1. Szymanski JJ, Sundby RT, Jones PA, Srihari D, Earland N, Harris PK, Feng W, Qaium F, Lei H, Roberts D, Landeau M, Bell J, Huang Y, Hoffman L, Spencer M, Spraker MB, Ding L, Widemann BC, Shern JF, Hirbe AC, Chaudhuri AA*. Cell-free DNA ultra-low-pass whole genome sequencing distinguishes malignant peripheral nerve sheath tumor (MPNST) from its benign precursor lesion. medRxiv. 2021 April. *Senior Corresponding Author
  2. Pellini B, Pejovic N, Feng W, Earland N, Harris PK, Usmani A, Szymanski JJ, Qaium F, Mudd J, Petty M, Jiang Y, Singh A, Maher CA, Henke LE, Park H, Ciorba MA, Kim H, Mutch MG, Pedersen KS, Tan BR, Hawkins WG, Fields RC, Chaudhuri AA*. ctDNA MRD Detection and Personalized Oncogenomic Analysis in Oligometastatic Colorectal Cancer From Plasma and Urine. JCO precision oncology. 2021 February; 5:378-388. *Senior Corresponding Author
  3. Otegbeye EE, Mitchem JB, Park H, Chaudhuri AA, Kim H, Mutch MG, Ciorba MA. Immunity, immunotherapy, and rectal cancer: a clinical and translational science review. Translational Research. 2020 Dec 8. PMID: 33307273
  4. Nabet BY, Esfahani MS, Moding EJ, Hamilton EG, Chabon JJ, Rizvi H, Steen CB, Chaudhuri AA, Liu CL, Hui AB, Almanza D, Stehr H, Gojenola L, Bonilla RF, Jin MC, Jeon YJ, Tseng D, Liu C, Merghoub T, Neal JW, Wakelee HA, Padda SK, Ramchandran KJ, Das M, Plodkowski AJ, Yoo C, Chen EL, Ko RB, Newman AM, Hellmann MD, Alizadeh AA, Diehn M. Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition. Cell. 2020 Oct;183(2):363-376. PMID: 33307267.
  5. Chaudhuri AA*, Pellini B, Pejovic N, Chauhan PS, Harris PK, Szymanski JJ, Smith ZL, Arora VK. Emerging Roles of Urine-Based Tumor DNA Analysis in Bladder Cancer Management. JCO Precision Oncology. 2020 July; 4:806-817. PMID: 32923907. *Co-Senior Author
  6. Dang HX, Chauhan PS, Ellis H, Feng W, Harris PK, Smith G, Qiao M, Dienstbach K, Beck R, Atkocius A, Qaium F, Luo J, Michalski JM, Picus J, Pachynski RK, Maher CA, Chaudhuri AA*. Cell-Free DNA Alterations in the AR Enhancer and Locus Predict Resistance to AR-Directed Therapy in Patients With Metastatic Prostate Cancer. JCO Precision Oncology. 2020 June; 4:680-713. PMID: 32903952. *Senior Corresponding Author
  7. Pellini P, Szymanski J, Chin R, Jones PA, Chaudhuri AA*. Liquid Biopsies Using Circulating Tumor DNA in Non-Small Cell Lung Cancer. Thoracic Surgery Clinics. 2020 May; 30(2):165-177. PMID: 32327175. *Senior Corresponding Author
  8. Chabon JJ, Hamilton EG, Kurtz DM, Esfahani MS, Moding EJ, Stehr H, Schroers-Martin J, Nabet BY, Chen B, Chaudhuri AA, Liu CL, Hui AB, Jin MC, Azad TD, Almanza D, Jeon Y, Nesselbush MC, Co Ting Keh L, Bonilla RF, Yoo CH, Ko RB, Chen EL, Merriott DJ, Massion PP, Mansfield AS, Jen J, Ren HZ, Lin SH, Costantino CL, Burr R, Tibshirani R, Gambhir SS, Berry GJ, Jensen KC, West RB, Neal JW, Wakelee HA, Loo BW, Kunder CA, Leung AN, Lui NS, Berry MF, Shrager JB, Nair VS, Haber DA, Sequist LV, Alizadeh AA, Diehn M. Integrating genomic features for non-invasive early lung cancer detection. Nature. 2020 March 25. PMID: 32269342
  9. Chan MB, Rogers CL, Chaudhuri AA, Flickinger JC, Khuntia D. Gunderson & Tepper’s Clinical Radiation Oncology. Tepper JE, Foote RL, Michalski JM, editors. Philadelphia: Elsevier; 2020. Chapter 33, Benign Brain Tumors: Meningiomas and Vestibular Schwannomas; p.508-527.
  10. Hellmann MD, Nabet BY, Rizvi H, Chaudhuri AA, Wells DK, Dunphy MP, Chabon JJ, Liu CL, Hui AB, Arbour KC, Luo J, Preeshagul IR, Moding EJ, Almanza D, Bonilla RF, Sauter JL, Choi H, Tenet M, Abu-Akeel M, Plodkowski AJ, Perez-Johnston R, Yoo CH, Ko RB, Stehr H, Gojenola L, Wakelee HA, Padda SK, Neal JW, Chaft JE, Kris MG, Rudin CM, Merghoub T, Li BT, Alizadeh AA, Diehn M. Circulating tumor DNA analysis to assess risk of progression after long-term response to PD-(L)1 blockade in NSCLC. Clinical Cancer Research. 2020 Feb 11. PMID: 32046999
  11. Moding EJ, Liu Y, Nabet BY, Chabon JJ, Chaudhuri AA, Hui AB, Bonilla RF, Ko RB, Yoo CH, Gojenola L, Jones CD, He J, Qiao Y, Xu T, Heymach JV, Tsao A, Liao Z, Gomez DR, Das M, Padda SK, Ramchandran KJ, Neal JW, Wakelee HA, Loo BW, Lin SH, Alizadeh AA, Diehn M. Circulating tumor DNA dynamics predict benefit from consolidation immunotherapy in locally advanced non-small-cell lung cancer. Nature Cancer. 2020 Jan 20.
  12. Samson PP, Spraker MB, Badiyan SN, Vlacich G, Robinson CG, Chaudhuri AA*. Local consolidative therapy for oligometastatic non-small cell lung cancer. Journal of Thoracic Disease. 2019 Dec;11(12):5649-5651. PMID: 32030290. *Senior Corresponding Author
  13. Barnell EK, Kang Y, Wurtzler EM, Griffith M, Chaudhuri AA*, Griffith OL*. Response to GASTRO-D-19-02091. Gastroenterology. 2019 Nov 16. PMID: 31743736. *Corresponding Author
  14. Azad TD, Chaudhuri AA, Fang P, Qiao Y, Esfahani MS, Chabon JJ, Hamilton EG, Yang YD, Lovejoy A, Newman AM, Kurtz DM, Jin M, Schroers-Martin J, Stehr H, Liu CL, Bik-Yu Hui A, Patel V, Maru D, Lin SH, Alizadeh AA, Diehn M. Circulating tumor DNA analysis for detection of minimal residual disease after chemoradiotherapy for localized esophageal cancer. Gastroenterology. 2019 Nov 8. PMID: 31711920
  15. Devarakonda S, Sankararaman S, Herzog B, Gold KA, Waqar SN, Ward JP, Raymond VM, Lanman RB, Chaudhuri AA, Owonikoko TK, Li BT, Poirier JT, Rudin CM, Govindan R, Morgensztern D. Circulating Tumor DNA Profiling in Small Cell Lung Cancer Identifies Potentially Targetable Alterations. Clinical Cancer Research. 2019 Jul 12. PMID: 31300452
  16. Barnell E, Kang Y, Wurtzler E, Griffith M, Chaudhuri AA*, Griffith OL*. Noninvasive Detection of High-risk Adenomas Using Stool-derived Eukaryotic RNA Sequences as Biomarkers. Gastroenterology. 2019 May 30. PMID: 31154021. *Corresponding Author
  17. Chaudhuri AA*, Chen K, Diehn M*, Loo BW*. Stereotactic ablative radiotherapy for central and ultra-central lung tumors. Therapeutic Radiology and Oncology. 2019 May 24. *Corresponding Author
  18. Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, Diehn M, Alizadeh AA. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nature Biotechnology. 2019 May 6. PMID: 31061481
  19. Chin R, Chen K, Usmani A, Chua C, Harris PK, Binkley MS, Azad TD, Dudley JC, Chaudhuri AA*. Detection of Solid Tumor Molecular Residual Disease using ctDNA. Molecular Diagnosis & Therapy. 2019 Apr 2. PMID: 30941670. *Senior Corresponding Author
  20. Dudley JC, Schroers-Martin J, Lazzareschi DV, Shi WY, Chen SB, Esfahani MS, Trivedi D, Chabon JJ, Chaudhuri AA, Stehr H, Liu CL, Lim H, Costa HA, Nabet BY, Sin MLY, Liao JC, Alizadeh AA, Diehn M. Detection and surveillance of bladder cancer using urine tumor DNA. Cancer Discovery. 2019 Apr; 9(4):500-509. PMID: 30578357
  21. Wallach J, Ho AL, Kim LH, Chaudhuri AA, Chaudhary N, Vaz-Guimaraes F, Chang SD. Quantitative analysis of the safety and efficacy of microvascular decompression for patients with trigeminal neuralgia above and below 65 years of age. Journal of Clinical Neuroscience. 2018 Sep;55:13-16.
  22. Turner B, Chaudhuri AA*. Principles of Clinical Cancer Research. Mell LK, Tran PT, Yu JB, Zhang Q, editors. New York: Springer Publishing Company; 2018. Chapter 29, Future Directions in Clinical Cancer Research; p.542-566. *Senior Corresponding Author
  23. Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, Carter JN, Merriott DJ, Dudley JC, Binkley MS, Modlin L, Padda SK, Gensheimer MF, West RB, Shrager JB, Neal JW, Wakelee HA, Loo BW Jr, Alizadeh AA, Diehn M. Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling. Cancer Discovery. 2017; 7(12):1394-1403. PMID: 29954647
  24. Qian Y, Zhu H, Pollom EL, Durkee BY, Chaudhuri AA, Gensheimer MF, Diehn M, Shultz DB, Loo BW Jr. Sinoatrial node toxicity after stereotactic ablative radiation therapy to lung tumors. Practical Radiation Oncology. 2017; 7(6):e525-e529. PMID: 28669706
  25. Binkley MS, King MT, Shrager JB, Bush K, Chaudhuri AA, Popat R, Gensheimer MF, Maxim PG, Henry Guo H, Diehn M, Nair VS, Loo BW Jr. Pulmonary function after lung tumor stereotactic ablative radiotherapy depends on regional ventilation within irradiated lung. Radiotherapy and Oncology. 2017; 123(2):270-275. PMID: 28460826
  26. 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. Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance. Cancer Discovery. 2017; 7(1):86-101. PMID: 27663899
  27. Chaudhuri AA, Binkley MS, Rigdon J, Carter JN, Aggarwal S, Dudley SA, Qian Y, Kumar KA, Hara WY, Gensheimer M, Nair VS, Maxim PG, Shultz DB, Bush K, Trakul N, Le QT, Diehn M, Loo BW Jr, Guo HH. Pre-treatment non-target lung FDG-PET uptake predicts symptomatic radiation pneumonitis following Stereotactic Ablative Radiotherapy (SABR). Radiotherapy and Oncology. 2016; 119(3):454-60. PMID: 27267049
  28. Chaudhuri AA, Chen JJ, Carter JN, Binkley MS, Kumar KA, Dudley SA, Sung AW, Loo BW Jr. Tracheal Diverticulum Following Paratracheal Hypofractionated Radiotherapy in the Setting of Prior and Subsequent Bevacizumab. Cureus. 2016; 8(4):e578. PMID: 27226939
  29. Binkley MS, Shrager JB, Chaudhuri A, Popat R, Maxim PG, Shultz DB, Diehn M, Loo BW Jr. Time course and predictive factors for lung volume reduction following stereotactic ablative radiotherapy (SABR) of lung tumors. Radiation Oncology. 2016; 11:40. PMID: 26975700
  30. Binkley MS, Hiniker SM, Chaudhuri A, Maxim PG, Diehn M, Loo BW Jr, Shultz DB. Dosimetric Factors and Toxicity in Highly Conformal Thoracic Reirradiation. International Journal of Radiation Oncology, Biology, Physics. 2016; 94(4):808-15. PMID: 26831903
  31. Chaudhuri AA, Simmons C Jr, Ellison D, Hemp J, Chung K. Atrial Myxoma Presenting as Myocardial Infarction Diagnosed by Echocardiography, Managed Endoscopically with Robot-Assisted Surgery. Cureus. 2016; 8(2):e484. PMID: 27014518
  32. Chaudhuri AA, Davis JT. Concomitant Granulomatosis with Polyangiitis and C3 Glomerulonephritis Causing Renal Failure. Cureus. 2016; 8(2):e482. PMID: 27004158
  33. Chaudhuri AA, Binkley MS, Aggarwal S, Qian Y, Carter JN, Shah R, Loo BW Jr. Severe Chest Wall Toxicity From Cryoablation in the Setting of Prior Stereotactic Ablative Radiotherapy. Cureus. 2016; 8(2):e477. PMID: 27004154
  34. Chaudhuri AA, Binkley MS, Osmundson EC, Alizadeh AA, Diehn M. Predicting Radiotherapy Responses and Treatment Outcomes Through Analysis of Circulating Tumor DNA. Seminars in Radiation Oncology. 2015; 25(4):305-12. PMID: 26384278
  35. Chaudhuri AA, Tang C, Binkley MS, Jin M, Wynne JF, von Eyben R, Hara WY, Trakul N, Loo BW Jr, Diehn M. Stereotactic ablative radiotherapy (SABR) for treatment of central and ultra-central lung tumors. Lung Cancer. 2015; 89(1):50-6. PMID: 25997421
  36. Chaudhuri AA, Xavier MF. Primary cutaneous diffuse large B cell lymphoma, leg type (PCDLBCL-LT) in the setting of prior radiation therapy. Journal of General Internal Medicine. 2015; 30(3):371-2. PMID: 25326162
  37. Chaudhuri AA, Binkley MS, Diehn M. Cancer Stem Cells: Emerging Concepts and Future Perspectives in Translational Oncology. Babashah S, editor. Switzerland: Springer; 2015. Chapter 25, Cancer Stem Cells and Tumor Radioresistance; p.519-532.
  38. Binkley MS, Shrager JB, Leung AN, Popat R, Trakul N, Atwood TF, Chaudhuri A, Maxim PG, Diehn M, Loo BW Jr. Lung volume reduction after stereotactic ablative radiation therapy of lung tumors: potential application to emphysema. International Journal of Radiation Oncology, Biology, Physics. 2014; 90(1):216-23. PMID: 25015205
  39. So AY, Sookram R, Chaudhuri AA, Minisandram A, Cheng D, Xie C, Lim EL, Flores YG, Jiang S, Kim JT, Keown C, Ramakrishnan P, Baltimore D. Dual mechanisms by which miR-125b represses IRF4 to induce myeloid and B-cell leukemias. Blood. 2014; 124(9):1502-12. PMID: 25006123
  40. Zhang M, Chaudhuri AA, Wallach J, Hara WY. Cyberknife Stereotactic Radiosurgery: Spine. Chang SD, Veeravagu A, editors. New York: Nova Science Publishers; 2014. Chapter 3, Imaging for Radiosurgery Treatment; p.27-44. PMID: 29954647
  41. Hu R, Huffaker TB, Kagele DA, Runtsch MC, Bake E, Chaudhuri AA, Round JL, O’Connell RM. MicroRNA-155 confers encephalogenic potential to Th17 cells by promoting effector gene expression. Journal of Immunology. 2013; 190(12):5972-80. PMID: 23686497
  42. Chaudhuri AA, So AY, Mehta A, Minisandram A, Sinha N, Jonsson VD, Rao DS, O’Connell RM, Baltimore D. Oncomir miR-125b regulates hematopoiesis by targeting the gene Lin28A. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109(11):4233-8. PMID: 22366319
  43. Chaudhuri AA, So AY, Sinha N, Gibson WS, Taganov KD, O’Connell RM, Baltimore D. MicroRNA-125b potentiates macrophage activation. Journal of Immunology. 2011; 187(10):5062-8. PMID: 22003200
  44. O’Connell RM, Kahn D, Gibson WS, Round JL, Scholz RL, Chaudhuri AA, Kahn ME, Rao DS, Baltimore D. MicroRNA-155 promotes autoimmune inflammation by enhancing inflammatory T cell development. Immunity. 2010; 33(4):607-19. PMID: 20888269
  45. O’Connell RM*, Chaudhuri AA*, Rao DS, Gibson WS, Balazs AB, Baltimore D. MicroRNAs enriched in hematopoietic stem cells differentially regulate long-term hematopoietic output. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107(32):14235-40. PMID: 20660734. *Equal contribution
  46. Rao DS, O’Connell RM, Chaudhuri AA, Garcia-Flores Y, Geiger TL, Baltimore D. MicroRNA-34a perturbs B lymphocyte development by repressing the forkhead box transcription factor Foxp1. Immunity. 2010; 33(1):48-59. PMID: 20598588
  47. O’Connell RM, Rao DS, Chaudhuri AA, Baltimore D. Physiological and pathological roles for microRNAs in the immune system. Nature Reviews Immunology. 2010; 10(2):111-22. PMID: 20098459
  48. O’Connell RM*, Chaudhuri AA*, Rao DS*, Baltimore D. Inositol phosphatase SHIP1 is a primary target of miR-155. Proceedings of the National Academy of Sciences of the United States of America. 2009; 106(17):7113-8. PMID: 19359473. *Equal contribution
  49. O’Connell RM, Rao DS, Chaudhuri AA, Boldin MP, Taganov KD, Nicoll J, Paquette RL, Baltimore D. Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. The Journal of Experimental Medicine. 2008; 205(3):585-94. PMID: 18299402
  50. Chaudhuri AA. Construction of a rational delta function using the reverse Cantor set and its application to quantum mechanics via pseudo-spectral methods. Trends in Applied Sciences Research. 2007; 2(1):1-14.
  51. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, Sharp PA, Tabin CJ, McManus MT. MicroRNA-responsive ‘sensor’ transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nature Genetics. 2004; 36(10):1079-83. PMID: 15361871