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Items: 1 to 50 of 79

1.

Qualitative and quantitative drug residue analyses: Chlortetracycline in white-tailed deer (Odocoileus virginianus) and supermarket meat by liquid chromatography tandem-mass spectrometry.

Anderson SC, Subbiah S, Gentles A, Oliver D, Stonum P, Brooks TA, Smith EE.

J Chromatogr B Analyt Technol Biomed Life Sci. 2018 Aug 15;1092:237-243. doi: 10.1016/j.jchromb.2018.05.027. Epub 2018 May 18.

PMID:
29913335
2.

GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma.

Zhang W, Bouchard G, Yu A, Shafiq M, Jamali M, Shrager JB, Ayers K, Bakr S, Gentles AJ, Diehn M, Quon A, West RB, Nair V, van de Rijn M, Napel S, Plevritis SK.

Cancer Res. 2018 Jul 1;78(13):3445-3457. doi: 10.1158/0008-5472.CAN-17-2928. Epub 2018 May 14.

PMID:
29760045
3.

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, 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 CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

4.

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.

5.

Brd4 regulates the expression of essential autophagy genes and Keap1 in AML cells.

Huang M, Zhu L, Garcia JS, Li MX, Gentles AJ, Mitchell BS.

Oncotarget. 2018 Feb 7;9(14):11665-11676. doi: 10.18632/oncotarget.24432. eCollection 2018 Feb 20.

6.

Subtype assignment of CLL based on B-cell subset associated gene signatures from normal bone marrow - A proof of concept study.

Nørgaard CH, Jakobsen LH, Gentles AJ, Dybkær K, El-Galaly TC, Bødker JS, Schmitz A, Johansen P, Herold T, Spiekermann K, Brown JR, Klitgaard JL, Johnsen HE, Bøgsted M.

PLoS One. 2018 Mar 7;13(3):e0193249. doi: 10.1371/journal.pone.0193249. eCollection 2018.

7.

Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response.

Champion M, Brennan K, Croonenborghs T, Gentles AJ, Pochet N, Gevaert O.

EBioMedicine. 2018 Jan;27:156-166. doi: 10.1016/j.ebiom.2017.11.028. Epub 2017 Dec 1.

8.

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma.

Brennan K, Shin JH, Tay JK, Prunello M, Gentles AJ, Sunwoo JB, Gevaert O.

Sci Rep. 2017 Dec 6;7(1):17064. doi: 10.1038/s41598-017-17298-x.

9.

Low BUB1 expression is an adverse prognostic marker in gastric adenocarcinoma.

Stahl D, Braun M, Gentles AJ, Lingohr P, Walter A, Kristiansen G, Gütgemann I.

Oncotarget. 2017 Jul 18;8(44):76329-76339. doi: 10.18632/oncotarget.19357. eCollection 2017 Sep 29.

10.

Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.

Zhou M, Leung A, Echegaray S, Gentles A, Shrager JB, Jensen KC, Berry GJ, Plevritis SK, Rubin DL, Napel S, Gevaert O.

Radiology. 2018 Jan;286(1):307-315. doi: 10.1148/radiol.2017161845. Epub 2017 Jul 20.

PMID:
28727543
11.

Data normalization considerations for digital tumor dissection.

Newman AM, Gentles AJ, Liu CL, Diehn M, Alizadeh AA.

Genome Biol. 2017 Jul 5;18(1):128. doi: 10.1186/s13059-017-1257-4.

12.

Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype.

Brennan K, Koenig JL, Gentles AJ, Sunwoo JB, Gevaert O.

EBioMedicine. 2017 Mar;17:223-236. doi: 10.1016/j.ebiom.2017.02.025. Epub 2017 Mar 1.

13.

Human AML-iPSCs Reacquire Leukemic Properties after Differentiation and Model Clonal Variation of Disease.

Chao MP, Gentles AJ, Chatterjee S, Lan F, Reinisch A, Corces MR, Xavy S, Shen J, Haag D, Chanda S, Sinha R, Morganti RM, Nishimura T, Ameen M, Wu H, Wernig M, Wu JC, Majeti R.

Cell Stem Cell. 2017 Mar 2;20(3):329-344.e7. doi: 10.1016/j.stem.2016.11.018. Epub 2017 Jan 12.

14.

Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance.

Jeong Y, Hoang NT, Lovejoy A, Stehr H, Newman AM, Gentles AJ, Kong W, Truong D, Martin S, Chaudhuri A, Heiser D, Zhou L, Say C, Carter JN, Hiniker SM, Loo BW Jr, West RB, Beachy P, Alizadeh AA, Diehn M.

Cancer Discov. 2017 Jan;7(1):86-101. doi: 10.1158/2159-8290.CD-16-0127. Epub 2016 Sep 23.

15.

Qualitative and Quantitative Drug residue analyses: Florfenicol in white-tailed deer (Odocoileus virginianus) and supermarket meat by liquid chromatography tandem-mass spectrometry.

Anderson SC, Subbiah S, Gentles A, Austin G, Stonum P, Brooks TA, Brooks C, Smith EE.

J Chromatogr B Analyt Technol Biomed Life Sci. 2016 Oct 15;1033-1034:73-79. doi: 10.1016/j.jchromb.2016.08.014. Epub 2016 Aug 10.

PMID:
27529828
16.

Pathophysiological significance and therapeutic targeting of germinal center kinase in diffuse large B-cell lymphoma.

Matthews JM, Bhatt S, Patricelli MP, Nomanbhoy TK, Jiang X, Natkunam Y, Gentles AJ, Martinez E, Zhu D, Chapman JR, Cortizas E, Shyam R, Chinichian S, Advani R, Tan L, Zhang J, Choi HG, Tibshirani R, Buhrlage SJ, Gratzinger D, Verdun R, Gray NS, Lossos IS.

Blood. 2016 Jul 14;128(2):239-48. doi: 10.1182/blood-2016-02-696856. Epub 2016 May 5.

17.

Identifying Network Perturbation in Cancer.

Grechkin M, Logsdon BA, Gentles AJ, Lee SI.

PLoS Comput Biol. 2016 May 4;12(5):e1004888. doi: 10.1371/journal.pcbi.1004888. eCollection 2016 May.

18.

An LSC epigenetic signature is largely mutation independent and implicates the HOXA cluster in AML pathogenesis.

Jung N, Dai B, Gentles AJ, Majeti R, Feinberg AP.

Nat Commun. 2015 Oct 7;6:8489. doi: 10.1038/ncomms9489.

19.

CD93 Marks a Non-Quiescent Human Leukemia Stem Cell Population and Is Required for Development of MLL-Rearranged Acute Myeloid Leukemia.

Iwasaki M, Liedtke M, Gentles AJ, Cleary ML.

Cell Stem Cell. 2015 Oct 1;17(4):412-21. doi: 10.1016/j.stem.2015.08.008. Epub 2015 Sep 18.

20.

Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer.

Gentles AJ, Bratman SV, Lee LJ, Harris JP, Feng W, Nair RV, Shultz DB, Nair VS, Hoang CD, West RB, Plevritis SK, Alizadeh AA, Diehn M.

J Natl Cancer Inst. 2015 Aug 18;107(10). pii: djv211. doi: 10.1093/jnci/djv211. Print 2015 Oct.

PMID:
26286589
21.

The prognostic landscape of genes and infiltrating immune cells across human cancers.

Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, Nair VS, Xu Y, Khuong A, Hoang CD, Diehn M, West RB, Plevritis SK, Alizadeh AA.

Nat Med. 2015 Aug;21(8):938-945. doi: 10.1038/nm.3909. Epub 2015 Jul 20.

22.

Gene expression analysis of plasmablastic lymphoma identifies downregulation of B-cell receptor signaling and additional unique transcriptional programs.

Chapman J, Gentles AJ, Sujoy V, Vega F, Dumur CI, Blevins TL, Bernal-Mizrachi L, Mosunjac M, Pimentel A, Zhu D, Lossos IS.

Leukemia. 2015 Nov;29(11):2270-3. doi: 10.1038/leu.2015.109. Epub 2015 Apr 24. No abstract available.

PMID:
25921246
23.

Robust enumeration of cell subsets from tissue expression profiles.

Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA.

Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30.

24.

Reprogramming of primary human Philadelphia chromosome-positive B cell acute lymphoblastic leukemia cells into nonleukemic macrophages.

McClellan JS, Dove C, Gentles AJ, Ryan CE, Majeti R.

Proc Natl Acad Sci U S A. 2015 Mar 31;112(13):4074-9. doi: 10.1073/pnas.1413383112. Epub 2015 Mar 16.

25.

A Simple Method for Estimating Interactions between a Treatment and a Large Number of Covariates.

Tian L, Alizadeh AA, Gentles AJ, Tibshirani R.

J Am Stat Assoc. 2014 Oct;109(508):1517-1532.

26.

Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation.

Green MR, Kihira S, Liu CL, Nair RV, Salari R, Gentles AJ, Irish J, Stehr H, Vicente-Dueñas C, Romero-Camarero I, Sanchez-Garcia I, Plevritis SK, Arber DA, Batzoglou S, Levy R, Alizadeh AA.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):E1116-25. doi: 10.1073/pnas.1501199112. Epub 2015 Feb 23.

27.

Sparse expression bases in cancer reveal tumor drivers.

Logsdon BA, Gentles AJ, Miller CP, Blau CA, Becker PS, Lee SI.

Nucleic Acids Res. 2015 Feb 18;43(3):1332-44. doi: 10.1093/nar/gku1290. Epub 2015 Jan 12.

28.

Mutant WT1 is associated with DNA hypermethylation of PRC2 targets in AML and responds to EZH2 inhibition.

Sinha S, Thomas D, Yu L, Gentles AJ, Jung N, Corces-Zimmerman MR, Chan SM, Reinisch A, Feinberg AP, Dill DL, Majeti R.

Blood. 2015 Jan 8;125(2):316-26. doi: 10.1182/blood-2014-03-566018. Epub 2014 Nov 14.

29.

Active idiotypic vaccination versus control immunotherapy for follicular lymphoma.

Levy R, Ganjoo KN, Leonard JP, Vose JM, Flinn IW, Ambinder RF, Connors JM, Berinstein NL, Belch AR, Bartlett NL, Nichols C, Emmanouilides CE, Timmerman JM, Gregory SA, Link BK, Inwards DJ, Freedman AS, Matous JV, Robertson MJ, Kunkel LA, Ingolia DE, Gentles AJ, Liu CL, Tibshirani R, Alizadeh AA, Denney DW Jr.

J Clin Oncol. 2014 Jun 10;32(17):1797-803. doi: 10.1200/JCO.2012.43.9273. Epub 2014 May 5.

30.

Targeting unique metabolic properties of breast tumor initiating cells.

Feng W, Gentles A, Nair RV, Huang M, Lin Y, Lee CY, Cai S, Scheeren FA, Kuo AH, Diehn M.

Stem Cells. 2014 Jul;32(7):1734-45. doi: 10.1002/stem.1662.

31.

Utility in prognostic value added by molecular profiles for diffuse large B-cell lymphoma.

Gentles AJ, Alizadeh AA.

Blood. 2013 Apr 11;121(15):3052-4. doi: 10.1182/blood-2013-01-477521. No abstract available.

32.

Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma.

Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA.

Blood. 2013 Feb 28;121(9):1604-11. doi: 10.1182/blood-2012-09-457283. Epub 2013 Jan 7.

33.

The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses.

Pachynski RK, Zabel BA, Kohrt HE, Tejeda NM, Monnier J, Swanson CD, Holzer AK, Gentles AJ, Sperinde GV, Edalati A, Hadeiba HA, Alizadeh AA, Butcher EC.

J Exp Med. 2012 Jul 30;209(8):1427-35. doi: 10.1084/jem.20112124. Epub 2012 Jul 2.

34.

Identification of LMO2 transcriptome and interactome in diffuse large B-cell lymphoma.

Cubedo E, Gentles AJ, Huang C, Natkunam Y, Bhatt S, Lu X, Jiang X, Romero-Camarero I, Freud A, Zhao S, Bacchi CE, Martínez-Climent JA, Sánchez-García I, Melnick A, Lossos IS.

Blood. 2012 Jun 7;119(23):5478-91. doi: 10.1182/blood-2012-01-403154. Epub 2012 Apr 19.

35.

The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors.

Willingham SB, Volkmer JP, Gentles AJ, Sahoo D, Dalerba P, Mitra SS, Wang J, Contreras-Trujillo H, Martin R, Cohen JD, Lovelace P, Scheeren FA, Chao MP, Weiskopf K, Tang C, Volkmer AK, Naik TJ, Storm TA, Mosley AR, Edris B, Schmid SM, Sun CK, Chua MS, Murillo O, Rajendran P, Cha AC, Chin RK, Kim D, Adorno M, Raveh T, Tseng D, Jaiswal S, Enger PØ, Steinberg GK, Li G, So SK, Majeti R, Harsh GR, van de Rijn M, Teng NN, Sunwoo JB, Alizadeh AA, Clarke MF, Weissman IL.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6662-7. doi: 10.1073/pnas.1121623109. Epub 2012 Mar 26.

36.

A few good genes: simple, biologically motivated signatures for cancer prognosis.

Gentles AJ, Alizadeh AA.

Cell Cycle. 2011 Nov 1;10(21):3615-6. doi: 10.4161/cc.10.21.17835. Epub 2011 Nov 1. No abstract available.

37.

Lymphomas that recur after MYC suppression continue to exhibit oncogene addiction.

Choi PS, van Riggelen J, Gentles AJ, Bachireddy P, Rakhra K, Adam SJ, Plevritis SK, Felsher DW.

Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17432-7. doi: 10.1073/pnas.1107303108. Epub 2011 Oct 3.

38.

Systems biology: confronting the complexity of cancer.

Gentles AJ, Gallahan D.

Cancer Res. 2011 Sep 15;71(18):5961-4. doi: 10.1158/0008-5472.CAN-11-1569. Epub 2011 Sep 6.

39.

Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment.

Alizadeh AA, Gentles AJ, Alencar AJ, Liu CL, Kohrt HE, Houot R, Goldstein MJ, Zhao S, Natkunam Y, Advani RH, Gascoyne RD, Briones J, Tibshirani RJ, Myklebust JH, Plevritis SK, Lossos IS, Levy R.

Blood. 2011 Aug 4;118(5):1350-8. doi: 10.1182/blood-2011-03-345272. Epub 2011 Jun 13.

40.

Clinical application of readout-segmented- echo-planar imaging for diffusion-weighted imaging in pediatric brain.

Holdsworth SJ, Yeom K, Skare S, Gentles AJ, Barnes PD, Bammer R.

AJNR Am J Neuroradiol. 2011 Aug;32(7):1274-9. doi: 10.3174/ajnr.A2481. Epub 2011 May 19.

41.

Discovering biological progression underlying microarray samples.

Qiu P, Gentles AJ, Plevritis SK.

PLoS Comput Biol. 2011 Apr;7(4):e1001123. doi: 10.1371/journal.pcbi.1001123. Epub 2011 Apr 14.

42.

Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker.

Jan M, Chao MP, Cha AC, Alizadeh AA, Gentles AJ, Weissman IL, Majeti R.

Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):5009-14. doi: 10.1073/pnas.1100551108. Epub 2011 Mar 7.

43.

Calreticulin is the dominant pro-phagocytic signal on multiple human cancers and is counterbalanced by CD47.

Chao MP, Jaiswal S, Weissman-Tsukamoto R, Alizadeh AA, Gentles AJ, Volkmer J, Weiskopf K, Willingham SB, Raveh T, Park CY, Majeti R, Weissman IL.

Sci Transl Med. 2010 Dec 22;2(63):63ra94. doi: 10.1126/scitranslmed.3001375.

44.

Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia.

Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA.

JAMA. 2010 Dec 22;304(24):2706-15. doi: 10.1001/jama.2010.1862.

45.

Recurrent interstitial 1p36 deletions: Evidence for germline mosaicism and complex rearrangement breakpoints.

Gajecka M, Saitta SC, Gentles AJ, Campbell L, Ciprero K, Geiger E, Catherwood A, Rosenfeld JA, Shaikh T, Shaffer LG.

Am J Med Genet A. 2010 Dec;152A(12):3074-83. doi: 10.1002/ajmg.a.33733.

46.

Efficacy of bortezomib in a direct xenograft model of primary effusion lymphoma.

Sarosiek KA, Cavallin LE, Bhatt S, Toomey NL, Natkunam Y, Blasini W, Gentles AJ, Ramos JC, Mesri EA, Lossos IS.

Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13069-74. doi: 10.1073/pnas.1002985107. Epub 2010 Jul 6.

47.

Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks.

Qiu P, Gentles AJ, Plevritis SK.

J Comput Biol. 2010 Feb;17(2):169-76. doi: 10.1089/cmb.2009.0052.

48.

Novel IL-21 signaling pathway up-regulates c-Myc and induces apoptosis of diffuse large B-cell lymphomas.

Sarosiek KA, Malumbres R, Nechushtan H, Gentles AJ, Avisar E, Lossos IS.

Blood. 2010 Jan 21;115(3):570-80. doi: 10.1182/blood-2009-08-239996. Epub 2009 Nov 20.

49.

Characterization of patient specific signaling via augmentation of Bayesian networks with disease and patient state nodes.

Sachs K, Gentles AJ, Youland R, Itani S, Irish J, Nolan GP, Plevritis SK.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:6624-7. doi: 10.1109/IEMBS.2009.5332563.

50.

A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients.

Gentles AJ, Alizadeh AA, Lee SI, Myklebust JH, Shachaf CM, Shahbaba B, Levy R, Koller D, Plevritis SK.

Blood. 2009 Oct 8;114(15):3158-66. doi: 10.1182/blood-2009-02-202465. Epub 2009 Jul 27.

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