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Items: 37

1.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2019 Aug 20;51(2):411-412. doi: 10.1016/j.immuni.2019.08.004. No abstract available.

2.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. Erratum in: Immunity. 2019 Aug 20;51(2):411-412.

3.

Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa.

Samal A, Craig JP, Coradetti ST, Benz JP, Eddy JA, Price ND, Glass NL.

Biotechnol Biofuels. 2017 Sep 21;10:225. doi: 10.1186/s13068-017-0901-2. eCollection 2017.

4.

Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.

Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS.

J Immunol. 2017 Jul 1;199(1):323-335. doi: 10.4049/jimmunol.1700172. Epub 2017 May 31.

5.

Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases.

Allen M, Carrasquillo MM, Funk C, Heavner BD, Zou F, Younkin CS, Burgess JD, Chai HS, Crook J, Eddy JA, Li H, Logsdon B, Peters MA, Dang KK, Wang X, Serie D, Wang C, Nguyen T, Lincoln S, Malphrus K, Bisceglio G, Li M, Golde TE, Mangravite LM, Asmann Y, Price ND, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N.

Sci Data. 2016 Oct 11;3:160089. doi: 10.1038/sdata.2016.89.

6.

Body Dissatisfaction in a Diverse Sample of Young Men Who Have Sex With Men: The P18 Cohort Study.

Siconolfi DE, Kapadia F, Moeller RW, Eddy JA, Kupprat SA, Kingdon MJ, Halkitis PN.

Arch Sex Behav. 2016 Jul;45(5):1227-39. doi: 10.1007/s10508-015-0592-3. Epub 2015 Sep 14.

7.

Fostering synergy between cell biology and systems biology.

Eddy JA, Funk CC, Price ND.

Trends Cell Biol. 2015 Aug;25(8):440-5. doi: 10.1016/j.tcb.2015.04.005. Epub 2015 May 23. Review.

8.

Acceptability of PrEP Uptake Among Racially/Ethnically Diverse Young Men Who Have Sex With Men: The P18 Study.

Pérez-Figueroa RE, Kapadia F, Barton SC, Eddy JA, Halkitis PN.

AIDS Educ Prev. 2015 Apr;27(2):112-25. doi: 10.1521/aeap.2015.27.2.112.

9.

IL-10 alters immunoproteostasis in APP mice, increasing plaque burden and worsening cognitive behavior.

Chakrabarty P, Li A, Ceballos-Diaz C, Eddy JA, Funk CC, Moore B, DiNunno N, Rosario AM, Cruz PE, Verbeeck C, Sacino A, Nix S, Janus C, Price ND, Das P, Golde TE.

Neuron. 2015 Feb 4;85(3):519-33. doi: 10.1016/j.neuron.2014.11.020. Epub 2015 Jan 22.

10.

Evidence for a Syndemic in Aging HIV-positive Gay, Bisexual, and Other MSM: Implications for a Holistic Approach to Prevention and Healthcare.

Halkitis PN, Kupprat SA, Hampton MB, Perez-Figueroa R, Kingdon M, Eddy JA, Ompad DC.

Nat Resour Model. 2012 Nov 1;36(2). doi: 10.1111/napa.12009.

11.

Sociodemographic Factors Contribute to Mental Health Disparities and Access to Services Among Young Men Who Have Sex with Men in New York City.

Storholm ED, Siconolfi DE, Halkitis PN, Moeller RW, Eddy JA, Bare MG.

J Gay Lesbian Ment Health. 2013;17(3). doi: 10.1080/19359705.2012.763080.

12.

Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas.

Wang C, Funk CC, Eddy JA, Price ND.

PLoS One. 2013 Oct 11;8(10):e76694. doi: 10.1371/journal.pone.0076694. eCollection 2013.

13.

AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures.

Earls JC, Eddy JA, Funk CC, Ko Y, Magis AT, Price ND.

BMC Bioinformatics. 2013 Mar 5;14:78. doi: 10.1186/1471-2105-14-78.

14.

Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain.

Ko Y, Ament SA, Eddy JA, Caballero J, Earls JC, Hood L, Price ND.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):3095-100. doi: 10.1073/pnas.1222897110. Epub 2013 Feb 5.

15.

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE.

Wang Y, Eddy JA, Price ND.

BMC Syst Biol. 2012 Dec 13;6:153. doi: 10.1186/1752-0509-6-153.

16.

Mechanistic modeling of aberrant energy metabolism in human disease.

Sangar V, Eddy JA, Simeonidis E, Price ND.

Front Physiol. 2012 Oct 25;3:404. doi: 10.3389/fphys.2012.00404. eCollection 2012.

17.

Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states.

Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND, Robinson GE.

Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):18020-5. doi: 10.1073/pnas.1114093108. Epub 2011 Sep 29.

18.

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052.

Milne CB, Eddy JA, Raju R, Ardekani S, Kim PJ, Senger RS, Jin YS, Blaschek HP, Price ND.

BMC Syst Biol. 2011 Aug 16;5:130. doi: 10.1186/1752-0509-5-130.

19.

Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup.

Magis AT, Earls JC, Ko YH, Eddy JA, Price ND.

Bioinformatics. 2011 Mar 15;27(6):872-3. doi: 10.1093/bioinformatics/btr033. Epub 2011 Jan 20.

20.

In silico models of cancer.

Edelman LB, Eddy JA, Price ND.

Wiley Interdiscip Rev Syst Biol Med. 2010 Jul-Aug;2(4):438-459. doi: 10.1002/wsbm.75. Review.

21.

Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug.

Yang J, Eddy JA, Pan Y, Hategan A, Tabus I, Wang Y, Cogdell D, Price ND, Pollock RE, Lazar AJ, Hunt KK, Trent JC, Zhang W.

Mol Cell Proteomics. 2010 Nov;9(11):2405-13. doi: 10.1074/mcp.M110.000240. Epub 2010 Jul 22.

22.

Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC).

Eddy JA, Hood L, Price ND, Geman D.

PLoS Comput Biol. 2010 May 27;6(5):e1000792. doi: 10.1371/journal.pcbi.1000792.

23.

Relative expression analysis for molecular cancer diagnosis and prognosis.

Eddy JA, Sung J, Geman D, Price ND.

Technol Cancer Res Treat. 2010 Apr;9(2):149-59. Review.

24.

Relative expression analysis for identifying perturbed pathways.

Eddy JA, Geman D, Price ND.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:5456-9. doi: 10.1109/IEMBS.2009.5334063.

25.

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology.

Milne CB, Kim PJ, Eddy JA, Price ND.

Biotechnol J. 2009 Dec;4(12):1653-70. doi: 10.1002/biot.200900234. Review.

26.

Dynamic analysis of integrated signaling, metabolic, and regulatory networks.

Lee JM, Gianchandani EP, Eddy JA, Papin JA.

PLoS Comput Biol. 2008 May 23;4(5):e1000086. doi: 10.1371/journal.pcbi.1000086. Erratum in: PLoS Comput Biol. 2008 Jun;4(6). doi: 10.1371/annotation/5594348b-de00-446a-bdd0-ec56e70b3553. Min Lee, Jong [corrected to Lee, Jong Min].

27.

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major.

Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA.

Mol Syst Biol. 2008;4:177. doi: 10.1038/msb.2008.15. Epub 2008 Mar 25.

28.

Solar considerations in the development of cutaneous melanoma.

Loggie BW, Eddy JA.

Semin Oncol. 1988 Dec;15(6):494-9.

PMID:
3206236
29.

Edison the scientist.

Eddy JA.

Appl Opt. 1979 Nov 15;18(22):3737. doi: 10.1364/AO.18.003737.

PMID:
20216688
30.

Anomalous solar rotation in the early 17th century.

Eddy JA, Gilman PA, Trotter DE.

Science. 1977 Nov 25;198(4319):824-9.

PMID:
17843405
31.

Skylab optics: an introduction.

Eddy JA.

Appl Opt. 1977 Apr 1;16(4):823. doi: 10.1364/AO.16.000823. No abstract available.

PMID:
20168600
32.

A practical question in astronomy.

Eddy JA.

Science. 1977 Feb 18;195(4279):670-1. No abstract available.

PMID:
17816412
33.

The maunder minimum.

Eddy JA.

Science. 1976 Jun 18;192(4245):1189-202. No abstract available.

PMID:
17771739
34.

Irrigation increases rainfall?

Eddy JA, Stidd CK, Fowler WB, Helvey JD.

Science. 1975 Apr 18;188(4185):279-81. No abstract available.

PMID:
17800405
35.

Astronomical alignment of the big horn medicine wheel.

Eddy JA.

Science. 1974 Jun 7;184(4141):1035-43. No abstract available.

PMID:
17736182
36.

Far infrared airborne spectroscopy.

Eddy JA, Lee RH, Léna PJ, Macqueen RM.

Appl Opt. 1970 Feb 1;9(2):439-46. doi: 10.1364/AO.9.000439.

PMID:
20076207
37.

The nurse and the hospitalized teenager.

Hammar SL, Eddy JA.

RN. 1966 Dec;29(12):68-71. No abstract available.

PMID:
5179846

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