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1.

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia.

Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP.

Genome Res. 2018 Apr;28(4):423-431. doi: 10.1101/gr.223693.117. Epub 2018 Mar 22.

2.

ImmPort, toward repurposing of open access immunological assay data for translational and clinical research.

Bhattacharya S, Dunn P, Thomas CG, Smith B, Schaefer H, Chen J, Hu Z, Zalocusky KA, Shankar RD, Shen-Orr SS, Thomson E, Wiser J, Butte AJ.

Sci Data. 2018 Feb 27;5:180015. doi: 10.1038/sdata.2018.15.

3.

Are minor alleles more likely to be risk alleles?

Kido T, Sikora-Wohlfeld W, Kawashima M, Kikuchi S, Kamatani N, Patwardhan A, Chen R, Sirota M, Kodama K, Hadley D, Butte AJ.

BMC Med Genomics. 2018 Jan 19;11(1):3. doi: 10.1186/s12920-018-0322-5.

4.

A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth.

Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M.

Sci Rep. 2018 Jan 9;8(1):226. doi: 10.1038/s41598-017-18246-5.

5.

Future cancer research priorities in the USA: a Lancet Oncology Commission.

Jaffee EM, Dang CV, Agus DB, Alexander BM, Anderson KC, Ashworth A, Barker AD, Bastani R, Bhatia S, Bluestone JA, Brawley O, Butte AJ, Coit DG, Davidson NE, Davis M, DePinho RA, Diasio RB, Draetta G, Frazier AL, Futreal A, Gambhir SS, Ganz PA, Garraway L, Gerson S, Gupta S, Heath J, Hoffman RI, Hudis C, Hughes-Halbert C, Ibrahim R, Jadvar H, Kavanagh B, Kittles R, Le QT, Lippman SM, Mankoff D, Mardis ER, Mayer DK, McMasters K, Meropol NJ, Mitchell B, Naredi P, Ornish D, Pawlik TM, Peppercorn J, Pomper MG, Raghavan D, Ritchie C, Schwarz SW, Sullivan R, Wahl R, Wolchok JD, Wong SL, Yung A.

Lancet Oncol. 2017 Nov;18(11):e653-e706. doi: 10.1016/S1470-2045(17)30698-8. Epub 2017 Oct 31. Review.

PMID:
29208398
6.

Risky Business: Meeting the Structural Needs of Transdisciplinary Science.

Wise PH, Shaw GM, Druzin ML, Darmstadt GL, Quaintance C, Mäkinen E, Relman DA, Quake SR, Butte AJ, Angst MS, Muglia LJ, Macones G, Driscoll D, Ober C, Simpson JL, Katz M, Howse J, Stevenson DK.

J Pediatr. 2017 Dec;191:255-258. doi: 10.1016/j.jpeds.2017.08.072. No abstract available.

PMID:
29173314
7.

xCell: digitally portraying the tissue cellular heterogeneity landscape.

Aran D, Hu Z, Butte AJ.

Genome Biol. 2017 Nov 15;18(1):220. doi: 10.1186/s13059-017-1349-1.

8.

PDX-MI: Minimal Information for Patient-Derived Tumor Xenograft Models.

Meehan TF, Conte N, Goldstein T, Inghirami G, Murakami MA, Brabetz S, Gu Z, Wiser JA, Dunn P, Begley DA, Krupke DM, Bertotti A, Bruna A, Brush MH, Byrne AT, Caldas C, Christie AL, Clark DA, Dowst H, Dry JR, Doroshow JH, Duchamp O, Evrard YA, Ferretti S, Frese KK, Goodwin NC, Greenawalt D, Haendel MA, Hermans E, Houghton PJ, Jonkers J, Kemper K, Khor TO, Lewis MT, Lloyd KCK, Mason J, Medico E, Neuhauser SB, Olson JM, Peeper DS, Rueda OM, Seong JK, Trusolino L, Vinolo E, Wechsler-Reya RJ, Weinstock DM, Welm A, Weroha SJ, Amant F, Pfister SM, Kool M, Parkinson H, Butte AJ, Bult CJ.

Cancer Res. 2017 Nov 1;77(21):e62-e66. doi: 10.1158/0008-5472.CAN-17-0582.

PMID:
29092942
9.

Comprehensive analysis of normal adjacent to tumor transcriptomes.

Aran D, Camarda R, Odegaard J, Paik H, Oskotsky B, Krings G, Goga A, Sirota M, Butte AJ.

Nat Commun. 2017 Oct 20;8(1):1077. doi: 10.1038/s41467-017-01027-z.

10.

Precision annotation of digital samples in NCBI's gene expression omnibus.

Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, Bhattacharya S, Sirota M, Musen MA, Butte AJ.

Sci Data. 2017 Sep 19;4:170125. doi: 10.1038/sdata.2017.125.

11.

Big data opens a window onto wellness.

Butte AJ.

Nat Biotechnol. 2017 Aug 8;35(8):720-721. doi: 10.1038/nbt.3934. No abstract available.

PMID:
28787419
12.

Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets.

Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ.

Nat Commun. 2017 Jul 12;8:16022. doi: 10.1038/ncomms16022.

13.

Cancer Cell-Autonomous Parainflammation Mimics Immune Cell Infiltration.

Lasry A, Aran D, Butte AJ, Ben-Neriah Y.

Cancer Res. 2017 Jul 15;77(14):3740-3744. doi: 10.1158/0008-5472.CAN-16-3383. Epub 2017 Jun 30.

PMID:
28667073
14.

Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling.

Chen B, Wei W, Ma L, Yang B, Gill RM, Chua MS, Butte AJ, So S.

Gastroenterology. 2017 Jun;152(8):2022-2036. doi: 10.1053/j.gastro.2017.02.039. Epub 2017 Mar 8.

PMID:
28284560
15.

Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer's disease.

Geifman N, Brinton RD, Kennedy RE, Schneider LS, Butte AJ.

Alzheimers Res Ther. 2017 Feb 17;9(1):10. doi: 10.1186/s13195-017-0237-y.

16.

RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data.

Shankar RD, Bhattacharya S, Jujjavarapu C, Andorf S, Wiser JA, Butte AJ.

Bioinformatics. 2017 Apr 1;33(7):1101-1103. doi: 10.1093/bioinformatics/btw719.

PMID:
28057685
17.

Solving Immunology?

Vodovotz Y, Xia A, Read EL, Bassaganya-Riera J, Hafler DA, Sontag E, Wang J, Tsang JS, Day JD, Kleinstein SH, Butte AJ, Altman MC, Hammond R, Sealfon SC.

Trends Immunol. 2017 Feb;38(2):116-127. doi: 10.1016/j.it.2016.11.006. Epub 2016 Dec 13. Review.

18.

In silico and in vitro drug screening identifies new therapeutic approaches for Ewing sarcoma.

Pessetto ZY, Chen B, Alturkmani H, Hyter S, Flynn CA, Baltezor M, Ma Y, Rosenthal HG, Neville KA, Weir SJ, Butte AJ, Godwin AK.

Oncotarget. 2017 Jan 17;8(3):4079-4095. doi: 10.18632/oncotarget.13385.

19.

Integrating Clinical Phenotype and Gene Expression Data to Prioritize Novel Drug Uses.

Paik H, Chen B, Sirota M, Hadley D, Butte AJ.

CPT Pharmacometrics Syst Pharmacol. 2016 Nov;5(11):599-607. doi: 10.1002/psp4.12108. Epub 2016 Nov 14.

20.

It takes a genome to understand a village: Population scale precision medicine.

Butte AJ.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12344-12346. Epub 2016 Oct 19. No abstract available.

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