Works by Freedman, Matthew L.

Results: 38

Plasma epigenomic profiling reveals treatment-emergent squamous transformation in prostate cancer.

Published in:

NPJ Precision Oncology, 2025, v. 9, n. 1, p. 1, doi. 10.1038/s41698-025-01031-3

By:

Semaan, Karl;
Nawfal, Rashad;
Canniff, John;
Savignano, Hunter;
Seo, Ji-Heui;
Siegmund, Stephanie E.;
Wu, Sarah J.;
Rotow, Julia K.;
Lee, Gwo-Shu Mary;
El Hajj Chehade, Razane;
Zhang, Ze;
Gulati, Gunsagar S.;
Phillips, Noa;
Lee, Garyoung Gary;
French, Christopher A.;
Hirsch, Michelle S.;
Jacene, Heather A.;
Choudhury, Atish D.;
Choueiri, Toni K.;
Freedman, Matthew L.

Publication type:

Article

Circulating KIM-1 is a minimally invasive biomarker correlated with treatment response to nivolumab in patients with metastatic renal cell carcinoma.

Published in:

Oncologist, 2023, v. 28, p. S2, doi. 10.1093/oncolo/oyad216.004

By:

Xu, Wenxin;
Vemula, Sai V;
Niman, Samuel M;
Liu, Xiaowen;
Takakura, Ayumi;
Huang, Zimo;
Choueiri, Toni K;
Freedman, Matthew L;
Catalano, Paul J;
Bonventre, Joseph V;
Gupta, Saurabh;
McDermott, David F;
Bhatt, Rupal S

Publication type:

Article

Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53758-5

By:

Altıntaş, Umut Berkay;
Seo, Ji-Heui;
Giambartolomei, Claudia;
Ozturan, Dogancan;
Fortunato, Brad J.;
Nelson, Geoffrey M.;
Goldman, Seth R.;
Adelman, Karen;
Hach, Faraz;
Freedman, Matthew L.;
Lack, Nathan A.

Publication type:

Article

Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases.

Published in:

Molecular Oncology, 2021, v. 15, n. 7, p. 1942, doi. 10.1002/1878-0261.12923

By:

Severson, Tesa M.;
Zhu, Yanyun;
De Marzo, Angelo M.;
Jones, Tracy;
Simons, Jonathan W.;
Nelson, William G.;
Yegnasubramanian, Srinivasan;
Freedman, Matthew L.;
Wessels, Lodewyk;
Bergman, Andries M.;
Haffner, Michael C.;
Zwart, Wilbert

Publication type:

Article

ASCL1 activates neuronal stem cell-like lineage programming through remodeling of the chromatin landscape in prostate cancer.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29963-5

By:

Nouruzi, Shaghayegh;
Ganguli, Dwaipayan;
Tabrizian, Nakisa;
Kobelev, Maxim;
Sivak, Olena;
Namekawa, Takeshi;
Thaper, Daksh;
Baca, Sylvan C.;
Freedman, Matthew L.;
Aguda, Adeleke;
Davies, Alastair;
Zoubeidi, Amina

Publication type:

Article

Androgen receptor and MYC equilibration centralizes on developmental super-enhancer.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27077-y

By:

Guo, Haiyang;
Wu, Yiming;
Nouri, Mannan;
Spisak, Sandor;
Russo, Joshua W.;
Sowalsky, Adam G.;
Pomerantz, Mark M.;
Wei, Zhao;
Korthauer, Keegan;
Seo, Ji-Heui;
Wang, Liyang;
Arai, Seiji;
Freedman, Matthew L.;
He, Housheng Hansen;
Chen, Shaoyong;
Balk, Steven P.

Publication type:

Article

Principles for the post-GWAS functional characterization of cancer risk loci.

Published in:

2011

By:

Freedman, Matthew L.;
Monteiro, Alvaro N. A.;
Gayther, Simon A.;
Coetzee, Gerhard A.;
Risch, Angela;
Plass, Christoph;
Casey, Graham;
De Biasi, Mariella;
Carlson, Chris;
Duggan, David;
James, Michael;
Liu, Pengyuan;
Tichelaar, Jay W.;
Vikis, Haris G.;
Ming You;
Mills, Ian G.

Publication type:

Opinion

Multiple regions within 8q24 independently affect risk for prostate cancer.

Published in:

Nature Genetics, 2007, v. 39, n. 5, p. 638, doi. 10.1038/ng2015

By:

Haiman, Christopher A.;
Patterson, Nick;
Freedman, Matthew L.;
Myers, Simon R.;
Pike, Malcolm C.;
Waliszewska, Alicja;
Neubauer, Julie;
Tandon, Arti;
Schirmer, Christine;
McDonald, Gavin J.;
Greenway, Steven C.;
Stram, Daniel O.;
Le Marchand, Loic;
Kolonel, Laurence N.;
Frasco, Melissa;
Wong, David;
Pooler, Loreall C.;
Ardlie, Kristin;
Oakley-Girvan, Ingrid;
Whittemore, Alice S.

Publication type:

Article

Transferability of tag SNPs in genetic association studies in multiple populations.

Published in:

Nature Genetics, 2006, v. 38, n. 11, p. 1298, doi. 10.1038/ng1899

By:

de Bakker, Paul I W.;
Burtt, Noël P.;
Graham, Robert R.;
Guiducci, Candace;
Yelensky, Roman;
Drake, Jared A.;
Bersaglieri, Todd;
Penney, Kathryn L.;
Butler, Johannah;
Young, Stanton;
Onofrio, Robert C.;
Lyon, Helen N.;
Stram, Daniel O.;
Haiman, Christopher A.;
Freedman, Matthew L.;
Xiaofeng Zhu;
Cooper, Richard;
Groop, Leif;
Kolonel, Laurence N.;
Henderson, Brian E.

Publication type:

Article

Demonstrating stratification in a European American population.

Published in:

Nature Genetics, 2005, v. 37, n. 8, p. 868, doi. 10.1038/ng1607

By:

Campbell, Catarina D.;
Ogburn, Elizabeth L.;
Lunetta, Kathryn L.;
Lyon, Helen N.;
Freedman, Matthew L.;
Groop, Leif C.;
Altshuler, David;
Ardlie, Kristin G.;
Hirschhorn, Joel N.

Publication type:

Article

Assessing the impact of population stratification on genetic association studies.

Published in:

Nature Genetics, 2004, v. 36, n. 4, p. 388, doi. 10.1038/ng1333

By:

Freedman, Matthew L.;
Reich, David;
Penney, Kathryn L.;
McDonald, Gavin J.;
Mignault, Andre A.;
Patterson, Nick;
Gabriel, Stacey B.;
Topol, Eric J.;
Smoller, Jordan W.;
Pato, Carlos N.;
Pato, Michele T.;
Petryshen, Tracey L.;
Kolonel, Laurence N.;
Lander, Eric S.;
Sklar, Pamela;
Henderson, Brian;
Hirschhorn, Joel N.;
Altshuler, David

Publication type:

Article

Genetic Variation in the HSD17B1 Gene and Risk of Prostate Cancer.

Published in:

PLoS Genetics, 2005, v. 1, n. 5, p. 603, doi. 10.1371/journal.pgen.0010068.eor

By:

Kraft, Peter;
Pharoah, Paul;
Chanock, Stephen J.;
Albanes, Demetrius;
Kolonel, Laurence N.;
Hayes, Richard B.;
Altshuler, David;
Andriole, Gerald;
Berg, Christine;
Boeing, Heiner;
Burtt, Noel P.;
Bueno-de-Mesquita, Bas;
Calle, Eugenia E.;
Cann, Howard;
Canzian, Federico;
Chen, Yen-Ching;
Crawford, David E.;
Dunning, Alison M.;
Feigelson, Heather S.;
Freedman, Matthew L.

Publication type:

Article

The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis.

Published in:

Nature Genetics, 2015, v. 47, n. 11, p. 1346, doi. 10.1038/ng.3419

By:

Li, Fugen;
Takeda, David Y;
Cejas, Paloma;
Shivdasani, Ramesh A;
Hahn, William C;
Brown, Myles;
Loda, Massimo;
Long, Henry W;
Freedman, Matthew L;
Pomerantz, Mark M;
Lenci, Romina;
Chonkar, Apurva;
Chabot, Matthew;
Cook, Jennifer;
Kantoff, Philip W;
Vazquez, Francisca;
Bowden, Michaela;
Lis, Rosina

Publication type:

Article

Comprehensive association testing of common genetic variation in DNA repair pathway genes in relationship with breast cancer risk in multiple populations.

Published in:

Human Molecular Genetics, 2008, v. 17, n. 6, p. 825, doi. 10.1093/hmg/ddm354

By:

Haiman, Christopher A.;
Hsu, Chris;
de Bakker, Paul I.W.;
Frasco, Melissa;
Sheng, Xin;
Van Den Berg, David;
Casagrande, John T.;
Kolonel, Laurence N.;
Le Marchand, Loic;
Hankinson, Susan E.;
Han, Jiali;
Dunning, Alison M.;
Pooley, Karen A.;
Freedman, Matthew L.;
Hunter, David J.;
Wu, Anna H.;
Stram, Daniel O.;
Henderson, Brian E.

Publication type:

Article

Common variation in BRCA2 and breast cancer risk: a haplotype-based analysis in the Multiethnic Cohort.

Published in:

Human Molecular Genetics, 2004, v. 13, n. 20, p. 2431, doi. 10.1093/hmg/ddh270

By:

Freedman, Matthew L.;
Penney, Kathryn L.;
Stram, Daniel O.;
Le Marchand, Loïc;
Hirschhorn, Joel N.;
Kolonel, Laurence N.;
Altshuler, David;
Henderson, Brian E.;
Haiman, Christopher A.

Publication type:

Article

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-35135-2

By:

Kneppers, Jeroen;
Severson, Tesa M.;
Siefert, Joseph C.;
Schol, Pieter;
Joosten, Stacey E. P.;
Yu, Ivan Pak Lok;
Huang, Chia-Chi Flora;
Morova, Tunç;
Altıntaş, Umut Berkay;
Giambartolomei, Claudia;
Seo, Ji-Heui;
Baca, Sylvan C.;
Carneiro, Isa;
Emberly, Eldon;
Pasaniuc, Bogdan;
Jerónimo, Carmen;
Henrique, Rui;
Freedman, Matthew L.;
Wessels, Lodewyk F. A.;
Lack, Nathan A.

Publication type:

Article

Clinical Uncertainty of Prostate Cancer Genetic Risk Panels.

Published in:

Science Translational Medicine, 2013, v. 5, n. 182, p. 1, doi. 10.1126/scitranslmed.3004696

By:

Pomerantz, Mark;
Freedman, Matthew L.

Publication type:

Article

Genetic Determinants of Circulating Insulin-Like Growth Factor (IGF)-I, IGF Binding Protein (BP)-1, and IGFBP-3 Levels in a Multiethnic Population.

Published in:

Journal of Clinical Endocrinology & Metabolism, 2007, v. 92, n. 9, p. 3660, doi. 10.1210/jc.2007-0790

By:

Cheng, Iona;
Henderson, Katherine DeLellis;
Haiman, Christopher A.;
Kolonel, Laurence N.;
Henderson, Brian E.;
Freedman, Matthew L.;
Marchand, Loïc Le

Publication type:

Article

Common Genetic Variation in the Sex Steroid Hormone-Binding Globulin (SHBG) Gene and Circulating SHBG Levels among Postmenopausal Women: The Multiethnic Cohort.

Published in:

Journal of Clinical Endocrinology & Metabolism, 2005, v. 90, n. 4, p. 2198, doi. 10.1210/jc.2004-1417

By:

Haiman, Christopher A.;
Riley, Stephanie E.;
Freedman, Matthew L.;
Setiawan, Veronica W.;
Conti, David V.;
Marchand, Loïc Le

Publication type:

Article

Power to detect selective allelic amplification in genome-wide scans of tumor data.

Published in:

Bioinformatics, 2010, v. 26, n. 4, p. 518, doi. 10.1093/bioinformatics/btp694

By:

Dewal, Ninad;
Freedman, Matthew L.;
LaFramboise, Thomas;
Pe'er, Itsik

Publication type:

Article

GENETIC DETERMINANTS OF PROSTATE CANCER RISK.

Published in:

BJU International, 2007, v. 100, n. 2, p. 241, doi. 10.1111/j.1464-410X.2007.06996.x

By:

Pomerantz, Mark M.;
Freedman, Matthew L.;
Kantoff, Philip W.

Publication type:

Article

A systematic approach to understand the functional consequences of non-protein coding risk regions.

Published in:

Cell Cycle, 2010, v. 9, n. 2, p. 256, doi. 10.4161/cc.9.2.10419

By:

Coetzee, Gerhard A.;
Li Jia;
Frenkel, Baruch;
Henderson, Brian E.;
Tanay, Amos;
Haiman, Christopher A.;
Freedman, Matthew L.

Publication type:

Article

Decomposing the Sources of Earnings Inequality: Assessing the Role of Reallocation.

Published in:

Industrial Relations, 2012, v. 51, n. 4, p. 779, doi. 10.1111/j.1468-232X.2012.00697.x

By:

Andersson, Fredrik;
Davis, Elizabeth E.;
Freedman, Matthew L.;
Lane, Julia I.;
Mccall, Brian P.;
Sandusky, Kristin

Publication type:

Article

Genetic and functional analysis of CHEK2 ( CHK2) variants in multiethnic cohorts.

Published in:

International Journal of Cancer, 2007, v. 121, n. 12, p. 2661, doi. 10.1002/ijc.23026

By:

Bell, Daphne W.;
Kim, Sang H.;
Godwin, Andrew K.;
Schiripo, Taryn A.;
Harris, Patricia L.;
Haserlat, Sara M.;
Wahrer, Doke C.R.;
Haiman, Christopher A.;
Daly, Mary B.;
Niendorf, Kristin B.;
Smith, Matthew R.;
Sgroi, Dennis C.;
Garber, Judy E.;
Olopade, Olufunmilayo I.;
Marchand, Loic Le;
Henderson, Brian E.;
Altshuler, David;
Haber, Daniel A.;
Freedman, Matthew L.

Publication type:

Article

Androgen receptor reprogramming demarcates prognostic, context-dependent gene sets in primary and metastatic prostate cancer.

Published in:

Clinical Epigenetics, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13148-022-01278-8

By:

Severson, Tesa;
Qiu, Xintao;
Alshalalfa, Mohammed;
Sjöström, Martin;
Quigley, David;
Bergman, Andries;
Long, Henry;
Feng, Felix;
Freedman, Matthew L.;
Zwart, Wilbert;
Pomerantz, Mark M.

Publication type:

Article

The association between germline BRCA2 variants and sensitivity to platinum-based chemotherapy among men with metastatic prostate cancer.

Published in:

Cancer (0008543X), 2017, v. 123, n. 18, p. 3532, doi. 10.1002/cncr.30808

By:

Pomerantz, Mark M.;
Spisák, Sandor;
Jia, Li;
Cronin, Angel M.;
Csabai, Istvan;
Ledet, Elisa;
Sartor, A. Oliver;
Rainville, Irene;
O'Connor, Edward P.;
Herbert, Zachary T.;
Szállási, Zoltan;
Oh, William K.;
Kantoff, Philip W.;
Garber, Judy E.;
Schrag, Deborah;
Kibel, Adam S.;
Freedman, Matthew L.

Publication type:

Article

Optimized high-throughput screening of non-coding variants identified from genome-wide association studies.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 3, p. e18, doi. 10.1093/nar/gkac1198

By:

Morova, Tunc;
Ding, Yi;
Huang, Chia-Chi F;
Sar, Funda;
Schwarz, Tommer;
Giambartolomei, Claudia;
Baca, Sylvan C;
Grishin, Dennis;
Hach, Faraz;
Gusev, Alexander;
Freedman, Matthew L;
Pasaniuc, Bogdan;
Lack, Nathan A

Publication type:

Article

CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.

Published in:

Nature Medicine, 2015, v. 21, n. 11, p. 1357, doi. 10.1038/nm.3975

By:

Spisák, Sándor;
Lawrenson, Kate;
Fu, Yanfang;
Csabai, István;
Cottman, Rebecca T;
Seo, Ji-Heui;
Haiman, Christopher;
Han, Ying;
Lenci, Romina;
Li, Qiyuan;
Tisza, Viktória;
Szállási, Zoltán;
Herbert, Zachery T;
Chabot, Matthew;
Pomerantz, Mark;
Solymosi, Norbert;
Gayther, Simon A;
Joung, J Keith;
Freedman, Matthew L

Publication type:

Article

CREB5 reprograms FOXA1 nuclear interactions to promote resistance to androgen receptor-targeting therapies.

Published in:

eLife, 2022, p. 1, doi. 10.7554/eLife.73223

By:

Hwang, Justin H.;
Arafeh, Rand;
Ji-Heui Seo;
Baca, Sylvan C.;
Ludwig, Megan;
Arnoff, Taylor E.;
Sawyer, Lydia;
Richter, Camden;
Tape, Sydney;
Bergom, Hannah E.;
McSweeney, Sean;
Rennhack, Jonathan P.;
Klingenberg, Sarah A.;
Cheung, Alexander T. M.;
Kwon, Jason;
So, Jonathan;
Kregel, Steven;
Van Allen, Eliezer M.;
Drake, Justin M.;
Freedman, Matthew L.

Publication type:

Article

Agglomeration, product heterogeneity and firm entry.

Published in:

Journal of Economic Geography, 2012, v. 12, n. 3, p. 601, doi. 10.1093/jeg/lbr022

By:

Freedman, Matthew L.;
Kosová, Renáta

Publication type:

Article

A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17325-y

By:

Walavalkar, Kaivalya;
Saravanan, Bharath;
Singh, Anurag Kumar;
Jayani, Ranveer Singh;
Nair, Ashwin;
Farooq, Umer;
Islam, Zubairul;
Soota, Deepanshu;
Mann, Rajat;
Shivaprasad, Padubidri V.;
Freedman, Matthew L.;
Sabarinathan, Radhakrishnan;
Haiman, Christopher A.;
Notani, Dimple

Publication type:

Article

Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15951-0

By:

Corona, Rosario I.;
Seo, Ji-Heui;
Lin, Xianzhi;
Hazelett, Dennis J.;
Reddy, Jessica;
Fonseca, Marcos A. S.;
Abassi, Forough;
Lin, Yvonne G.;
Mhawech-Fauceglia, Paulette Y.;
Shah, Sohrab P.;
Huntsman, David G.;
Gusev, Alexander;
Karlan, Beth Y.;
Berman, Benjamin P.;
Freedman, Matthew L.;
Gayther, Simon A.;
Lawrenson, Kate

Publication type:

Article

Aspirin Use, 8q24 Single Nucleotide Polymorphism rs6983267, and Colorectal Cancer According to CTNNB1 Alterations.

Published in:

JNCI: Journal of the National Cancer Institute, 2013, v. 105, n. 24, p. 1852, doi. 10.1093/jnci/djt331

By:

Nan, Hongmei;
Morikawa, Teppei;
Suuriniemi, Miia;
Imamura, Yu;
Werner, Lillian;
Kuchiba, Aya;
Yamauchi, Mai;
Hunter, David J.;
Kraft, Peter;
Giovannucci, Edward L.;
Fuchs, Charles S.;
Ogino, Shuji;
Freedman, Matthew L.;
Chan, Andrew T.

Publication type:

Article

Replication of Prostate Cancer Risk Loci in a Japanese Case–Control Association Study.

Published in:

JNCI: Journal of the National Cancer Institute, 2009, v. 101, n. 19, p. 1330, doi. 10.1093/jnci/djp287

By:

Yamada, Hiroki;
Penney, Kathryn L.;
Takahashi, Hiroyuki;
Katoh, Takahiko;
Yamano, Yuko;
Yamakado, Minoru;
Kimura, Takahiro;
Kuruma, Hidetoshi;
Kamata, Yuko;
Egawa, Shin;
Freedman, Matthew L.

Publication type:

Article

Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer.

Published in:

eLife, 2017, p. 1, doi. 10.7554/eLife.27861

By:

Shah, Neel;
Ping Wang;
Wongvipat, John;
Karthaus, Wouter R.;
Abida, Wassim;
Armenia, Joshua;
Rockowitz, Shira;
Drier, Yotam;
Bernstein, Bradley E.;
Long, Henry W.;
Freedman, Matthew L.;
Arora, Vivek K.;
Deyou Zheng;
Sawyers, Charles L.

Publication type:

Article

Common Genetic Variation in IGF1 and Prostate Cancer Risk in the Multiethnic Cohort.

Published in:

JNCI: Journal of the National Cancer Institute, 2006, v. 98, n. 2, p. 123, doi. 10.1093/jnci/djj013

By:

Cheng, Iona;
Stram, Daniel 0.;
Penney, Kathryn L.;
Pike, Malcolm;
Marchand, Loïc Le;
Kolonel, Laurence N.;
Hirschhorn, Joel;
Altshuler, David;
Henderson, Brian E.;
Freedman, Matthew L.

Publication type:

Article

Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.

Published in:

Human Molecular Genetics, 2014, v. 23, n. 19, p. 5294, doi. 10.1093/hmg/ddu228

By:

Li, Qiyuan;
Stram, Alexander;
Chen, Constance;
Kar, Siddhartha;
Gayther, Simon;
Pharoah, Paul;
Haiman, Christopher;
Stranger, Barbara;
Kraft, Peter;
Freedman, Matthew L.

Publication type:

Article

A comprehensive analysis of common IGF1, IGFBP1 and IGFBP3 genetic variation with prospective IGF-I and IGFBP-3 blood levels and prostate cancer risk among Caucasians†.

Published in:

Human Molecular Genetics, 2010, v. 19, n. 15, p. 3089, doi. 10.1093/hmg/ddq210

By:

Schumacher, Fredrick R.;
Cheng, Iona;
Freedman, Matthew L.;
Mucci, Lorelei;
Allen, Naomi E.;
Pollak, Michael N.;
Hayes, Richard B.;
Stram, Daniel O.;
Canzian, Federico;
Henderson, Brian E.;
Hunter, David J.;
Virtamo, Jarmo;
Manjer, Jonas;
Gaziano, J. Michael;
Kolonel, Laurence N.;
Tjønneland, Anne;
Albanes, Demetrius;
Calle, Eugenia E.;
Giovannucci, Edward;
Crawford, E. David

Publication type:

Article