The latest can be found at Google Scholar.
2020-now
Single cell genomics in AML: extending the frontiers of AML research. Ediriwickrema A, Gentles AJ, Majeti R. Blood. 2022 Aug 4:blood.2021014670. doi: 10.1182/blood.2021014670. PMID: 35926108
Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma. Espín-Pérez A, Brennan K, Ediriwickrema AS, Gevaert O, Lossos IS, Gentles AJ. NPJ Precis Oncol. 2022 Jul 21;6(1):53. doi: 10.1038/s41698-022-00295-3.PMID: 35864305
Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA. Zhang W, Li I, Reticker-Flynn NE, Good Z, Chang S, Samusik N, Saumyaa S, Li Y, Zhou X, Liang R, Kong CS, Le QT, Gentles AJ, Sunwoo JB, Nolan GP, Engleman EG, Plevritis SK. Nat Methods. 2022 Jun;19(6):759-769. doi: 10.1038/s41592-022-01498-z. Epub 2022 Jun 2.PMID: 35654951
Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. Reticker-Flynn NE, Zhang W, Belk JA, Basto PA, Escalante NK, Pilarowski GOW, Bejnood A, Martins MM, Kenkel JA, Linde IL, Bagchi S, Yuan R, Chang S, Spitzer MH, Carmi Y, Cheng J, Tolentino LL, Choi O, Wu N, Kong CS, Gentles AJ, Sunwoo JB, Satpathy AT, Plevritis SK, Engleman EG. Cell. 2022 May 26;185(11):1924-1942.. PMID: 35525247
NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Brennan K, Zheng H, Fahrner JA, Shin JH, Gentles AJ, Schaefer B, Sunwoo JB, Bernstein JA, Gevaert O. Hum Mol Genet. 2022 Jul 7;31(13):2164-2184. doi: 10.1093/hmg/ddac026.P MID: 35094088
Clonal architecture predicts clinical outcomes and drug sensitivity in acute myeloid leukemia. Benard BA, Leak LB, Azizi A, Thomas D, Gentles AJ, Majeti R.Nat Commun. 2021 Dec 13;12(1):7244. doi: 10.1038/s41467-021-27472-5. PMID: 34903734
Atlas of clinically distinct cell states and ecosystems across human solid tumors. Luca BA, Steen CB, Matusiak M, Azizi A, Varma S, Zhu C, Przybyl J, Espín-Pérez A, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Cell. 2021 Sep 28:S0092-8674(21)01061-8. doi: 10.1016/j.cell.2021.09.014. Online ahead of print. PMID: 34597583
The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles AJ, Newman AM, Alizadeh AA. Cancer Cell. 2021 Sep 14:S1535-6108(21)00451-7. doi: 10.1016/j.ccell.2021.08.011. Online ahead of print. PMID: 34597589
HGAL inhibits lymphoma dissemination by interacting with multiple Cytoskeletal proteins. Jiang X, Lu X, Gentles AJ, Zhao D, Wander SA, Zhang Y, Natkunam Y, Slingerland J, Reis IM, Rabinovich B, Abdulreda MH, Moy VT, Lossos IS. Blood Adv. 2021 Sep 20:bloodadvances.2021004304. doi: 10.1182/bloodadvances.2021004304. Online ahead of print. PMID: 34543391
High-grade serous ovarian tumor cells modulate NK cell function to create an immune-tolerant microenvironment. Gonzalez VD, Huang YW, Delgado-Gonzalez A, Chen SY, Donoso K, Sachs K, Gentles AJ, Allard GM, Kolahi KS, Howitt BE, Porpiglia E, Fantl WJ. Cell Rep. 2021 Aug 31;36(9):109632. doi: 10.1016/j.celrep.2021.109632. PMID: 34469729
Landscape of innate lymphoid cells in human head and neck cancer reveals divergent NK cell states in the tumor microenvironment. Moreno-Nieves UY, Tay JK, Saumyaa S, Horowitz NB, Shin JH, Mohammad IA, Luca B, Mundy DC, Gulati GS, Bedi N, Chang S, Chen C, Kaplan MJ, Rosenthal EL, Holsinger FC, Divi V, Baik FM, Sirjani DB, Gentles AJ, Newman AM, Freud AG, Sunwoo JB. Proc Natl Acad Sci U S A. 2021 Jul 13;118(28):e2101169118. doi: 10.1073/pnas.2101169118. PMID: 34244432
Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling. Weber EW, Parker KR, Sotillo E, Lynn RC, Anbunathan H, Lattin J, Good Z, Belk JA, Daniel B, Klysz D, Malipatlolla M, Xu P, Bashti M, Heitzeneder S, Labanieh L, Vandris P, Majzner RG, Qi Y, Sandor K, Chen LC, Prabhu S, Gentles AJ, Wandless TJ, Satpathy AT, Chang HY, Mackall CL. Science. 2021 Apr 2;372(6537):eaba1786. doi: 10.1126/science.aba1786. PMID: 33795428
Prognostic Gene Expression, Stemness and Immune Microenvironment in Pediatric Tumors. Stahl D, Knoll R, Gentles AJ, Vokuhl C, Buness A, Gütgemann I. Cancers (Basel). 2021 Feb 18;13(4):854. doi: 10.3390/cancers13040854. PMID: 33670534
Conditional expression of HGAL leads to the development of diffuse large B-cell lymphoma in mice. Raboso-Gallego J, Casado-García A, Jiang X, Isidro-Hernández M, Gentles AJ, Zhao S, Natkunam Y, Blanco O, Domínguez V, Pintado B, Alonso-López D, De Las Rivas J, Vicente-Dueñas C, Lossos IS, Sanchez-Garcia I. Blood. 2021 Apr 1;137(13):1741-1753. doi: 10.1182/blood.2020004996. PMID: 33024996
Maternal Anti-Dengue IgG Fucosylation Predicts Susceptibility to Dengue Disease in Infants. Thulin NK, Brewer RC, Sherwood R, Bournazos S, Edwards KG, Ramadoss NS, Taubenberger JK, Memoli M, Gentles AJ, Jagannathan P, Zhang S, Libraty DH, Wang TT. Cell Rep. 2020 May 12;31(6):107642. doi: 10.1016/j.celrep.2020.107642. PMID: 32402275
A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. Gentles AJ, Hui AB, Feng W, Azizi A, Nair RV, Bouchard G, Knowles DA, Yu A, Jeong Y, Bejnood A, Forgó E, Varma S, Xu Y, Kuong A, Nair VS, West R, van de Rijn M, Hoang CD, Diehn M, Plevritis SK. Genome Biol. 2020 May 7;21(1):107. doi: 10.1186/s13059-020-02019-x. PMID: 32381040
CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. Han K, Pierce SE, Li A, Spees K, Anderson GR, Seoane JA, Lo YH, Dubreuil M, Olivas M, Kamber RA, Wainberg M, Kostyrko K, Kelly MR, Yousefi M, Simpkins SW, Yao D, Lee K, Kuo CJ, Jackson PK, Sweet-Cordero A, Kundaje A, Gentles AJ, Curtis C, Winslow MM, Bassik MC. Nature. 2020 Apr;580(7801):136-141. doi: 10.1038/s41586-020-2099-x. Epub 2020 Mar 11. PMID: 32238925
MYC and Twist1 cooperate to drive metastasis by eliciting crosstalk between cancer and innate immunity. Dhanasekaran R, Baylot V, Kim M, Kuruvilla S, Bellovin DI, Adeniji N, Rajan Kd A, Lai I, Gabay M, Tong L, Krishnan M, Park J, Hu T, Barbhuiya MA, Gentles AJ, Kannan K, Tran PT, Felsher DW. Elife. 2020 Jan 14;9:e50731. doi: 10.7554/eLife.50731. PMID: 31933479
2010-2020
Prognostic profiling of the immune cell microenvironment in Ewing´s Sarcoma Family of Tumors. Stahl D, Gentles AJ, Thiele R, Gütgemann I. Oncoimmunology. 2019 Oct 13;8(12):e1674113. doi: 10.1080/2162402X.2019.1674113. eCollection 2019. PMID: 31741777
Perfusion MRI-Based Fractional Tumor Burden Differentiates between Tumor and Treatment Effect in Recurrent Glioblastomas and Informs Clinical Decision-Making. Iv M, Liu X, Lavezo J, Gentles AJ, Ghanem R, Lummus S, Born DE, Soltys SG, Nagpal S, Thomas R, Recht L, Fischbein N. AJNR Am J Neuroradiol. 2019 Oct;40(10):1649-1657. doi: 10.3174/ajnr.A6211. Epub 2019 Sep 12. PMID: 31515215
LMO2 Confers Synthetic Lethality to PARP Inhibition in DLBCL. Parvin S, Ramirez-Labrada A, Aumann S, Lu X, Weich N, Santiago G, Cortizas EM, Sharabi E, Zhang Y, Sanchez-Garcia I, Gentles AJ, Roberts E, Bilbao-Cortes D, Vega F, Chapman JR, Verdun RE, Lossos IS. Cancer Cell. 2019 Sep 16;36(3):237-249.e6. doi: 10.1016/j.ccell.2019.07.007. Epub 2019 Aug 22. PMID: 31447348
Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma. Jain N, Hartert K, Tadros S, Fiskus W, Havranek O, Ma MCJ, Bouska A, Heavican T, Kumar D, Deng Q, Moore D, Pak C, Liu CL, Gentles AJ, Hartmann E, Kridel R, Smedby KE, Juliusson G, Rosenquist R, Gascoyne RD, Rosenwald A, Giancotti F, Neelapu SS, Westin J, Vose JM, Lunning MA, Greiner T, Rodig S, Iqbal J, Alizadeh AA, Davis RE, Bhalla K, Green MR. Sci Transl Med. 2019 Jun 19;11(497):eaav5599. doi: 10.1126/scitranslmed.aav5599. PMID: 31217338
Determining cell type abundance and expression from bulk tissues with digital cytometry. Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, Diehn M, Alizadeh AA. Nat Biotechnol. 2019 Jul;37(7):773-782. doi: 10.1038/s41587-019-0114-2. Epub 2019 May 6. PMID: 31061481
Data mining for mutation-specific targets in acute myeloid leukemia. Benard B, Gentles AJ, Köhnke T, Majeti R, Thomas D. Leukemia. 2019 Apr;33(4):826-843. doi: 10.1038/s41375-019-0387-y. Epub 2019 Feb 6. PMID: 30728456
Quantification of Macrophages in High-Grade Gliomas by Using Ferumoxytol-enhanced MRI: A Pilot Study. Iv M, Samghabadi P, Holdsworth S, Gentles A, Rezaii P, Harsh G, Li G, Thomas R, Moseley M, Daldrup-Link HE, Vogel H, Wintermark M, Cheshier S, Yeom KW. Radiology. 2019 Jan;290(1):198-206. doi: 10.1148/radiol.2018181204. Epub 2018 Nov 6. PMID: 30398435
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
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. PMID: 29628290
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. PMID: 29625051
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. PMID: 29545928
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. PMID: 29513759
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. PMID: 29331675
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. PMID: 29213088
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. PMID: 29100315
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
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. PMID: 28679399
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. PMID: 28314692
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. PMID: 28089908
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. PMID: 27663899
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. PMID: 27151888
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. PMID: 27145341
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. PMID: 26444494
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. PMID: 26387756
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):djv211. doi: 10.1093/jnci/djv211. Print 2015 Oct. PMID: 26286589
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. PMID: 26193342
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. PMID: 25921246
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. PMID: 25822800
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. PMID: 25775523
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. doi: 10.1080/01621459.2014.951443. PMID: 25729117
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. PMID: 25713363
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. PMID: 25583238 F
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. PMID: 25398938
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. PMID: 24799467
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. PMID: 24497069
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. PMID: 23580636
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. PMID: 23297126
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. PMID: 22753924
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. PMID: 22517897
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. PMID: 22451913
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. PMID: 22037208
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. PMID: 21969595
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. PMID: 21896642
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. PMID: 21670469
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. PMID: 21596809
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. PMID: 21533210
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. PMID: 21383193
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. PMID: 21178137
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. PMID: 21177505
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. PMID: 21108392
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. PMID: 20615981
Pre-2010
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. PMID: 20078227
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. PMID: 19965678
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. Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:6624-7. doi: 10.1109/IEMBS.2009.5332563. PMID: 19963681
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. PMID: 19636063
Molecular outcome prediction in diffuse large-B-cell lymphoma. Alizadeh AA, Gentles AJ, Lossos IS, Levy R. N Engl J Med. 2009 Jun 25;360(26):2794-5. doi: 10.1056/NEJMc0902616. PMID: 19553658
Further delineation of nonhomologous-based recombination and evidence for subtelomeric segmental duplications in 1p36 rearrangements. D’Angelo CS, Gajecka M, Kim CA, Gentles AJ, Glotzbach CD, Shaffer LG, Koiffmann CP. Hum Genet. 2009 Jun;125(5-6):551-63. doi: 10.1007/s00439-009-0650-9. Epub 2009 Mar 7. PMID: 19271239
Fast calculation of pairwise mutual information for gene regulatory network reconstruction. Qiu P, Gentles AJ, Plevritis SK. Comput Methods Programs Biomed. 2009 May;94(2):177-80. doi: 10.1016/j.cmpb.2008.11.003. Epub 2009 Jan 22. PMID: 19167129
Boolean implication networks derived from large scale, whole genome microarray datasets. Sahoo D, Dill DL, Gentles AJ, Tibshirani R, Plevritis SK. Genome Biol. 2008 Oct 30;9(10):R157. doi: 10.1186/gb-2008-9-10-r157. PMID: 18973690
Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13). Gajecka M, Gentles AJ, Tsai A, Chitayat D, Mackay KL, Glotzbach CD, Lieber MR, Shaffer LG. Genome Res. 2008 Nov;18(11):1733-42. doi: 10.1101/gr.077453.108. Epub 2008 Sep 2. PMID: 18765821
Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Shachaf CM, Gentles AJ, Elchuri S, Sahoo D, Soen Y, Sharpe O, Perez OD, Chang M, Mitchel D, Robinson WH, Dill D, Nolan GP, Plevritis SK, Felsher DW. Cancer Res. 2008 Jul 1;68(13):5132-42. doi: 10.1158/0008-5472.CAN-07-6192. PMID: 18593912
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC; Broad Institute Genome Sequencing Platform; Broad Institute Whole Genome Assembly Team, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Nature. 2007 May 10;447(7141):167-77. doi: 10.1038/nature05805. PMID: 17495919
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J. Genome Res. 2007 Jul;17(7):992-1004. doi: 10.1101/gr.6070707. Epub 2007 May 10. PMID: 17495012
SINEs, evolution and genome structure in the opossum. Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, Pollock DD. Gene. 2007 Jul 1;396(1):46-58. doi: 10.1016/j.gene.2007.02.028. Epub 2007 Mar 19. PMID: 17442506
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. Kohany O, Gentles AJ, Hankus L, Jurka J. BMC Bioinformatics. 2006 Oct 25;7:474. doi: 10.1186/1471-2105-7-474. PMID: 17064419
Retroposition of processed pseudogenes: the impact of RNA stability and translational control. Pavlicek A, Gentles AJ, Paces J, Paces V, Jurka J. Trends Genet. 2006 Feb;22(2):69-73. doi: 10.1016/j.tig.2005.11.005. Epub 2005 Dec 13. PMID: 16356584
Origin and diversification of minisatellites derived from human Alu sequences. Jurka J, Gentles AJ. Gene. 2006 Jan 3;365:21-6. doi: 10.1016/j.gene.2005.09.029. Epub 2005 Dec 15. PMID: 16343813 73
Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. Pavlicek A, House R, Gentles AJ, Jurka J, Morrow BE. Genome Res. 2005 Nov;15(11):1487-95. doi: 10.1101/gr.4281205. PMID: 16251458
Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons. Gentles AJ, Kohany O, Jurka J. Mol Biol Evol. 2005 Oct;22(10):1983-91. doi: 10.1093/molbev/msi188. Epub 2005 Jun 8. PMID: 15944437
Genome comparisons and analysis. Karlin S, Mrázek J, Gentles AJ. Curr Opin Struct Biol. 2003 Jun;13(3):344-52. doi: 10.1016/s0959-440x(03)00073-3. PMID: 12831886
Associations between human disease genes and overlapping gene groups and multiple amino acid runs. Karlin S, Chen C, Gentles AJ, Cleary M. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17008-13. doi: 10.1073/pnas.262658799. Epub 2002 Dec 9. PMID: 12473749
Genes, pseudogenes, and Alu sequence organization across human chromosomes 21 and 22. Chen C, Gentles AJ, Jurka J, Karlin S. Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2930-5. doi: 10.1073/pnas.052692099. Epub 2002 Feb 26. PMID: 11867739
Amino acid runs in eukaryotic proteomes and disease associations. Karlin S, Brocchieri L, Bergman A, Mrazek J, Gentles AJ. Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):333-8. doi: 10.1073/pnas.012608599. PMID: 11782551
Genomics. Annotation of the Drosophila genome. Karlin S, Bergman A, Gentles AJ. Nature. 2001 May 17;411(6835):259-60. doi: 10.1038/35077152. PMID: 11357119
Genome-scale compositional comparisons in eukaryotes. Gentles AJ, Karlin S. Genome Res. 2001 Apr;11(4):540-6. doi: 10.1101/gr.163101. PMID: 11282969
Why are human G-protein-coupled receptors predominantly intronless? Gentles AJ, Karlin S. Trends Genet. 1999 Feb;15(2):47-9. doi: 10.1016/s0168-9525(98)01648-5. PMID: 10098406
Ancient Quantum History
Chiral symmetry breaking in axial gauge QCD from the Dyson-Schwinger equations. Gentles AJ, Ross DA. 1996
The Quark propagator from the Dyson-Schwinger equations. 1. The chiral solution. Cudell JR, Gentles AJ, Ross DA 1995. Nucl.Phys.B 440 521-542. e-Print: hep-ph/9407220
Nonperturbative QCD on the continuum: Solving the Dyson-Schwinger equations. Gentles AJ 1994. NATO Advanced Study Institute: Fronties in Particle Physics 145-152.