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Timothy M. Baran, Ph.D.

Timothy M. Baran, Ph.D.

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About Me

Timothy Baran received his B.S. in Electrical and Computer & Systems Engineering from Rensselaer Polytechnic Institute in 2007. He came to the University of Rochester in 2007 and received his Ph.D. in Optics in 2013. Following this, Dr. Baran joined the faculty as an Instructor in the Department of ...
Timothy Baran received his B.S. in Electrical and Computer & Systems Engineering from Rensselaer Polytechnic Institute in 2007. He came to the University of Rochester in 2007 and received his Ph.D. in Optics in 2013. Following this, Dr. Baran joined the faculty as an Instructor in the Department of Imaging Sciences in 2013. He was promoted to Research Assistant Professor in 2015, and joined the tenure-track faculty as an Assistant Professor in 2020.

Faculty Appointments

Assistant Professor - Department of Imaging Sciences (SMD)

Assistant Professor - Department of Biomedical Engineering (SMD) - Joint

Assistant Professor - Department of The Institute for Optics (RC) - Joint

Credentials

Education

PhD | University of Rochester. Optics. 2013

BS | Rensselaer Polytechnic Institute. Electrical Engineering. 2007

Awards

Lasers in Surgery and Medicine Young Investigators Award. 2013

Optical Society of America Biomedical Optics Meeting Student Award. 2012

Rochester Precision Optics Award for Outstanding Graduate Project. 2010

Research

Publications

Journal Articles

Feasibility of antimicrobial photodynamic therapy for treatment of breast abscesses: Retrospective Monte Carlo simulation study.

Baran TM, Nguyen L, Palumbo S, Weiss A, Duric N

Photochemistry and photobiology.. 2025 March 4 Epub 03/04/2025.

Impact of Early Direct Patient Notification on Follow-Up Completion for Nonurgent Actionable Incidental Radiologic Findings.

Loftus JR, Kadom N, Baran TM, Hans K, Waldman D, Wandtke B

Journal of the American College of Radiology : JACR.. 2024 April 21 (4):558-566. Epub 01/12/2024.

WATUNet: a deep neural network for segmentation of volumetric sweep imaging ultrasound.

Khaledyan D, Marini TJ, O'Connell A, Meng S, Kan J, Brennan G, Zhao Y, Baran TM, Parker KJ

Machine learning: science and technology.. 2024 March 15 (1):015042. Epub 03/08/2024.

Safety and Feasibility of Photodynamic Therapy for Percutaneous Image-guided Abdominopelvic Abscess Drainage: Phase 1 Trial.

Baran TM, Bass DA, Christensen L, Longbine E, Favella MD, Foster TH, Sharma AK

Radiology.. 2024 March 310 (3):e232667. Epub 1900 01 01.

Treatment planning for photodynamic therapy of abscess cavities using patient-specific optical properties measured prior to illumination.

Li Z, Hannan MN, Sharma AK, Baran TM

Physics in medicine and biology.. 2024 February 2869 (5)Epub 02/28/2024.

First in human measurements of abscess cavity optical properties and methylene blue uptake prior to photodynamic therapy by diffuse reflectance spectroscopy.

Hannan MN, Sharma AK, Baran TM

Journal of biomedical optics.. 2024 February 29 (2):027002. Epub 02/27/2024.

Application of transfer learning for rapid calibration of spatially resolved diffuse reflectance probes for extraction of tissue optical properties.

Hannan MN, Baran TM

Journal of biomedical optics.. 2024 February 29 (2):027004. Epub 02/28/2024.

Treatment planning for photodynamic therapy of abscess cavities using patient-specific optical properties measured prior to illumination.

Li Z, Hannan MN, Sharma AK, Baran TM

medRxiv : the preprint server for health sciences.. 2023 November 6 Epub 11/06/2023.

Application of Transfer Learning for Rapid Calibration of Spatially-resolved Diffuse Reflectance Probes for Extraction of Tissue Optical Properties.

Hannan MN, Baran TM

bioRxiv : the preprint server for biology.. 2023 November 5 Epub 11/05/2023.

Reactive oxygen species drive foraging decisions in Caenorhabditis elegans.

Bischer AP, Baran TM, Wojtovich AP

Redox biology.. 2023 November 67 :102934. Epub 10/13/2023.

Photodynamic therapy is a safe and feasible adjunct to percutaneous drainage of deep tissue abscesses: Results of a first in humans Phase 1 clinical trial.

Baran TM, Bass DA, Christensen L, Longbine E, Favella MD, Foster TH, Sharma AK

medRxiv : the preprint server for health sciences.. 2023 October 16 Epub 10/16/2023.

First in human measurements of abscess cavity optical properties and methylene blue uptake prior to photodynamic therapy by diffuse reflectance spectroscopy.

Hannan MN, Sharma AK, Baran TM

medRxiv : the preprint server for health sciences.. 2023 October 16 Epub 10/16/2023.

Photodynamic Therapy of an Abdominal Abscess at the Time of Percutaneous Drainage.

Baran TM, Sharma AK

Cardiovascular and interventional radiology.. 2023 September 46 (9):1292-1294. Epub 07/18/2023.

Standardized Criteria for Identification of Cardiac Tamponade on Non-Electrocardiogram-gated Computed Tomography: Correlation With Echocardiographic Findings.

Bothwell KD, Ling FS, Ambrosini R, Baran TM, Lorca MC, Chaturvedi A

Journal of thoracic imaging.. 2023 July 138 (4):W44-W51. Epub 12/13/2022.

Diagnosis of Pregnancy Complications Using Blind Ultrasound Sweeps Performed by Individuals Without Prior Formal Ultrasound Training.

Toscano M, Marini T, Lennon C, Erlick M, Silva H, Crofton K, Serratelli W, Rana N, Dozier AM, Castaneda B, Baran TM, Drennan K

Obstetrics and gynecology.. 2023 May 1141 (5):937-948. Epub 04/05/2023.

Breast Ultrasound Volume Sweep Imaging: A New Horizon in Expanding Imaging Access for Breast Cancer Detection.

Marini TJ, Castaneda B, Iyer R, Baran TM, Nemer O, Dozier AM, Parker KJ, Zhao Y, Serratelli W, Matos G, Ali S, Ghobryal B, Visca A, O'Connell A

Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine.. 2023 April 42 (4):817-832. Epub 07/08/2022.

Sustainable volume sweep imaging lung teleultrasound in Peru: Public health perspectives from a new frontier in expanding access to imaging.

Marini TJ, Castaneda B, Satheesh M, Zhao YT, Reátegui-Rivera CM, Sifuentes W, Baran TM, Kaproth-Joslin KA, Ambrosini R, Rios-Mayhua G, Dozier AM

Frontiers in health services.. 2023 3 :1002208. Epub 04/03/2023.

Methylene blue photodynamic therapy of bacterial species found in human abscesses: Planktonic, biofilm, and 3D silicone models.

Chan H, Pavelka MS, Baran TM

Proceedings of SPIE--the International Society for Optical Engineering.. 2023 12358 Epub 03/14/2023.

Preliminary measurements of optical properties in human abscess cavities prior to methylene blue photodynamic therapy.

Hannan MN, Sharma AK, Baran TM

Proceedings of SPIE--the International Society for Optical Engineering.. 2023 12359 Epub 03/14/2023.

No sonographer, no radiologist: Assessing accuracy of artificial intelligence on breast ultrasound volume sweep imaging scans.

Marini TJ, Castaneda B, Parker K, Baran TM, Romero S, Iyer R, Zhao YT, Hah Z, Park MH, Brennan G, Kan J, Meng S, Dozier A, O'Connell A

PLOS digital health.. 2022 November 1 (11):e0000148. Epub 11/23/2022.

Volume sweep imaging lung teleultrasound for detection of COVID-19 in Peru: a multicentre pilot study.

Marini TJ, Kaproth-Joslin K, Ambrosini R, Baran TM, Dozier AM, Zhao YT, Satheesh M, Mahony Reátegui-Rivera C, Sifuentes W, Rios-Mayhua G, Castaneda B

BMJ open.. 2022 October 312 (10):e061332. Epub 10/03/2022.

Functional brain mapping in patients with chronic back pain shows age-related differences.

Baran TM, Lin FV, Geha P

Pain.. 2022 August 1163 (8):e917-e926. Epub 11/15/2021.

Diagnostic Performance of the Ovarian-Adnexal Reporting and Data System (O-RADS) Ultrasound Risk Score in Women in the United States.

Jha P, Gupta A, Baran TM, Maturen KE, Patel-Lippmann K, Zafar HM, Kamaya A, Antil N, Barroilhet L, Sadowski EA

JAMA network open.. 2022 June 15 (6):e2216370. Epub 06/01/2022.

Ovarian Cancer Detection in Average-Risk Women: Classic- versus Nonclassic-appearing Adnexal Lesions at US.

Gupta A, Jha P, Baran TM, Maturen KE, Patel-Lippmann K, Zafar HM, Kamaya A, Antil N, Barroilhet L, Sadowski E

Radiology.. 2022 June 303 (3):603-610. Epub 03/22/2022.

Brain Small-Worldness Properties and Perceived Fatigue in Mild Cognitive Impairment.

Kukla B, Anthony M, Chen S, Turnbull A, Baran TM, Lin FV

The journals of gerontology. Series A, Biological sciences and medical sciences.. 2022 March 377 (3):541-546. Epub 1900 01 01.

Effects of patient-specific treatment planning on eligibility for photodynamic therapy of deep tissue abscess cavities: retrospective Monte Carlo simulation study.

Li Z, Nguyen L, Bass DA, Baran TM

Journal of biomedical optics.. 2022 February 27 (8)Epub 1900 01 01.

No sonographer, no radiologist: New system for automatic prenatal detection of fetal biometry, fetal presentation, and placental location.

Arroyo J, Marini TJ, Saavedra AC, Toscano M, Baran TM, Drennan K, Dozier A, Zhao YT, Egoavil M, Tamayo L, Ramos B, Castaneda B

PloS one.. 2022 17 (2):e0262107. Epub 02/09/2022.

Fluorescence and diffuse reflectance provide similar accuracy in recovering fluorophore concentration at short source-detector separations.

Roccabruna JR, Bridger KG, Baran TM

Journal of modern optics.. 2022 69 (12):699-704. Epub 05/11/2022.

Optical property recovery with spatially-resolved diffuse reflectance at short source-detector separations using a compact fiber-optic probe.

Bridger KG, Roccabruna JR, Baran TM

Biomedical optics express.. 2021 December 112 (12):7388-7404. Epub 11/09/2021.

Testing telediagnostic thyroid ultrasound in Peru: a new horizon in expanding access to imaging in rural and underserved areas.

Marini TJ, Weiss SL, Gupta A, Zhao YT, Baran TM, Garra B, Shafiq I, Oppenheimer DC, Egoavil MS, Ortega RL, Quinn RA, Kan J, Dozier AM, Tamayo L, Carlotto C, Castaneda B

Journal of endocrinological investigation.. 2021 December 44 (12):2699-2708. Epub 05/10/2021.

Lung ultrasound volume sweep imaging for respiratory illness: a new horizon in expanding imaging access.

Marini TJ, Weis JM, Baran TM, Kan J, Meng S, Yeo A, Zhao YT, Ambrosini R, Cleary S, Rubens D, Chess M, Castaneda B, Dozier A, O'Connor T, Garra B, Kaproth-Joslin K

BMJ open respiratory research.. 2021 November 8 (1)Epub 1900 01 01.

Improving CT assessment for pulmonary hypertension in patients with severe aortic stenosis, correlation with right heart catheterization.

Chaturvedi A, Baran TM, Ambrosini R, Krishnamoorthy V

Clinical imaging.. 2021 September 77 :122-129. Epub 02/03/2021.

Rethinking Time-to-Exchange: Outcomes of Nephrostomy Tube Placement in Pregnancy.

Kapoor SR, Maldow DJ, Baran TM, Sharma AK

Journal of vascular and interventional radiology : JVIR.. 2021 August 32 (8):1231-1233. Epub 1900 01 01.

Increased segregation of structural brain networks underpins enhanced broad cognitive abilities of cognitive training.

Chen Q, Baran TM, Turnbull A, Zhang Z, Rebok GW, Lin FV

Human brain mapping.. 2021 July 42 (10):3202-3215. Epub 05/06/2021.

Testing telediagnostic obstetric ultrasound in Peru: a new horizon in expanding access to prenatal ultrasound.

Toscano M, Marini TJ, Drennan K, Baran TM, Kan J, Garra B, Dozier AM, Ortega RL, Quinn RA, Zhao YT, Egoavil MS, Tamayo L, Carlotto C, Castaneda B

BMC pregnancy and childbirth.. 2021 April 2621 (1):328. Epub 04/26/2021.

New Ultrasound Telediagnostic System for Low-Resource Areas: Pilot Results From Peru.

Marini TJ, Oppenheimer DC, Baran TM, Rubens DJ, Toscano M, Drennan K, Garra B, Miele FR, Garra G, Noone SJ, Tamayo L, Carlotto C, Trujillo L, Waks E, Garra K, Egoavil MS, Berrospi J, Castaneda B

Journal of ultrasound in medicine : official journal of the American Institute of Ultrasound in Medicine.. 2021 March 40 (3):583-595. Epub 08/14/2020.

Staphylococcus aureus Tolerance and Genomic Response to Photodynamic Inactivation.

Snell SB, Gill AL, Haidaris CG, Foster TH, Baran TM, Gill SR

mSphere.. 2021 January 66 (1)Epub 01/06/2021.

Testing telediagnostic right upper quadrant abdominal ultrasound in Peru: A new horizon in expanding access to imaging in rural and underserved areas.

Marini TJ, Oppenheimer DC, Baran TM, Rubens DJ, Dozier A, Garra B, Egoavil MS, Quinn RA, Kan J, Ortega RL, Zhao YT, Tamayo L, Carlotto C, Castaneda B

PloS one.. 2021 16 (8):e0255919. Epub 08/11/2021.

Longitudinal stability of medial temporal lobe connectivity is associated with tau-related memory decline.

Chen Q, Turnbull A, Baran TM, Lin FV

eLife.. 2020 December 319 Epub 12/31/2020.

Brain structural connectomes indicate shared neural circuitry involved in subjective experience of cognitive and physical fatigue in older adults.

Baran TM, Zhang Z, Anderson AJ, McDermott K, Lin F

Brain imaging and behavior.. 2020 December 14 (6):2488-2499. Epub 1900 01 01.

Quantification of reactive oxygen species production by the red fluorescent proteins KillerRed, SuperNova and mCherry.

Onukwufor JO, Trewin AJ, Baran TM, Almast A, Foster TH, Wojtovich AP

Free radical biology & medicine.. 2020 February 1147 :1-7. Epub 12/10/2019.

Cognitively supernormal older adults maintain a unique structural connectome that is resistant to Alzheimer's pathology.

Chen Q, Baran TM, Rooks B, O'Banion MK, Mapstone M, Zhang Z, Lin F,

NeuroImage. Clinical.. 2020 28 :102413. Epub 09/08/2020.

Insula and putamen centered functional connectivity networks reflect healthy agers' subjective experience of cognitive fatigue in multiple tasks.

Anderson AJ, Ren P, Baran TM, Zhang Z, Lin F

Cortex; a journal devoted to the study of the nervous system and behavior.. 2019 October 119 :428-440. Epub 08/14/2019.

Accuracy of Non-Electrocardiographically Gated Thoracic CT Angiography for Right Atrial and Right Ventricular Enlargement.

Nuffer Z, Baran TM, Krishnamoorthy V, Kaproth-Joslin K, Chaturvedi A

Radiology. Cardiothoracic imaging.. 2019 October 1 (4):e190008. Epub 10/31/2019.

Photodynamic therapy of deep tissue abscess cavities: Retrospective image-based feasibility study using Monte Carlo simulation.

Baran TM, Choi HW, Flakus MJ, Sharma AK

Medical physics.. 2019 July 46 (7):3259-3267. Epub 05/21/2019.

Cognitive fatigue and cortical-striatal network in old age.

Ren P, Anderson AJ, McDermott K, Baran TM, Lin F

Aging.. 2019 April 1711 (8):2312-2326. Epub 1900 01 01.

Longitudinal Functional Brain Mapping in Supernormals.

Wang X, Ren P, Baran TM, Raizada RDS, Mapstone M, Lin F,

Cerebral cortex.. 2019 January 129 (1):242-252. Epub 1900 01 01.

Non-invasive monitoring of alternative splicing outcomes to identify candidate therapies for myotonic dystrophy type 1.

Hu N, Antoury L, Baran TM, Mitra S, Bennett CF, Rigo F, Foster TH, Wheeler TM

Nature communications.. 2018 December 79 (1):5227. Epub 12/07/2018.

Risk of Pulmonary Embolism in Patients With Isolated Great Saphenous Vein Thrombus.

Gupta A, Pandya V, Baran T, Dogra VS

Ultrasound quarterly.. 2018 September 34 (3):167-169. Epub 1900 01 01.

Quantification of light-induced miniSOG superoxide production using the selective marker, 2-hydroxyethidium.

Barnett ME, Baran TM, Foster TH, Wojtovich AP

Free radical biology & medicine.. 2018 February 20116 :134-140. Epub 01/31/2018.

Photofrin® photodynamic therapy with intratumor photosensitizer injection provides similar tumor response while reducing systemic skin photosensitivity: Pilot murine study

Baran TM.

Lasers in Surgery and Medicine. 2018; 50(5): 476-482.

Amyloid and FDG PET of Successful Cognitive Aging: Global and Cingulate-Specific Differences.

Baran TM, Lin FV,

Journal of Alzheimer's disease : JAD.. 2018 66 (1):307-318. Epub 1900 01 01.

Long-Term Patency of Arteriovenous Fistulae Salvaged by Balloon Angioplasty with and without Accessory Vein Embolization: A Retrospective Study.

Sawas A, Baran TM, Foster TH, Reis J, Wing RE, Kashyap R, Brhel D, Sasson T

Journal of vascular and interventional radiology : JVIR.. 2017 May 28 (5):714-721. Epub 02/09/2017.

The cingulate cortex of older adults with excellent memory capacity

Lin, F; Ren, P; Mapstone, M; Meyers, SP; Porsteinsson, A; Baran, TM.

Cortex. 2017; 86: 83-92.

Identification of Left Ventricle Failure on Pulmonary Artery CTA: Diagnostic Significance of Decreased Aortic & Left Ventricle Enhancement

Chaturvedi, A; Thompson, JP; Kaproth-Joslin, K; Hobbs, SK; Schwarz, KQ; Krishnamoorthy, VK; Chaturvedi, A; Baran, TM.

Emergency Radiology. 2017; 24(5): 487–496.

Recovery of optical properties using interstitial cylindrical diffusers as source and detector fibers.

Baran TM

Journal of biomedical optics.. 2016 July 121 (7):77001. Epub 1900 01 01.

Indwelling Stent Embedded with Light-Emitting Diodes for Photodynamic Therapy of Malignant Biliary Obstruction.

Baran TM, Mironov O, Sharma AK, Foster TH

Cardiovascular and interventional radiology.. 2016 June 39 (6):916-9. Epub 11/19/2015.

Insula and Inferior Frontal Gyrus' Activities Protect Memory Performance Against Alzheimer's Disease Pathology in Old Age

Lin, F; Ren, P; Lo, RY; Chapman, BP; Jacobs, A; Baran, TM; Porsteinsson, AP; Foxe, JJ.

Journal of Alzheimer's Disease. 2016; 55(2): 669-678.

Horizontal long axis imaging plane for evaluation of right ventricular function on cardiac magnetic resonance imaging

Chaturvedi, A.; Whitnah, J.; Maki, J.H.; Baran, T.M.; Mitsumori, L.M.

Journal of Clinical Imaging Science. 2016; 6: 52.

Cylindrical diffuser axial detection profile is dependent on fiber design.

Baran TM

Journal of biomedical optics.. 2015 April 20 (4):040502. Epub 1900 01 01.

Comparison of flat cleaved and cylindrical diffusing fibers as treatment sources for interstitial photodynamic therapy.

Baran TM, Foster TH

Medical physics.. 2014 February 41 (2):022701. Epub 1900 01 01.

Recovery of intrinsic fluorescence from single-point interstitial measurements for quantification of doxorubicin concentration.

Baran TM, Foster TH

Lasers in surgery and medicine.. 2013 October 45 (8):542-50. Epub 08/23/2013.

Determination of optical properties by interstitial white light spectroscopy using a custom fiber optic probe.

Baran TM, Fenn MC, Foster TH

Journal of biomedical optics.. 2013 October 18 (10):107007. Epub 1900 01 01.

Optical property measurements establish the feasibility of photodynamic therapy as a minimally invasive intervention for tumors of the kidney.

Baran TM, Wilson JD, Mitra S, Yao JL, Messing EM, Waldman DL, Foster TH

Journal of biomedical optics.. 2012 September 17 (9):98002-1. Epub 1900 01 01.

Fluence rate-dependent photobleaching of intratumorally administered Pc 4 does not predict tumor growth delay.

Baran TM, Foster TH

Photochemistry and photobiology.. 2012 88 (5):1273-9. Epub 06/06/2012.

New Monte Carlo model of cylindrical diffusing fibers illustrates axially heterogeneous fluorescence detection: simulation and experimental validation.

Baran TM, Foster TH

Journal of biomedical optics.. 2011 August 16 (8):085003. Epub 1900 01 01.

Factors influencing tumor response to photodynamic therapy sensitized by intratumor administration of methylene blue.

Baran TM, Giesselman BR, Hu R, Biel MA, Foster TH

Lasers in surgery and medicine.. 2010 October 42 (8):728-35. Epub 1900 01 01.