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Items: 1 to 50 of 305

1.

PLATYPUS: A Multiple-View Learning Predictive Framework for Cancer Drug Sensitivity Prediction.

Graim K, Friedl V, Houlahan KE, Stuart JM.

Pac Symp Biocomput. 2019;24:136-147.

2.

Risk factors for acquisition of meningococcal carriage in the African meningitis belt.

Cooper LV, Robson A, Trotter CL, Aseffa A, Collard JM, Daugla DM, Diallo A, Hodgson A, Jusot JF, Omotara B, Sow S, Hassan-King M, Manigart O, Nascimento M, Woukeu A, Chandramohan D, Borrow R, Maiden MCJ, Greenwood B, Stuart JM; MenAfriCar Consortium.

Trop Med Int Health. 2019 Apr;24(4):392-400. doi: 10.1111/tmi.13203. Epub 2019 Feb 6.

3.

Reply to A. Dalla Volta et al.

Aggarwal R, Huang J, Alumkal J, Feng FY, Zhang L, Stuart JM, Small EJ.

J Clin Oncol. 2019 Feb 1;37(4):351-352. doi: 10.1200/JCO.18.01487. Epub 2018 Dec 17. No abstract available.

PMID:
30557523
4.

Narrative review of methods and findings of recent studies on the carriage of meningococci and other Neisseria species in the African Meningitis Belt.

Greenwood BM, Aseffa A, Caugant DA, Diallo K, Kristiansen PA, Maiden MCJ, Stuart JM, Trotter CL.

Trop Med Int Health. 2019 Feb;24(2):143-154. doi: 10.1111/tmi.13185. Epub 2018 Dec 6. Review.

5.

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC.

Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

6.

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN Jr, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY.

Cell. 2018 Oct 18;175(3):889. doi: 10.1016/j.cell.2018.10.019. No abstract available.

7.

Valection: design optimization for validation and verification studies.

Cooper CI, Yao D, Sendorek DH, Yamaguchi TN, P'ng C, Houlahan KE, Caloian C, Fraser M; SMC-DNA Challenge Participants, Ellrott K, Margolin AA, Bristow RG, Stuart JM, Boutros PC.

BMC Bioinformatics. 2018 Sep 25;19(1):339. doi: 10.1186/s12859-018-2391-z.

8.

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer.

Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, Cieslik MP, Parolia A, Beer TM, Thomas G, Chi KN, Gleave M, Lack NA, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Ryan CJ, Fong L, Kim W, Friedlander T, Chou J, Li H, Das R, Li H, Moussavi-Baygi R, Goodarzi H, Gilbert LA, Lara PN Jr, Evans CP, Goldstein TC, Stuart JM, Tomlins SA, Spratt DE, Cheetham RK, Cheng DT, Farh K, Gehring JS, Hakenberg J, Liao A, Febbo PG, Shon J, Sickler B, Batzoglou S, Knudsen KE, He HH, Huang J, Wyatt AW, Dehm SM, Ashworth A, Chinnaiyan AM, Maher CA, Small EJ, Feng FY.

Cell. 2018 Jul 26;174(3):758-769.e9. doi: 10.1016/j.cell.2018.06.039. Epub 2018 Jul 19. Erratum in: Cell. 2018 Oct 18;175(3):889.

9.

Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.

Aggarwal R, Huang J, Alumkal JJ, Zhang L, Feng FY, Thomas GV, Weinstein AS, Friedl V, Zhang C, Witte ON, Lloyd P, Gleave M, Evans CP, Youngren J, Beer TM, Rettig M, Wong CK, True L, Foye A, Playdle D, Ryan CJ, Lara P, Chi KN, Uzunangelov V, Sokolov A, Newton Y, Beltran H, Demichelis F, Rubin MA, Stuart JM, Small EJ.

J Clin Oncol. 2018 Aug 20;36(24):2492-2503. doi: 10.1200/JCO.2017.77.6880. Epub 2018 Jul 9.

10.

Integrated Molecular Characterization of Testicular Germ Cell Tumors.

Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, Kulis T, Cárcano FM, Leraas KM, Lichtenberg TM, Brooks D, Cherniack AD, Cho J, Heiman DI, Kasaian K, Liu M, Noble MS, Xi L, Zhang H, Zhou W, ZenKlusen JC, Hutter CM, Felau I, Zhang J, Schultz N, Getz G, Meyerson M, Stuart JM; Cancer Genome Atlas Research Network, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA.

Cell Rep. 2018 Jun 12;23(11):3392-3406. doi: 10.1016/j.celrep.2018.05.039.

11.

The role of Syk in peripheral T cells.

Park JE, Majumdar S, Brand DD, Rosloniec EF, Yi AK, Stuart JM, Kang AH, Myers LK.

Clin Immunol. 2018 Jul;192:50-57. doi: 10.1016/j.clim.2018.04.007. Epub 2018 Apr 16.

12.

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.

Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

13.

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.

Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G; Cancer Genome Atlas Research Network.

Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033.

14.

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer.

Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM; Cancer Genome Atlas Network, Stuart JM, Benz CC, Laird PW.

Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022.

15.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK; Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C.

Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063.

16.

Environmental Toxin Acrolein Alters Levels of Endogenous Lipids, Including TRP Agonists: A Potential Mechanism for Headache Driven by TRPA1 Activation.

Leishman E, Kunkler PE, Manchanda M, Sangani K, Stuart JM, Oxford GS, Hurley JH, Bradshaw HB.

Neurobiol Pain. 2017 Jan-Jul;1:28-36. doi: 10.1016/j.ynpai.2017.03.001. Epub 2017 May 17.

17.

Germline contamination and leakage in whole genome somatic single nucleotide variant detection.

Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC.

BMC Bioinformatics. 2018 Jan 31;19(1):28. doi: 10.1186/s12859-018-2046-0.

18.

Reactive vaccination as a control strategy for pneumococcal meningitis outbreaks in the African meningitis belt: Analysis of outbreak data from Ghana.

Cooper LV, Stuart JM, Okot C, Asiedu-Bekoe F, Afreh OK, Fernandez K, Ronveaux O, Trotter CL.

Vaccine. 2018 Jan 20. pii: S0264-410X(17)31832-7. doi: 10.1016/j.vaccine.2017.12.069. [Epub ahead of print]

19.

Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer.

Newton Y, Rassekh SR, Deyell RJ, Shen Y, Jones MR, Dunham C, Yip S, Leelakumari S, Zhu J, McColl D, Swatloski T, Salama SR, Ng T, Hendson G, Lee AF, Ma Y, Moore R, Mungall AJ, Haussler D, Stuart JM, Jantzen C, Laskin J, Jones SJM, Marra MA, Morozova O.

JCO Precis Oncol. 2018;2. doi: 10.1200/PO.17.00198. Epub 2018 Apr 19.

20.

Prophetic Granger Causality to infer gene regulatory networks.

Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM.

PLoS One. 2017 Dec 6;12(12):e0170340. doi: 10.1371/journal.pone.0170340. eCollection 2017.

21.

Meningococcal carriage within households in the African meningitis belt: A longitudinal pilot study.

Basta NE, Berthe A, Keita M, Onwuchekwa U, Tamboura B, Traore A, Hassan-King M, Manigart O, Nascimento M, Stuart JM, Trotter C, Blake J, Carr AD, Gray SJ, Newbold LS, Deng Y, Wolfson J, Halloran ME, Greenwood B, Borrow R, Sow SO.

J Infect. 2018 Feb;76(2):140-148. doi: 10.1016/j.jinf.2017.11.006. Epub 2017 Nov 29.

22.

Impact of serogroup A meningococcal conjugate vaccine for Africa.

Stuart JM.

Hum Vaccin Immunother. 2018 May 4;14(5):1116-1117. doi: 10.1080/21645515.2017.1412022. Epub 2018 Jan 16.

23.

TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal.

Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM.

Cancer Res. 2017 Nov 1;77(21):e111-e114. doi: 10.1158/0008-5472.CAN-17-0580.

24.

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma'ayan A, Sorger PK.

Nat Commun. 2017 Oct 30;8(1):1186. doi: 10.1038/s41467-017-01383-w.

25.

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.

Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA.

Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4.

26.

The Role of Leukocyte-Associated Ig-like Receptor-1 in Suppressing Collagen-Induced Arthritis.

Kim S, Easterling ER, Price LC, Smith SL, Coligan JE, Park JE, Brand DD, Rosloniec EF, Stuart JM, Kang AH, Myers LK.

J Immunol. 2017 Oct 15;199(8):2692-2700. doi: 10.4049/jimmunol.1700271. Epub 2017 Sep 8.

27.

Investigation of correlates of protection against pharyngeal carriage of Neisseria meningitidis genogroups W and Y in the African meningitis belt.

Cooper LV, Boukary RM, Aseffa A, Mihret W, Collard JM, Daugla D, Hodgson A, Sokhna C, Omotara B, Sow S, Quaye SL, Diallo K, Manigart O, Maiden MCJ, Findlow H, Borrow R, Stuart JM, Greenwood BM, Trotter CL.

PLoS One. 2017 Aug 10;12(8):e0182575. doi: 10.1371/journal.pone.0182575. eCollection 2017.

28.

Targeting Adaptive Pathways in Metastatic Treatment-Resistant Prostate Cancer: Update on the Stand Up 2 Cancer/Prostate Cancer Foundation-Supported West Coast Prostate Cancer Dream Team.

Aggarwal R, Beer TM, Gleave M, Stuart JM, Rettig M, Evans CP, Youngren J, Alumkal JJ, Huang J, Thomas G, Witte O, Small EJ.

Eur Urol Focus. 2016 Dec;2(5):469-471. doi: 10.1016/j.euf.2016.10.011. Epub 2016 Nov 14.

PMID:
28723508
29.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN.

Cell Rep. 2017 Jun 27;19(13):2878-2880. doi: 10.1016/j.celrep.2017.06.008. No abstract available.

30.

Impact of MenAfriVac in nine countries of the African meningitis belt, 2010-15: an analysis of surveillance data.

Trotter CL, Lingani C, Fernandez K, Cooper LV, Bita A, Tevi-Benissan C, Ronveaux O, Préziosi MP, Stuart JM.

Lancet Infect Dis. 2017 Aug;17(8):867-872. doi: 10.1016/S1473-3099(17)30301-8. Epub 2017 May 22.

PMID:
28545721
31.

Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad.

Diallo K, Gamougam K, Daugla DM, Harrison OB, Bray JE, Caugant DA, Lucidarme J, Trotter CL, Hassan-King M, Stuart JM, Manigart O, Greenwood BM, Maiden MCJ.

BMC Genomics. 2017 May 22;18(1):398. doi: 10.1186/s12864-017-3789-0.

32.

Revealing cancer subtypes with higher-order correlations applied to imaging and omics data.

Graim K, Liu TT, Achrol AS, Paull EO, Newton Y, Chang SD, Harsh GR 4th, Cordero SP, Rubin DL, Stuart JM.

BMC Med Genomics. 2017 Mar 31;10(1):20. doi: 10.1186/s12920-017-0256-3.

33.

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles.

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN.

Cell Rep. 2017 Mar 14;18(11):2780-2794. doi: 10.1016/j.celrep.2017.02.033. Erratum in: Cell Rep. 2017 Jun 27;19(13):2878-2880.

34.

Can infant vaccination prevent pneumococcal meningitis outbreaks in sub-Saharan Africa?

Stuart JM.

Trop Med Int Health. 2017 May;22(5):514-515. doi: 10.1111/tmi.12860. Epub 2017 Mar 29. No abstract available.

35.

Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment.

Liu TT, Achrol AS, Mitchell LA, Rodriguez SA, Feroze A, Iv M, Kim C, Chaudhary N, Gevaert O, Stuart JM, Harsh GR, Chang SD, Rubin DL.

Neuro Oncol. 2017 Jul 1;19(7):997-1007. doi: 10.1093/neuonc/now270.

36.

TRACING CO-REGULATORY NETWORK DYNAMICS IN NOISY, SINGLE-CELL TRANSCRIPTOME TRAJECTORIES.

Cordero P, Stuart JM.

Pac Symp Biocomput. 2017;22:576-587. doi: 10.1142/9789813207813_0053.

37.

Characterization of the Syk-Dependent T Cell Signaling Response to an Altered Peptide.

Park JE, Rotondo JA, Cullins DL, Brand DD, Yi AK, Stuart JM, Kang AH, Myers LK.

J Immunol. 2016 Dec 15;197(12):4569-4575. Epub 2016 Nov 11.

38.

TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer.

Si H, Lu H, Yang X, Mattox A, Jang M, Bian Y, Sano E, Viadiu H, Yan B, Yau C, Ng S, Lee SK, Romano RA, Davis S, Walker RL, Xiao W, Sun H, Wei L, Sinha S, Benz CC, Stuart JM, Meltzer PS, Van Waes C, Chen Z.

Oncogene. 2016 Nov 3;35(44):5781-5794. doi: 10.1038/onc.2016.112. Epub 2016 May 2.

39.

Alternative Molecular Methods for Improved Detection of Meningococcal Carriage and Measurement of Bacterial Density.

Manigart O, Okeakpu J, Odutola A, Jarju S, Foster-Nyarko E, Diallo K, Roca A, Kampmann B, D'Alessandro U, Sow S, Antonio M, Maiden MJ, Borrow R, Stuart JM, Trotter CL, Greenwood BM.

J Clin Microbiol. 2016 Nov;54(11):2743-2748. Epub 2016 Aug 31.

40.

Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.

Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM.

Cell. 2016 Aug 11;166(4):1041-1054. doi: 10.1016/j.cell.2016.07.007. Epub 2016 Aug 4.

41.

Decreased expression levels of Ifi genes is associated to the increased resistance to spontaneous arthritis disease in mice deficiency of IL-1RA.

Liu X, Jiao Y, Cao Y, Deng N, Ma Y, Hasty KA, Kang A, Chen H, Stuart JM, Gu W.

BMC Immunol. 2016 Aug 2;17(1):25. doi: 10.1186/s12865-016-0163-y.

42.

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.

Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong CH, Wei CL, Smith RD, Callister SJ, Stuart JM, Worden AZ.

PLoS One. 2016 Jul 19;11(7):e0155839. doi: 10.1371/journal.pone.0155839. eCollection 2016.

43.

Correction: A Seroepidemiological Study of Serogroup A Meningococcal Infection in the African Meningitis Belt.

Manigart O, Trotter C, Findlow H, Aseffa A, Mihret W, Moti Demisse T, Yeshitela B, Osei I, Hodgson A, Quaye SL, Sow S, Coulibaly M, Diallo K, Traore A, Collard JM, Moustapha Boukary R, Djermakoye O, Mahamane AE, Jusot JF, Sokhna C, Alavo S, Doucoure S, Ba EH, Dieng M, Diallo A, Daugla DM, Omotara B, Chandramohan D, Hassan-King M, Nascimento M, Woukeu A, Borrow R, Stuart JM, Greenwood B.

PLoS One. 2016 Jul 5;11(7):e0158938. doi: 10.1371/journal.pone.0158938. eCollection 2016.

44.

Non-invasive dual fluorescence in vivo imaging for detection of macrophage infiltration and matrix metalloproteinase (MMP) activity in inflammatory arthritic joints.

Cho H, Bhatti FU, Yoon TW, Hasty KA, Stuart JM, Yi AK.

Biomed Opt Express. 2016 Apr 14;7(5):1842-52. doi: 10.1364/BOE.7.001842. eCollection 2016 May 1.

45.

N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells.

Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A, Meyerowitz JG, Mathis C, Cheng D, Stuart JM, Shokat KM, Gustafson WC, Huang J, Witte ON.

Cancer Cell. 2016 Apr 11;29(4):536-547. doi: 10.1016/j.ccell.2016.03.001. Epub 2016 Mar 31.

46.

Pharyngeal carriage of Neisseria species in the African meningitis belt.

Diallo K, Trotter C, Timbine Y, Tamboura B, Sow SO, Issaka B, Dano ID, Collard JM, Dieng M, Diallo A, Mihret A, Ali OA, Aseffa A, Quaye SL, Bugri A, Osei I, Gamougam K, Mbainadji L, Daugla DM, Gadzama G, Sambo ZB, Omotara BA, Bennett JS, Rebbetts LS, Watkins ER, Nascimento M, Woukeu A, Manigart O, Borrow R, Stuart JM, Greenwood BM, Maiden MCJ.

J Infect. 2016 Jun;72(6):667-677. doi: 10.1016/j.jinf.2016.03.010. Epub 2016 Mar 23.

47.

Pathway-Based Genomics Prediction using Generalized Elastic Net.

Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM.

PLoS Comput Biol. 2016 Mar 9;12(3):e1004790. doi: 10.1371/journal.pcbi.1004790. eCollection 2016 Mar.

48.

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22.

49.

A Seroepidemiological Study of Serogroup A Meningococcal Infection in the African Meningitis Belt.

Manigart O, Trotter C, Findlow H, Assefa A, Mihret W, Moti Demisse T, Yeshitela B, Osei I, Hodgson A, Quaye SL, Sow S, Coulibaly M, Diallo K, Traore A, Collard JM, Moustapha Boukary R, Djermakoye O, Mahamane AE, Jusot JF, Sokhna C, Alavo S, Doucoure S, Ba el H, Dieng M, Diallo A, Daugla DM, Omotara B, Chandramohan D, Hassan-King M, Nascimento M, Woukeu A, Borrow R, Stuart JM, Greenwood B.

PLoS One. 2016 Feb 12;11(2):e0147928. doi: 10.1371/journal.pone.0147928. eCollection 2016. Erratum in: PLoS One. 2016;11(7):e0158938.

50.

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES.

Sokolov A, Paull EO, Stuart JM.

Pac Symp Biocomput. 2016;21:405-16.

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