A complete list of publications by Dr. Bratman can be reviewed on Google Scholar and Pubmed.

Publication Highlights:

Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. Sci Adv. 2022 Jan 28. doi: 10.1126/sciadv.abi8618. Link

Leung E, Han K, Zou J, Zhen Z, Zheng Y, Wang TT, Rostami A, Siu LL, Pugh TJ, Bratman SV. HPV sequencing facilitates ultrasensitive detection of HPV circulating tumor DNA. Clin Cancer Res. 2021 Sep 27. doi: 10.1158/1078-0432.CCR-19-2384. Link

Burgener JM, Zou J, Zhen Z, Zheng Y, Shen SY, Huang SH, Keshavarzi S, Xu W, Liu FF, Liu G, Waldron J, Weinreb I, Spreafico A, Siu LL, de Almeida JR, Goldstein DP, Hoffman MM, De Carvalho DD, Bratman SV. Tumor-naïve multimodal profiling of circulating tumor DNA in head and neck squamous cell carcinoma. Clin Cancer Res. 2021 Jun 24. doi: 10.1158/1078-0432.CCR-21-0110. Link

Abelson S, Zeng A, Ng S, Wang TT, Minden M, Pugh TJ, Shlush LI, Murphy T, Chan S, Dick JE, Bratman SV. Integration of intra-sample contextual error signatures for improved detection of somatic mutations from deep sequencing. Sci Adv. 2020 Dec 9;6(50):eabe3722. doi: 10.1126/sciadv.abe3722. Link

Rostami A, Yu C, Bratman SV. Serial Cell-free DNA Assessments in Preclinical Models. STAR Protocols. 2020 Dec 18;1:100145. doi: 10.1016/ j.xpro.2020.100145. Link

Malkin EZ, Bratman SV. Bioactive DNA from extracellular vesicles and particles. Cell Death Dis. 2020 Jul 27;11(7):584. doi: 10.1038/s41419-020-02803-4. Link

Bratman SV, Yang SYC, Iafolla MAJ, Liu Z, Hansen AR, Bedard PL, Lheureux S, Spreafico A, Razak AA, Shchegrova S, Louie M, Billings P, Zimmermann B, Sethi H, Aleshin A, Torti D, Marsh K, Eagles J, Cirlan I, Hanna Y, Clothier DL, Lien SC, Ohashi PS, Xu W, Siu LL, Pugh TJ. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nature Cancer. 2020 Aug 3. doi: 10.1038/s43018-020-0096-5. Link

Rostami A, Lambie M, Yu C, Stambolic V, Waldron JN, Bratman SV. Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics. Cell Reports. 2020 Jun 30;31(13):107830. doi: 10.1016/j.celrep.2020.107830. Link

De Michino S, Aparnathi M, Rostami A, Lok BH, Bratman SV. The utility of liquid biopsies in radiation oncology. Int J Radiat Oncol Biol Phys. 2020 May 14. pii: S0360-3016(20)31132-9. doi: 10.1016/j.ijrobp.2020.05.008. Link

Cescon DW, Bratman SV, Chan SM, Siu LL. Circulating tumor DNA and liquid biopsy in oncology. Nature Cancer. 2020;1(3):276-90. doi: 10.1038/s43018-020-0043-5. Link

*Manem VSK, *Lambie M, Smirnov P, Kofia V, Freeman M, Koritzinsky M, Abazeed ME, Haibe-Kains B, Bratman SV. Modeling cellular response in large-scale radiogenomic databases to advance precision radiotherapy. Cancer Res. 2019 Sep 26. pii: canres.0179.2019. doi: 10.1158/0008-5472.CAN-19-0179. Link

Wang TT, Abelson S, Zou J, Li T, Zhao Z, Dick JE, Shlush LI, Pugh TJ, Bratman SV. High efficiency error suppression for accurate detection of low-frequency variants. Nucleic Acids Res. 2019 Sep 5;47(15):e87. doi: 10.1093/nar/gkz474. Link

*Shen SY, *Burgener JM, Bratman SV, De Carvalho DD. Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA. Nat Protoc. 2019 Aug 30. doi: 10.1038/s41596-019-0202-2. Link

Lee S, Cabanero M, Hyrcza M, Butler MO, Liu FF, Hansen A, Huang SH, Tsao M, Song Y, Lu L, Xu W, Chepeha D, Goldstein D, Weinreb I, Bratman SV. Computer-Assisted Image Analysis of the Tumor Microenvironment on an Oral Tongue Squamous Cell Carcinoma Tissue Microarray. Clin Transl Radiat Oncol. 2019 Jul;17:32-39. Link

Murphy T, Zou J, Daher-Reyes GS, Arruda A, Gupta V, McNamara CJ, Minden MD, Schimmer AD, Sibai H, Yee KWL, Korulla M, Stockley T, Kamel-Reid S, Maze D, Tierens A, Bratman SV, Schuh AC, Chan SM. Impact of preleukemic mutations and their persistence on hematologic recovery after induction chemotherapy for AML. Blood Adv. 2019 Aug 13;3(15):2307-2311. doi: 10.1182/bloodadvances.2019000306. Link

Araujo DV, Bratman SV, Siu LL. Designing circulating tumor DNA-based interventional clinical trials in oncology. Genome Med. 2019 Apr 19;11(1):22. doi: 10.1186/s13073-019-0634-x. Link

Zhao X, Ghoraie LS, Psarianos P, Yip K, Goldstein D, Gilbert R, Witterick I, Pang H, Hussain A, Lee JH, Williams J, Bratman SV, Ailles L, Haibe-Kains B, Liu FF. Metabolic regulation of dermal fibroblasts contributes to skin extracellular matrix homeostasis and fibrosis. Nat Metab. 2019 Jan 7;1:147-157. Link

Inoue M, Nakashima R, Enomoto M, Koike Y, Zhao X, Yip K, Huang SH, Waldron JN, Ikura M, Liu FF, Bratman SV. Plasma redox imbalance caused by albumin oxidation promotes lung-predominant NETosis and pulmonary cancer metastasis. Nat Commun. 2018 Nov 30;9(1):5116. doi: 10.1038/s41467-018-07550-x. Link

*Shen SY, *Singhania R, *Fehringer G, *Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018 Nov;563(7732):579-583. doi: 10.1038/s41586-018-0703-0. Epub 2018 Nov 14. Link

Kwan J, Su J, Huang SH, Ghoraie LS, Xu W, Chan B , Yip KW, Giuliani M, Bayley A, Kim J, Hope AJ, Ringash J, Cho J, McNiven A, Hansen A, Goldstein D, de Almeida J, Aerts HJ, Waldron JN, Haibe-Kains B, O'Sullivan B, Bratman SV, Liu FF. Radiomic Biomarkers to Refine Risk Models for Distant Metastasis in HPV-related Oropharyngeal Carcinoma. Int J Radiat Oncol Biol Phys. 2018 Nov 15;102(4):1107-1116. doi: 10.1016/j.ijrobp.2018.01.057. Epub 2018 Feb 1. Link

Karamboulas C, Bruce JP, Hope AJ, Meens J, Huang SH, Erdmann N, Pereira K, Goldstein DP, Weinreb I, Su J, O’Sullivan B, Tiedemann R, Liu FF, Pugh TJ, Bratman SV, Xu W, Ailles L. Patient-Derived Xenografts for Prognostication and Personalized Treatment for Head and Neck Squamous Cell Carcinoma. Cell Rep. 2018 Oct 30;25(5):1318-1331.e4. doi: 10.1016/j.celrep.2018.10.004. Link

*Han K,  *Leung E,  Barbera L,  Barnes E,  Croke J,  Di Grappa MA,  Fyles A,  Metser U,  Milosevic M,  Pintilie M,  Wolfson R,  Zhao Z, Bratman SV. Circulating Human Papillomavirus DNA as a Biomarker of Response in Patients With Locally Advanced Cervical Cancer Treated With Definitive Chemoradiation. JCO Precis Oncol. 2018 Sep;2:1-8. Link

Abelson S, Collord G, Ng SWK, Weissbrod O, Mendelson Cohen N, Niemeyer E, Barda N, Zuzarte PC, Heisler L, Sundaravadanam Y, Luben R, Hayat S, Wang TT, Zhao Z, Cirlan I, Pugh TJ, Soave D, Ng K, Latimer C, Hardy C, Raine K, Jones D, Hoult D, Britten A, McPherson JD, Johansson M, Mbabaali F, Eagles J, Miller JK, Pasternack D, Timms L, Krzyzanowski P, Awadalla P, Costa R, Segal E, Bratman SV, Beer P, Behjati S, Martincorena I, Wang JCY, Bowles KM, Quirós JR, Karakatsani A, La Vecchia C, Trichopoulou A, Salamanca-Fernández E, Huerta JM, Barricarte A, Travis RC, Tumino R, Masala G, Boeing H, Panico S, Kaaks R, Krämer A, Sieri S, Riboli E, Vineis P, Foll M, McKay J, Polidoro S, Sala N, Khaw KT, Vermeulen R, Campbell PJ, Papaemmanuil E, Minden MD, Tanay A, Balicer RD, Wareham NJ, Gerstung M, Dick JE, Brennan P, Vassiliou GS, Shlush LI. Prediction of acute myeloid leukaemia risk in healthy individuals. Nature. 2018 Jul;559(7714):400-404. doi: 10.1038/s41586-018-0317-6. Epub 2018 Jul 9. Link

Horowitz G, Hosni A, Yu E, Xu W, Lu L, Au M, Dixon P, Brown D, Chepeha DB, Gilbert RW, Goldstein DP, Gullane PJ, Irish JC, Bayley A, Cho J, Giuliani M, Huang SH, Hope A, Kim J, O’Sullivan B, Ringash J, Waldron J, Weinreb I, Ordonez BP, Bratman SV, de Almeida JR. Prevalence, Prognosis, and Treatment Implications of Retropharyngeal Nodes in Unknown Primary Head and Neck Carcinoma. Oral Oncol. 2018 Jul;82:162-167. Link

Bristow RG, Alexander B, Baumann M, Bratman SV, Brown JM, Camphausen K, Choyke P, Citrin D, Contessa JN, Dicker A, Kirsch DG, Krause M, Le QT, Milosevic M, Morris ZS, Sarkaria JN, Sondel PM, Tran PT, Wilson GD, Willers H, Wong RKS, Harari PM. Combining precision radiotherapy with molecular targeting and immunomodulatory agents: a guideline by the American Society for Radiation Oncology. Lancet Oncol. 2018 May;19(5):e240-e251. Link

Burgener JM, Rostami A, De Carvalho DD, Bratman SV. Cell-Free DNA as a Post-Treatment Surveillance Strategy: Current Status. Semin Oncol. 2017 Oct;44(5):330-346. doi: 10.1053/j.seminoncol.2018.01.009. Link

Juergens RA, Bratman SV, Tsao MS, Laurie SA, Kuruvilla MS, Razak A, Hansen AR. Biology and Patterns of Response to EGFR-Inhibition in Squamous Cell Cancers of the Lung and Head & Neck. Cancer Treatment Reviews. 2017. Link

Muhanna N, Di Grappa MA, Chan HHL, Khan T, Jin CS, Zheng Y, Irish JC, Bratman SV. Cell-Free DNA Kinetics in a Pre-Clinical Model of Head and Neck Cancer. Sci Rep. 2017 Dec 1;7(1):16723. doi: 10.1038/s41598-017-17079-6. Link

Kis O, Kaedbey R, Chow S, Danesh A, Dowar M, Li T, Li Z, Liu J, Mansour M, Masih-Khan E, Zhang T, Bratman SV, Oza AM, Kamel-Reid S, Trudel S, Pugh TJ. Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates. Nat Commun. 2017 May 11;8:15086. doi: 10.1038/ncomms15086. Link

Kim KY, Le QT, Yom SS, Bratman SV, El Mubarak HS, Kim RHW, Sander ME, Conley BA. Current State of PCR-Based Epstein-Barr Virus DNA Testing for Nasopharyngeal Cancer. J Natl Cancer Inst. 2017 Apr 1;109(4). doi: 10.1093/jnci/djx007. Link

Rostami A, and Bratman SV. Utilizing circulating tumour DNA in radiation oncology. Radiother Oncol. 2017 Sep;124(3):357-364. doi: 10.1016/j.radonc.2017.07.004. Epub 2017 Jul 20. Link

Hosni A, Dixon PR, Rishi A, Au M, Xu W, Song Y, Chepeha DB, Goldstein DP, Huang SH, Kim J, O'Sullivan B, Waldron J, Bratman SV, de Almeida JR. Radiotherapy Characteristics and Outcomes for Head and Neck Carcinoma of Unknown Primary vs T1 Base-of-Tongue Carcinoma. JAMA Otolaryngol Head Neck Surg. 2016 Dec 1;142(12):1208-1215. doi: 10.1001/jamaoto.2016.3083. Link

Lowes LE, Bratman SV, Dittamore R, Done S, Kelley SO, Mai S, Morin RD, Wyatt AW, Allan AL. Circulating Tumor Cells (CTC) and Cell-Free DNA (cfDNA) Workshop 2016: Scientific opportunities and logistics for cancer clinical trial incorporation. Int J Mol Sci. 2016 Sep 8;17(9). pii: E1505. doi: 10.3390/ijms17091505. Link

*Bratman SV, *Bruce JP, O’Sullivan B, Pugh TJ, Xu W, Yip KW, Liu FF. Human Papillomavirus Genotype Association With Survival in Head and Neck Squamous Cell Carcinoma. JAMA Oncol. 2016 Jun 1;2(6):823-6. Link

Newman AM, Lovejoy AF, Klass DM, Kurtz DM, Chabon JJ, Scherer F, Stehr H, Liu CL, Bratman SV, Say C, Zhou L, Carter JN, West RB, Sledge GW Jr, Shrager JB, Loo BW Jr, Neal JW, Wakelee HA, Diehn M, Alizadeh AA. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016 May 1;34(5):547-55. Link

Bruce JP, Yip K, Bratman SV, Ito E, and Liu FF. Nasopharyngeal cancer: molecular landscape. J Clin Oncol. 2015 Oct 10;33(29):3346-55. Link

Kurtz DM, Green MR, Bratman SV, Scherer F, Liu CL, Kunder CA, Takahashi K, Glover C, Keane C, Kihira S, Visser B, Callahan J, Kong KA, Faham M, Corbelli KS, Miklos D, Advani RH, Levy R, Hicks RJ, Hertzberg M, Ohgami RS, Gandhi MK, Diehn M, Alizadeh AA. Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing. Blood. 2015 Jun 11;125(24):3679-87. doi: 10.1182/blood-2015-03-635169. Epub 2015 Apr 17. Link

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. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat Med. 2015 Aug;21(8):938-945. doi: 10.1038/nm.3909. Epub 2015 Jul 20. Link

Bratman SV, Newman AM, Alizadeh AA, Diehn M. Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq. Expert Rev Mol Diagn. 2015 Jun 1;15(6):715-9. Link

*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.  Integrating tumor and stromal gene expression signatures with clinical indices for survival stratification of early-stage non-small cell lung cancer. J Natl Cancer Inst. 2015 Aug 18;107(10). pii: djv211. doi: 10.1093/jnci/djv211. Print 2015 Oct. Link

Newman AM, Bratman SV, Stehr H, Lee LJ, Liu CL, Diehn M, Alizadeh AA. FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution. Bioinformatics. 2014 Dec;30(23):3390-3. Link

*Newman AM, *Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, Shrager JB, Loo BW Jr, Alizadeh AA, Diehn M. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014 May;20(5):548-54. Link