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Items: 1 to 50 of 236

1.

Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis.

Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ.

JAMA Netw Open. 2019 Mar 1;2(3):e190606. doi: 10.1001/jamanetworkopen.2019.0606.

PMID:
30874779
2.

Translational informatics of population health: How large biomolecular and clinical datasets unite.

Lussier YA, Butte AJ, Li H, Chen R, Moore JH.

Pac Symp Biocomput. 2019;24:455-459.

3.

A pilot study showing a stronger H1N1 influenza vaccination response during pregnancy in women who subsequently deliver preterm.

Andorf S, Bhattacharya S, Gaudilliere B, Shaw GM, Stevenson DK, Butte AJ, Sirota M.

J Reprod Immunol. 2019 Feb 27;132:16-20. doi: 10.1016/j.jri.2019.02.004. [Epub ahead of print]

PMID:
30852461
4.

Prototype of running clinical trials in an untrustworthy environment using blockchain.

Wong DR, Bhattacharya S, Butte AJ.

Nat Commun. 2019 Feb 22;10(1):917. doi: 10.1038/s41467-019-08874-y.

5.

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage.

Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, Chak S, Naikawadi RP, Wolters PJ, Abate AR, Butte AJ, Bhattacharya M.

Nat Immunol. 2019 Feb;20(2):163-172. doi: 10.1038/s41590-018-0276-y. Epub 2019 Jan 14.

PMID:
30643263
6.

A call for deep-learning healthcare.

Norgeot B, Glicksberg BS, Butte AJ.

Nat Med. 2019 Jan;25(1):14-15. doi: 10.1038/s41591-018-0320-3. No abstract available.

PMID:
30617337
7.

Author Correction: Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, Muglia LJ, Ober C, England SK, Macones G, Driscoll D, Parry S, Shaw GM, Stevenson DK, Simpson JL, Thomson E, Butte AJ; March of Dimes Prematurity Research Centers.

Sci Data. 2018 Dec 18;5(1):3. doi: 10.1038/s41597-018-0004-3.

8.

Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health.

Cheng F, Liang H, Butte AJ, Eng C, Nussinov R.

Pharmacol Rev. 2019 Jan;71(1):1-19. doi: 10.1124/pr.118.016253. Epub 2018 Dec 13. Review.

9.

Closing the Evidence Gap in Interstitial Lung Disease: The Promise of Real World Data.

Farrand E, Anstrom KJ, Bernard G, Butte AJ, Iribarren C, Ley B, Martinez F, Collard HR.

Am J Respir Crit Care Med. 2018 Nov 19. doi: 10.1164/rccm.201807-1209PP. [Epub ahead of print]

PMID:
30452876
10.

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 Nov 13;25(7):1995. doi: 10.1016/j.celrep.2018.11.013. No abstract available.

11.

Enabling precision medicine in neonatology, an integrated repository for preterm birth research.

Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, England SK, Parry S, Shaw GM, Simpson JL, Thomson E, Butte AJ; March of Dimes Prematurity Research Centers.

Sci Data. 2018 Nov 6;5:180219. doi: 10.1038/sdata.2018.219. Erratum in: Sci Data. 2018 Dec 18;5(1):3.

12.

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. Erratum in: Cell Rep. 2018 Nov 13;25(7):1995.

13.

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
14.

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.

15.

Open data informatics and data repurposing for IBD.

Rudrapatna VA, Butte AJ.

Nat Rev Gastroenterol Hepatol. 2018 Dec;15(12):715-716. doi: 10.1038/s41575-018-0050-5. No abstract available.

PMID:
30061595
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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
22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

50.

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

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