Research Summary

Pratik Mukherjee, MD, PhD, is a Professor in Residence in the Department Radiology and Biomedical Imaging, Bioengineering, and he is an attending neuroradiologist at the University of California, San Francisco. He is the Director of the Center for Imaging of Neurodegenerative Disease (CIND) based at the San Francisco VA Medical Center. He also directs the Neural Connectivity Laboratory (NCL) at UCSF China Basin.

Dr. Mukherjee received his PhD in Neuroscience from Rockefeller University, New York in 1994 and his MD from Cornell University, New York, in 1995. He completed his internship in Internal Medicine at New York Hospital - Cornell Medical Center, followed by a residency in Radiology and fellowship in Neuroradiology at Washington University Medical Center in St. Louis, Missouri, completed in 2002.

Dr. Mukherjee's primary clinical research is the study of neurodevelopmental disorders and traumatic brain injury (TBI) using advanced MRI. His research has been focused on technical development, neuroscience and clinical applications of advanced imaging methods for mapping structure and function of the human brain, especially diffusion MRI, which is a popular technique for assessing the development and integrity of white matter and for mapping axonal fiber pathways.

Dr. Mukherjee has served as Principal Investigator or Co-Principal Investigator for several NIH grants. His work has also been funded by grants from the Dept. of Defense, the Simons Foundation, McDonnell Foundation, Dana Foundation, Wallace Research Foundation, GE Healthcare and the GE-NFL Head Health Initiative. He has published over 150 peer-reviewed papers.

Research Funding

  • September 1, 2021 - August 31, 2025 - Transforming Research and Clinical Knowledge in Older Veterans with Acute Traumatic Brain Injury (TRACK-VA) , Principal Investigator . Sponsor: US Department of Veterans Affairs, CSRD Merit, Sponsor Award ID: CX002346-01
  • January 1, 2021 - December 31, 2024 - Predicting Outcomes in Pediatric Hemorrhagic Stroke with Personalized Connectomics: Project 2 , . Sponsor: American Heart Association/American Stroke Association Bugher Foundation, Sponsor Award ID: A136503
  • July 8, 2019 - April 30, 2024 - Neural Mechanisms of Sensory OverResponsivity , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01MH116950
  • September 30, 2017 - July 31, 2022 - MRI CORTICOGRAPHY: DEVELOPING NEXT GENERATION MICROSCALE HUMAN CORTEX MRI SCANNER , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01EB025162
  • October 1, 2020 - September 30, 2021 - ShEEP-IC: Request to purchase MAGNETOM Skyra 3T complete concurrent field monitoring and motion correction system upgrade , Principal Investigator . Sponsor: NIH, Sponsor Award ID: IS1BX005513
  • February 1, 2017 - September 30, 2021 - Multi-level assessment and rehabilitation of combat mild traumatic brain injury , Principal Investigator . Sponsor: NIH, Sponsor Award ID: I01RX002300
  • September 30, 2013 - August 31, 2020 - Transforming Research and Clinical Knowledge in Traumatic Brain Injury , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01NS086090
  • January 1, 2019 - September 30, 2019 - ShEEP IC Request to purchase MAGNETOM Terra 7T coil upgrade , Principal Investigator . Sponsor: NIH, Sponsor Award ID: IS1BX004816
  • September 26, 2014 - November 30, 2018 - MRI Corticography (MRCoG): Micro-scale Human Cortical Imaging , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: R24MH106096
  • January 1, 2018 - September 30, 2018 - ShEEP IC Request to purchase MAGNETOM 7T PTx upgrade , Principal Investigator . Sponsor: NIH, Sponsor Award ID: IS1BX004415
  • February 1, 2017 - July 31, 2018 - Artificial Intelligence for Imaging of Neurological Emergencies , Principal Investigator . Sponsor: California Initiative to Advance Precision Medicine (CIAPM), Sponsor Award ID:
  • July 15, 2009 - June 30, 2015 - Macrostructural and Microstructural Imaging Biomarkers of Traumatic Brain Injury , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01NS060776

Education

Yale University, New Haven, CT, B.A., 1988, Computer Science & Psychology
Rockefeller Univ., New York, NY, Ph.D., 1994, Neuroscience
Cornell University, New York, NY, M.D., 1995, Medicine

Honors & Awards

  • 1988-95
    Medical Scientist Training Program Grant, National Institutes of Health
  • 1994
    S. Koide Memorial Fellowship, Rockefeller University
  • 1999
    Roentgen Resident/Fellow Research Award, Radiological Society of North America
  • 2001
    Berlex/ASNR Award in Basic Science Research, American Society of Neuroradiology

Selected Publications

  1. Andres Nunez, Rachel Thomas, Katie Brecker, Catherine Demos, Sonia Jain, Xiaoying Sun, Joseph Giacino, Michael McCrea, David Okonkwo, Claudia Robertson, Pratik Mukherjee, Kevin Wang, Ava Puccio, Andrea Schneider, Danielle Sandsmark, Geoffrey Manley, Alexa Walter, Ramon Diaz-Arrastia. Angiopoietin2 (Ang2) Levels are Associated with Increased Severity and Unfavorable Outcomes in Traumatic Brain Injury (TBI): A TRACK-TBI Study (S17.001). Neurology. 2025 Apr 8; 104(7_Supplement_1).  View on PubMed
  2. Anna Mueller, Rachel Thomas, Katie Brecker, Catherine Demos, George Sigal, Sonia Jain, Xiaoying Sun, Joseph Giacino, Michael McCrea, Alexa Walter, David Okonkwo, Claudia Robertson, Nancy Temkin, Pratik Mukherjee, Ava Puccio, Andrea Schneider, Danielle Sandsmark, Geoffrey Manley, Ramon Diaz-Arrastia. Plasma Placental Growth Factor (PlGF) is Elevated After Traumatic Brain Injury (TBI) (P6-7.009). Neurology. 2025 Apr 8; 104(7_Supplement_1).  View on PubMed
  3. John K. Yue, Sonia Jain, Ava Puccio, Xiaoying Sun, Thomas van Essen, Romit Samanta, Patrick Belton, Esther Yuh, Lindsay Nelson, Mahmoud Elguindy, Joye Tracey, Shawn Eagle, Frederick Korley, Andrea Schneider, Pratik Mukherjee, Raquel Gardner. 343 Diagnostic and Prognostic Utility of Inflammatory Cytokines and Acute Phase Proteins in Traumatic Brain Injury: Results From the 18-Center TRACK-TBI Study. Neurosurgery. 2025 Apr 1; 71(Supplement_1):83-83.  View on PubMed
  4. Harris M, Yue JK, Jain S, Sun X, Puccio AM, Gardner RC, Wang KKW, Okonkwo DO, Yuh EL, Mukherjee P, Nelson LD, Taylor SR, Markowitz AJ, Diaz-Arrastia R, Manley GT, Korley FK, TRACK-TBI Investigators. Effect of blood alcohol on the diagnostic accuracy of glial fibrillary acidic protein and ubiquitin carboxy-terminal hydrolase L1 for traumatic intracranial hemorrhage: A TRACK-TBI study. Acad Emerg Med. 2025 Feb 18.  View on PubMed
  5. art Kals, Lindsay Wilson, Daniel F. Levey, Livia Parodi, Ewout W. Steyerberg, Sylvia Richardson, Feng He, Xiaoying Sun, Sonia Jain, Aarno Palotie, Samuli Ripatti, Jonathan Rosand, Geoff T. Manley, Andrew I.R. Maas, Murray B. Stein, David K. Menon, The Genetic Associations In Neurotrauma Consortium, Cecilia Ackerlund, Hadie Adams, Krisztina Amrein, Nada Andelic, Lasse Andreassen, Audny Anke, Anna Antoni, Gérard Audibert, Philippe Azouvi, Maria Luisa Azzolini, Ronald Bartels, Pál Barzó, Romuald Beauvais, Ronny Beer, Bo-Michael Bellander, Antonio Belli, Habib Benali, Maurizio Berardino, Luigi Beretta, Morten Blaabjerg, Peter Bragge, Alexandra Brazinova, Vibeke Brinck, Joanne Brooker, Camilla Brorsson, Andras Buki, Monika Bullinger, Manuel Cabeleira, Alessio Caccioppola, Emiliana Calappi, Maria Rosa Calvi, Peter Cameron, Guillermo Carbayo Lozano, Marco Carbonara, Ana M. Castaño-León, Simona Cavallo, Giorgio Chevallard, Arturo Chieregato, Giuseppe Citerio, Hans Clusmann, Mark Steven Coburn, Jonathan Coles, Jamie D. Cooper, Marta Correia, Amra Covic, Nicola Curry, Endre Czeiter, Marek Czosnyka, Claire Dahyot-Fizelier, Paul Dark, Helen Dawes, Véronique De Keyser, Vincent Degos, Francesco Della Corte, Hugo den Boogert, Bart Depreitere, Ðula Ðilvesi, Abhishek Dixit, Emma Donoghue, Jens Dreier, Guy-Loup Dulière, Ari Ercole, Patrick Esser, Erzsébet Ezer, Martin Fabricius, Valery L. Feigin, Kelly Foks, Shirin Frisvold, Alex Furmanov, Pablo Gagliardo, Damien Galanaud, Dashiell Gantner, Guoyi Gao, Pradeep George, Alexandre Ghuysen, Lelde Giga, Ben Glocker, Jagoš Golubovic, Pedro A. Gomez, Johannes Gratz, Benjamin Gravesteijn, Francesca Grossi, Russell L. Gruen, Deepak Gupta, Juanita A. Haagsma, Iain Haitsma, Raimund Helbok, Eirik Helseth, Lindsay Horton, Jilske Huijben, Peter J. Hutchinson, Bram Jacobs, Stefan Jankowski, Mike Jarrett, Ji-yao Jiang, Faye Johnson, Kelly Jones, Mladen Karan, Angelos G. Kolias, Erwin Kompanje, Daniel Kondziella, Lars-Owe Koskinen, Noémi Kovács, Ana Kowark, Alfonso Lagares, Linda Lanyon, Steven Laureys, Fiona Lecky, Didier Ledoux, Rolf Lefering, Valerie Legrand, Aurelie Lejeune, Leon Levi, Roger Lightfoot, Hester Lingsma, Marc Maegele, Marek Majdan, Alex Manara, Hugues Maréchal, Costanza Martino, Julia Mattern, Charles McFadyen, Catherine McMahon, Béla Melegh, Tomas Menovsky, Ana Mikolic, Benoit Misset, Visakh Muraleedharan, Lynnette Murray, Ancuta Negru, David Nelson, Virginia Newcombe, Daan Nieboer, József Nyirádi, Matej Oresic, Fabrizio Ortolano, Olubukola Otesile, Paul M. Parizel, Jean-François Payen, Natascha Perera, Vincent Perlbarg, Paolo Persona, Wilco Peul, Anna Piippo-Karjalainen, Matti Pirinen, Dana Pisica, Horia Ples, Suzanne Polinder, Inigo Pomposo, Jussi P. Posti, Louis Puybasset, Andreea Radoi, Arminas Ragauskas, Rahul Raj, Malinka Rambadagalla, Veronika Rehorcíková, Isabel Retel Helmrich, Jonathan Rhodes, Sophie Richter, Saulius Rocka, Cecilie Roe, Olav Roise, Jeffrey Rosenfeld, Christina Rosenlund, Guy Rosenthal, Rolf Rossaint, Sandra Rossi, Daniel Rueckert, Martin Rusnák, Juan Sahuquillo, Oliver Sakowitz, Renan Sanchez-Porras, Janos Sandor, Nadine Schäfer, Silke Schmidt, Herbert Schoechl, Guus Schoonman, Rico Frederik Schou, Elisabeth Schwendenwein, Charlie Sewalt, Ranjit D. Singh, Toril Skandsen, Peter Smielewski, Abayomi Sorinola, Emmanuel Stamatakis, Simon Stanworth, Robert Stevens, William Stewart, Nino Stocchetti, Nina Sundström, Riikka Takala, Viktória Tamás, Tomas Tamosuitis, Mark Steven Taylor, Braden Te Ao, Olli Tenovuo, Alice Theadom, Aurore Thibaut, Matt Thomas, Dick Tibboel, Marjolijn Timmers, Christos Tolias, Tony Trapani, Cristina Maria Tudora, Andreas Unterberg, Peter Vajkoczy, Egils Valeinis, Shirley Vallance, Zoltán Vámos, Mathieu van der Jagt, Joukje van der Naalt, Gregory Van der Steen, Jeroen T.J.M. van Dijck, Inge A. van Erp, Thomas A. van Essen, Wim Van Hecke, Caroline van H.... Genetic vulnerability and adverse mental health outcomes following mild traumatic brain injury: a meta-analysis of CENTER-TBI and TRACK-TBI cohorts. EClinicalMedicine. 2024 Dec 1; 78:102956.  View on PubMed
  6. Brandes-Aitken A, Powers R, Wren J, Chu R, Shapiro KA, Steele M, Mukherjee P, Marco EJ. Sensory processing subtypes relate to distinct emotional and behavioral phenotypes in a mixed neurodevelopmental cohort. Sci Rep. 2024 11 26; 14(1):29326.  View on PubMed
  7. Karbasforoushan H, Wren-Jarvis J, Hwang A, Santiago R, Raptentsetsang S, Cai LT, Xiao J, Maruyama BA, Abrams GM, Novakovic-Agopian T, Mukherjee P. Goal-Oriented Attentional Self-Regulation Training in Chronic Mild Traumatic Brain Injury is Linked to Microstructural Plasticity in Prefrontal White Matter. J Neurotrauma. 2025 Jan; 42(1-2):46-56.  View on PubMed
  8. Yue JK, Kanter JH, Barber JK, Huang MC, van Essen TA, Elguindy MM, Foreman B, Korley FK, Belton PJ, Pisica D, Lee YM, Kitagawa RS, Vassar MJ, Sun X, Satris GG, Wong JC, Ferguson AR, Huie JR, Wang KKW, Deng H, Wang VY, Bodien YG, Taylor SR, Madhok DY, McCrea MA, Ngwenya LB, DiGiorgio AM, Tarapore PE, Stein MB, Puccio AM, Giacino JT, Diaz-Arrastia R, Lingsma HF, Mukherjee P, Yuh EL, Robertson CS, Menon DK, Maas AIR, Markowitz AJ, Jain S, Okonkwo DO, Temkin NR, Manley GT, TRACK-TBI Investigators. Clinical profile of patients with acute traumatic brain injury undergoing cranial surgery in the United States: report from the 18-centre TRACK-TBI cohort study. Lancet Reg Health Am. 2024 Nov; 39:100915.  View on PubMed
  9. Edlow BL, Boerwinkle VL, Annen J, Boly M, Gosseries O, Laureys S, Mukherjee P, Puybasset L, Stevens RD, Threlkeld ZD, Newcombe VFJ, Fernandez-Espejo D, Curing Coma Campaign and its Contributing Members. Correction: Common Data Elements for Disorders of Consciousness: Recommendations from the Working Group on Neuroimaging. Neurocrit Care. 2024 Oct 11.  View on PubMed
  10. Qiming Cui, Duygu Tosun, Pratik Mukherjee, Reza Abbasi-Asl. 7T MRI Synthesization from 3T Acquisitions. Lecture Notes in Computer Science. 2024 Oct 3; 15007:35-44.  View on PubMed
  11. Yue JK, Etemad LL, Elguindy MM, van Essen TA, Belton PJ, Nelson LD, McCrea MA, Vreeburg RJG, Gotthardt CJ, Tracey JX, Coskun BC, Krishnan N, Halabi C, Eagle SR, Korley FK, Robertson CS, Duhaime AC, Satris GG, Tarapore PE, Huang MC, Madhok DY, Giacino JT, Mukherjee P, Yuh EL, Valadka AB, Puccio AM, Okonkwo DO, Sun X, Jain S, Manley GT, DiGiorgio AM, TRACK-TBI Investigators, Badjatia N, Barber J, Bodien YG, Fabian B, Ferguson AR, Foreman B, Gardner RC, Gopinath S, Grandhi R, Russell Huie J, Dirk Keene C, Lingsma HF, MacDonald CL, Markowitz AJ, Merchant R, Ngwenya LB, Rodgers RB, Schneider ALC, Schnyer DM, Taylor SR, Temkin NR, Torres-Espin A, Vassar MJ, Wang KKW, Wong JC, Zafonte RD. Prior traumatic brain injury is a risk factor for in-hospital mortality in moderate to severe traumatic brain injury: a TRACK-TBI cohort study. Trauma Surg Acute Care Open. 2024; 9(1):e001501.  View on PubMed
  12. Wintermark M, Allen JW, Anzai Y, Das T, Flanders AE, Galanaud D, Gean A, Haller S, Lv H, Hirvonen J, Jordan JE, Lee R, Lui YW, Sundgren PC, Mukherjee P, Moen KG, Muto M, Ng K, Niogi SN, Rovira A, de Bruxellas NL, Smits M, Tsiouris AJ, Van Goethem J, Vyvere TV, Whitlow C, Wiesmann M, Yamada K, Zakharova N, Parizel PM. Standardized reporting for Head CT Scans in patients suspected of traumatic brain injury (TBI): An international expert endeavor. Neuroradiology. 2024 Sep; 66(9):1513-1526.  View on PubMed
  13. Kundu S, Sair H, Sherr EH, Mukherjee P, Rohde GK. Discovering the gene-brain-behavior link in autism via generative machine learning. Sci Adv. 2024 Jun 14; 10(24):eadl5307.  View on PubMed
  14. Yue JK, Yuh EL, Elguindy MM, Sun X, van Essen TA, Deng H, Belton PJ, Satris GG, Wong JC, Valadka AB, Korley FK, Robertson CS, McCrea MA, Stein MB, Diaz-Arrastia R, Wang KKW, Temkin NR, DiGiorgio AM, Tarapore PE, Huang MC, Markowitz AJ, Puccio AM, Mukherjee P, Okonkwo DO, Jain S, Manley GT. Isolated Traumatic Subarachnoid Hemorrhage on Head Computed Tomography Scan May Not Be Isolated: A Transforming Research and Clinical Knowledge in Traumatic Brain Injury Study (TRACK-TBI) Study. J Neurotrauma. 2024 06; 41(11-12):1310-1322.  View on PubMed
  15. John K. Yue, Leila Etemad, Jason Barber, Gabriela Satris, Patrick Belton, Debbie Madhok, Sabah Hamidi, Joye Tracey, Esther Yuh, Pratik Mukherjee, Michael C. Huang, Phiroz E. Tarapore, Ava Puccio, David O. Okonkwo, Geoffrey T. Manley, Nancy Temkin, Anthony DiGiorgio. 176 Repetitive Traumatic Brain Injuries Are Associated With Poorer Outcomes at 1-Year and 3-7 Years After Index Injury. Neurosurgery. 2024 Apr 1; 70(Supplement_1):43-44.  View on PubMed
  16. John K. Yue, Esther Yuh, Mahmoud Elguindy, Xiaoying Sun, Thomas van Essen, Hansen Deng, Gabriela Satris, Justin Wong, Anthony Michael DiGiorgio, Phiroz E. Tarapore, Michael C. Huang, Amy Markowitz, Pratik Mukherjee, Sonia Jain, Geoffrey T. Manley. 248 Isolated Traumatic Subarachnoid Hemorrhage on Head Computed Tomography Scan May Not Be Isolated. Neurosurgery. 2024 Apr 1; 70(Supplement_1):68-69.  View on PubMed
  17. Werner JK, Albrecht J, Capaldi VF, Jain S, Sun X, Mukherjee P, Williams SG, Collen J, Diaz-Arrastia R, Manley GT, Krystal AD, Wickwire E, TRACK-TBI Investigators. Association of Biomarkers of Neuronal Injury and Inflammation With Insomnia Trajectories After Traumatic Brain Injury: A TRACK-TBI Study. Neurology. 2024 Apr 23; 102(8):e209269.  View on PubMed
  18. Yue JK, Lee YM, Sun X, van Essen TA, Elguindy MM, Belton PJ, Pisica D, Mikolic A, Deng H, Kanter JH, McCrea MA, Bodien YG, Satris GG, Wong JC, Ambati VS, Grandhi R, Puccio AM, Mukherjee P, Valadka AB, Tarapore PE, Huang MC, DiGiorgio AM, Markowitz AJ, Yuh EL, Okonkwo DO, Steyerberg EW, Lingsma HF, Menon DK, Maas AIR, Jain S, Manley GT, The TRACK-TBI Investigators . Performance of the IMPACT and CRASH prognostic models for traumatic brain injury in a contemporary multicenter cohort: a TRACK-TBI study. J Neurosurg. 2024 Aug 01; 141(2):417-429.  View on PubMed
  19. Puccio AM, Yue JK, Korley FK, Okonkwo DO, Diaz-Arrastia R, Yuh EL, Ferguson AR, Mukherjee P, Wang KKW, Taylor SR, Deng H, Markowitz AJ, Sun X, Jain S, Manley GT. Diagnostic Utility of Glial Fibrillary Acidic Protein Beyond 12 Hours After Traumatic Brain Injury: A TRACK-TBI Study. J Neurotrauma. 2024 06; 41(11-12):1353-1363.  View on PubMed
  20. Cai LT, Moon J, Camacho PB, Anderson AT, Chwa WJ, Sutton BP, Markowitz AJ, Palacios EM, Rodriguez A, Manley GT, Shankar S, Bremer PT, Mukherjee P, Madduri RK, TRACK-TBI Investigators. MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline. Neuroinformatics. 2024 Apr; 22(2):177-191.  View on PubMed

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