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Items: 1 to 50 of 225

1.

The 10,000 Immunomes Project: Building a Resource for Human Immunology.

Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ.

Cell Rep. 2018 Oct 9;25(2):513-522.e3. doi: 10.1016/j.celrep.2018.09.021.

2.

Robust prediction of clinical outcomes using cytometry data.

Hu Z, Glicksberg BS, Butte AJ.

Bioinformatics. 2018 Aug 31. doi: 10.1093/bioinformatics/bty768. [Epub ahead of print]

PMID:
30169745
3.

MetaCyto: A Tool for Automated Meta-analysis of Mass and Flow Cytometry Data.

Hu Z, Jujjavarapu C, Hughey JJ, Andorf S, Lee HC, Gherardini PF, Spitzer MH, Thomas CG, Campbell J, Dunn P, Wiser J, Kidd BA, Dudley JT, Nolan GP, Bhattacharya S, Butte AJ.

Cell Rep. 2018 Jul 31;24(5):1377-1388. doi: 10.1016/j.celrep.2018.07.003.

4.

Open data informatics and data repurposing for IBD.

Rudrapatna VA, Butte AJ.

Nat Rev Gastroenterol Hepatol. 2018 Jul 30. doi: 10.1038/s41575-018-0050-5. [Epub ahead of print] No abstract available.

PMID:
30061595
5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans.

Shen-Orr SS, Furman D, Kidd BA, Hadad F, Lovelace P, Huang YW, Rosenberg-Hasson Y, Mackey S, Grisar FA, Pickman Y, Maecker HT, Chien YH, Dekker CL, Wu JC, Butte AJ, Davis MM.

Cell Syst. 2016 Oct 26;3(4):374-384.e4. doi: 10.1016/j.cels.2016.09.009. Epub 2016 Oct 13.

26.

Differential Phasing between Circadian Clocks in the Brain and Peripheral Organs in Humans.

Hughey JJ, Butte AJ.

J Biol Rhythms. 2016 Dec;31(6):588-597. doi: 10.1177/0748730416668049. Epub 2016 Oct 4.

27.

Digitally deconvolving the tumor microenvironment.

Aran D, Butte AJ.

Genome Biol. 2016 Aug 22;17(1):175. doi: 10.1186/s13059-016-1036-7. Review.

28.

Widespread parainflammation in human cancer.

Aran D, Lasry A, Zinger A, Biton M, Pikarsky E, Hellman A, Butte AJ, Ben-Neriah Y.

Genome Biol. 2016 Jul 8;17(1):145. doi: 10.1186/s13059-016-0995-z.

29.

Identification of matrix metalloproteinase-12 as a candidate molecule for prevention and treatment of cardiometabolic disease.

Amor M, Moreno Viedma V, Sarabi A, Grün NG, Itariu B, Leitner L, Steiner I, Bilban M, Kodama K, Butte AJ, Staffler G, Zeyda M, Stulnig TM.

Mol Med. 2016 Oct;22:487-496. doi: 10.2119/molmed.2016.00068. Epub 2016 Jun 30.

30.

Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies.

Rennert RC, Januszyk M, Sorkin M, Rodrigues M, Maan ZN, Duscher D, Whittam AJ, Kosaraju R, Chung MT, Paik K, Li AY, Findlay M, Glotzbach JP, Butte AJ, Gurtner GC.

Nat Commun. 2016 Jun 21;7:11945. doi: 10.1038/ncomms11945.

31.

A patient-level data meta-analysis of standard-of-care treatments from eight prostate cancer clinical trials.

Geifman N, Butte AJ.

Sci Data. 2016 May 10;3:160027. doi: 10.1038/sdata.2016.27.

32.

Cross-tissue Analysis of Gene and Protein Expression in Normal and Cancer Tissues.

Kosti I, Jain N, Aran D, Butte AJ, Sirota M.

Sci Rep. 2016 May 4;6:24799. doi: 10.1038/srep24799.

33.

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.

Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB.

PLoS Comput Biol. 2016 Apr 26;12(4):e1004885. doi: 10.1371/journal.pcbi.1004885. eCollection 2016 Apr.

34.

Expression-Based Genome-Wide Association Study Links Vitamin D-Binding Protein With Autoantigenicity in Type 1 Diabetes.

Kodama K, Zhao Z, Toda K, Yip L, Fuhlbrigge R, Miao D, Fathman CG, Yamada S, Butte AJ, Yu L.

Diabetes. 2016 May;65(5):1341-9. doi: 10.2337/db15-1308. Epub 2016 Mar 16.

35.

Corrigendum: Systematic pan-cancer analysis of tumour purity.

Aran D, Sirota M, Butte AJ.

Nat Commun. 2016 Feb 5;7:10707. doi: 10.1038/ncomms10707. No abstract available.

36.

ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.

Hughey JJ, Hastie T, Butte AJ.

Nucleic Acids Res. 2016 May 5;44(8):e80. doi: 10.1093/nar/gkw030. Epub 2016 Jan 26.

37.

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN.

Immunity. 2016 Jan 19;44(1):194-206. doi: 10.1016/j.immuni.2015.12.006. Epub 2016 Jan 12.

39.

Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome.

Li X, Kang J, Pan Q, Sikora-Wohlfeld W, Zhao D, Meng C, Bai C, Patwardhan A, Chen R, Ren H, Butte AJ, Ding K.

Oncol Rep. 2016 Mar;35(3):1519-28. doi: 10.3892/or.2015.4501. Epub 2015 Dec 21.

PMID:
26707089
40.

Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression.

Geifman N, Bhattacharya S, Butte AJ.

J Am Med Inform Assoc. 2016 May;23(3):617-26. doi: 10.1093/jamia/ocv166. Epub 2015 Dec 11.

41.

Leveraging big data to transform target selection and drug discovery.

Chen B, Butte AJ.

Clin Pharmacol Ther. 2016 Mar;99(3):285-97. doi: 10.1002/cpt.318. Review.

42.

Systematic pan-cancer analysis of tumour purity.

Aran D, Sirota M, Butte AJ.

Nat Commun. 2015 Dec 4;6:8971. doi: 10.1038/ncomms9971. Erratum in: Nat Commun. 2016;7:10707.

43.

Opening clinical trial data: are the voluntary data-sharing portals enough?

Geifman N, Bollyky J, Bhattacharya S, Butte AJ.

BMC Med. 2015 Nov 11;13:280. doi: 10.1186/s12916-015-0525-y.

44.

Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds.

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

CPT Pharmacometrics Syst Pharmacol. 2015 Oct;4(10):576-84. doi: 10.1002/psp4.12009. Epub 2015 Sep 29.

45.

Serological targeted analysis of an ITIH4 peptide isoform: a preterm birth biomarker and its associated SNP implications.

Tan Z, Hu Z, Cai EY, Alev C, Yang T, Li Z, Sung J, El-Sayed YY, Shaw GM, Stevenson DK, Butte AJ, Sheng G, Sylvester KG, Cohen HJ, Ling XB.

J Genet Genomics. 2015 Sep 20;42(9):507-10. doi: 10.1016/j.jgg.2015.06.001. Epub 2015 Jun 14. No abstract available.

PMID:
26408095
46.

Reanalysis of the Rituximab in ANCA-Associated Vasculitis trial identifies granulocyte subsets as a novel early marker of successful treatment.

Nasrallah M, Pouliot Y, Hartmann B, Dunn P, Thomson E, Wiser J, Butte AJ.

Arthritis Res Ther. 2015 Sep 21;17:262. doi: 10.1186/s13075-015-0778-z.

47.

Achieving high-sensitivity for clinical applications using augmented exome sequencing.

Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R.

Genome Med. 2015 Jul 16;7:71. doi: 10.1186/s13073-015-0197-4. eCollection 2015.

48.

Relating hepatocellular carcinoma tumor samples and cell lines using gene expression data in translational research.

Chen B, Sirota M, Fan-Minogue H, Hadley D, Butte AJ.

BMC Med Genomics. 2015;8 Suppl 2:S5. doi: 10.1186/1755-8794-8-S2-S5. Epub 2015 May 29.

49.

The receptor CD44 is associated with systemic insulin resistance and proinflammatory macrophages in human adipose tissue.

Liu LF, Kodama K, Wei K, Tolentino LL, Choi O, Engleman EG, Butte AJ, McLaughlin T.

Diabetologia. 2015 Jul;58(7):1579-86. doi: 10.1007/s00125-015-3603-y. Epub 2015 May 9.

PMID:
25952479
50.

A survey of current trends in computational drug repositioning.

Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z.

Brief Bioinform. 2016 Jan;17(1):2-12. doi: 10.1093/bib/bbv020. Epub 2015 Mar 31. Review.

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