, Pineda M, Rudloff U, Quezado M, Pichurin PN, Hulick PJ, Weissman SM, Newlin A, Rubinstein WS, Sampson JE, Hamman K, Goldgar D, Poplawski N, Phillips K, Schofield L, Armstrong J, Kiraly-Borri C, Suthers GK, Huntsman DG, Foulkes WD, Carneiro F, Lindor NM, Edwards SL, French JD, Waddell N, Meltzer PS, Worthley DL, Schrader KA, Chenevix-Trench G.

Am J Hum Genet. 2016 May 5;98(5):830-842. doi: 10.1016/j.ajhg.2016.03.001. Epub 2016 Apr 14.

10.

Whole Genome Sequencing of Newly Established Pancreatic Cancer Lines Identifies Novel Somatic Mutation (c.2587G>A) in Axon Guidance Receptor Plexin A1 as Enhancer of Proliferation and Invasion.

Sorber R, Teper Y, Abisoye-Ogunniyan A, Waterfall JJ, Davis S, Killian JK, Pineda M, Ray S, McCord MR, Pflicke H, Burkett SS, Meltzer PS, Rudloff U.

PLoS One. 2016 Mar 10;11(3):e0149833. doi: 10.1371/journal.pone.0149833. eCollection 2016.

11.

Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling.

Grøntved L, Waterfall JJ, Kim DW, Baek S, Sung MH, Zhao L, Park JW, Nielsen R, Walker RL, Zhu YJ, Meltzer PS, Hager GL, Cheng SY.

Nat Commun. 2015 Apr 28;6:7048. doi: 10.1038/ncomms8048.

12.

Avalanching mutations in biallelic mismatch repair deficiency syndrome.

Waterfall JJ, Meltzer PS.

Nat Genet. 2015 Mar;47(3):194-6. doi: 10.1038/ng.3227.

PMID:
25711864
13.

Recurrent epimutation of SDHC in gastrointestinal stromal tumors.

Killian JK, Miettinen M, Walker RL, Wang Y, Zhu YJ, Waterfall JJ, Noyes N, Retnakumar P, Yang Z, Smith WI Jr, Killian MS, Lau CC, Pineda M, Walling J, Stevenson H, Smith C, Wang Z, Lasota J, Kim SY, Boikos SA, Helman LJ, Meltzer PS.

Sci Transl Med. 2014 Dec 24;6(268):268ra177. doi: 10.1126/scitranslmed.3009961.

PMID:
25540324
14.

Building through breaking: the development of cancer neochromosomes.

Waterfall JJ, Meltzer PS.

Cancer Cell. 2014 Nov 10;26(5):593-5. doi: 10.1016/j.ccell.2014.10.013. Epub 2014 Nov 10.

15.

The role of mutation of metabolism-related genes in genomic hypermethylation.

Waterfall JJ, Killian JK, Meltzer PS.

Biochem Biophys Res Commun. 2014 Dec 5;455(1-2):16-23. doi: 10.1016/j.bbrc.2014.08.003. Epub 2014 Aug 8. Review.

PMID:
25111818
16.

High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias.

Waterfall JJ, Arons E, Walker RL, Pineda M, Roth L, Killian JK, Abaan OD, Davis SR, Kreitman RJ, Meltzer PS.

Nat Genet. 2014 Jan;46(1):8-10. doi: 10.1038/ng.2828. Epub 2013 Nov 17.

17.

Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor.

Killian JK, Kim SY, Miettinen M, Smith C, Merino M, Tsokos M, Quezado M, Smith WI Jr, Jahromi MS, Xekouki P, Szarek E, Walker RL, Lasota J, Raffeld M, Klotzle B, Wang Z, Jones L, Zhu Y, Wang Y, Waterfall JJ, O'Sullivan MJ, Bibikova M, Pacak K, Stratakis C, Janeway KA, Schiffman JD, Fan JB, Helman L, Meltzer PS.

Cancer Discov. 2013 Jun;3(6):648-57. doi: 10.1158/2159-8290.CD-13-0092. Epub 2013 Apr 2.

18.

Defining the status of RNA polymerase at promoters.

Core LJ, Waterfall JJ, Gilchrist DA, Fargo DC, Kwak H, Adelman K, Lis JT.

Cell Rep. 2012 Oct 25;2(4):1025-35. doi: 10.1016/j.celrep.2012.08.034. Epub 2012 Oct 10.

19.

Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins.

Chatterjee R, Zhao J, He X, Shlyakhtenko A, Mann I, Waterfall JJ, Meltzer P, Sathyanarayana BK, FitzGerald PC, Vinson C.

G3 (Bethesda). 2012 Oct;2(10):1243-56. doi: 10.1534/g3.112.004002. Epub 2012 Oct 1.

20.

Targeting epigenetic misregulation in synovial sarcoma.

Waterfall JJ, Meltzer PS.

Cancer Cell. 2012 Mar 20;21(3):323-4. doi: 10.1016/j.ccr.2012.02.023.

21.

A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology.

Killian JK, Bilke S, Davis S, Walker RL, Jaeger E, Killian MS, Waterfall JJ, Bibikova M, Fan JB, Smith WI Jr, Meltzer PS.

Am J Pathol. 2011 Jul;179(1):55-65. doi: 10.1016/j.ajpath.2011.03.022. Epub 2011 May 13.

22.

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.

Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL.

Cell. 2011 May 13;145(4):622-34. doi: 10.1016/j.cell.2011.03.042. Epub 2011 May 5. Erratum in: Cell. 2011 Jun 24;145(7):1156.

23.

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells.

Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT.

Genes Dev. 2011 Apr 1;25(7):742-54. doi: 10.1101/gad.2005511.

24.

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters.

Core LJ, Waterfall JJ, Lis JT.

Science. 2008 Dec 19;322(5909):1845-8. doi: 10.1126/science.1162228. Epub 2008 Dec 4.

25.

Variational method for estimating the rate of convergence of Markov-chain Monte Carlo algorithms.

Casey FP, Waterfall JJ, Gutenkunst RN, Myers CR, Sethna JP.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Oct;78(4 Pt 2):046704. Epub 2008 Oct 20.

PMID:
18999558
26.

Extracting falsifiable predictions from sloppy models.

Gutenkunst RN, Casey FP, Waterfall JJ, Myers CR, Sethna JP.

Ann N Y Acad Sci. 2007 Dec;1115:203-11. Epub 2007 Oct 9.

PMID:
17925353
27.

Universally sloppy parameter sensitivities in systems biology models.

Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP.

PLoS Comput Biol. 2007 Oct;3(10):1871-78. Epub 2007 Aug 15.

28.

Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model.

Casey FP, Baird D, Feng Q, Gutenkunst RN, Waterfall JJ, Myers CR, Brown KS, Cerione RA, Sethna JP.

IET Syst Biol. 2007 May;1(3):190-202.

PMID:
17591178
29.

Sloppy-model universality class and the Vandermonde matrix.

Waterfall JJ, Casey FP, Gutenkunst RN, Brown KS, Myers CR, Brouwer PW, Elser V, Sethna JP.

Phys Rev Lett. 2006 Oct 13;97(15):150601. Epub 2006 Oct 12.

PMID:
17155311

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