Shikhar Uttam

  • Strassburg, C., Pitlor, D., Singhi, A.D., Gottschalk, R.A., & Uttam, S. (2026). MitoChontrol: Adaptive mitochondrial filtering for robust single-cell RNA sequencing quality control. bioRxiv, 2026.04.04.716517.Cold Spring Harbor Laboratory. doi: 10.64898/2026.04.04.716517.
  • Kochetov, B., & Uttam, S. (2025). Local mean suppression filter for effective background identification in fluorescence images. Comput Biol Med, 192(Pt B), 110296.Elsevier. doi: 10.1016/j.compbiomed.2025.110296.
  • Noceda, M.G., Kher, G., Uttam, S., & Barton, J.P. (2025). Clonal heterogeneity and antigenic stimulation shape persistence of the latent reservoir of HIV. In Ribeiro, R.M. (Ed.). PLoS Comput Biol, 21(9), e1013433.Public Library of Science (PLoS). doi: 10.1371/journal.pcbi.1013433.
  • Raphael, I., Xiong, Z., Sneiderman, C.T., Raphael, R.A., Mash, M., Schwegman, L., Jackson, S.A., O'Brien, C., Anderson, K.J., Sever, R.E., Hendrikse, L.D., Vincze, S.R., Diaz, A., Felker, J., Nazarian, J., Nechemia-Arbely, Y., Hu, B., Kammula, U.S., Agnihotri, S., Rich, J.N., Broniscer, A., Drappatz, J., Abel, T.J., Uttam, S., Hwang, E.I., Pearce, T.M., Taylor, M.D., Nisnboym, M., Forsthuber, T.G., Pollack, I.F., Chikina, M., Rajasundaram, D., & Kohanbash, G. (2025). The T cell receptor landscape of childhood brain tumors. Sci Transl Med, 17(790), eadp0675.American Association for the Advancement of Science (AAAS). doi: 10.1126/scitranslmed.adp0675.
  • Kochetov, B., Bell, P., Garcia, P.S., Shalaby, A.S., Raphael, R., Raymond, B., Leibowitz, B.J., Schoedel, K., Brand, R.M., Brand, R.E., Yu, J., Zhang, L., Diergaarde, B., Schoen, R.E., Singhi, A., & Uttam, S. (2024). UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples. bioRxiv, 2023.11.13.566842.Cold Spring Harbor Laboratory. doi: 10.1101/2023.11.13.566842.
  • Kochetov, B., Bell, P.D., Garcia, P.S., Shalaby, A.S., Raphael, R., Raymond, B., Leibowitz, B.J., Schoedel, K., Brand, R.M., Brand, R.E., Yu, J., Zhang, L., Diergaarde, B., Schoen, R.E., Singhi, A., & Uttam, S. (2024). UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples. Commun Biol, 7(1), 1062.Springer Nature. doi: 10.1038/s42003-024-06714-4.
  • Liu, Y., & Uttam, S. (2024). Perspective on quantitative phase imaging to improve precision cancer medicine. J Biomed Opt, 29(Suppl 2), S22705.SPIE, the international society for optics and photonics. doi: 10.1117/1.JBO.29.S2.S22705.
  • Muoio, D., Laspata, N., Dannenberg, R.L., Curry, C., Darkoa-Larbi, S., Hedglin, M., Uttam, S., & Fouquerel, E. (2024). PARP2 promotes Break Induced Replication-mediated telomere fragility in response to replication stress. Nat Commun, 15(1), 2857.Springer Nature. doi: 10.1038/s41467-024-47222-7.
  • Brand, R.M., Dudley, B., Karloski, E., Zyhowski, A., Raphael, R., Pitlor, D., Metter, E.J., Pai, R., Lee, K., Brand, R.E., & Uttam, S. (2023). Immune microenvironment profiling of normal appearing colorectal mucosa biopsied over repeat patient visits reproducibly separates lynch syndrome patients based on their history of colon cancer. Front Oncol, 13, 1174831.Frontiers. doi: 10.3389/fonc.2023.1174831.
  • Brand, R.M., Pitlor, D., Metter, E.J., Dudley, B., Karloski, E., Zyhowski, A., Brand, R.E., & Uttam, S. (2023). rxCOV is a quantitative metric for assessing immunoassay analyte fidelity. Sci Rep, 13(1), 88.Springer Nature. doi: 10.1038/s41598-022-27309-1.
  • Uttam, S., Hashash, J.G., LaFace, J., Binion, D., Regueiro, M., Hartman, D.J., Brand, R.E., & Liu, Y. (2023). Data from Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. doi: 10.1158/1940-6207.c.6547369.v1.
  • Uttam, S., Hashash, J.G., LaFace, J., Binion, D., Regueiro, M., Hartman, D.J., Brand, R.E., & Liu, Y. (2023). Supplementary Data from Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. doi: 10.1158/1940-6207.22534066.v1.
  • Uttam, S., Hashash, J.G., LaFace, J., Binion, D., Regueiro, M., Hartman, D.J., Brand, R.E., & Liu, Y. (2023). Data from Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. doi: 10.1158/1940-6207.c.6547369.
  • Uttam, S., Hashash, J.G., LaFace, J., Binion, D., Regueiro, M., Hartman, D.J., Brand, R.E., & Liu, Y. (2023). Supplementary Data from Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. doi: 10.1158/1940-6207.22534066.
  • Das, R., McGrath, K., Seiser, N., Smith, K., Uttam, S., Brand, R.E., Fasanella, K.E., Khalid, A., Chennat, J.S., Sarkaria, S., Singh, H., Slivka, A., Zeh, H.J., Zureikat, A.H., Hogg, M.E., Lee, K.K., Paniccia, A., Ongchin, M.C., Pingpank, J.F., Boone, B.A., Dasyam, A.K., Bahary, N., Gorantla, V.C., Rhee, J.C., Thomas, R., Ellsworth, S., Landau, M.S., Ohori, N.P., Henn, P., Shyu, S., Theisen, B.K., & Singhi, A.D. (2022). Tumor Size Differences Between Preoperative Endoscopic Ultrasound and Postoperative Pathology for Neoadjuvant-Treated Pancreatic Ductal Adenocarcinoma Predict Patient Outcome. Clin Gastroenterol Hepatol, 20(4), 886-897.Elsevier. doi: 10.1016/j.cgh.2020.11.041.
  • Thota, P.N., Nasibli, J., Kumar, P., Sanaka, M.R., Chak, A., Zhang, X., Liu, X., Uttam, S., & Liu, Y. (2022). Prediction of neoplastic progression in Barrett's esophagus using nanoscale nuclear architecture mapping: a pilot study. Gastrointest Endosc, 95(6), 1239-1246.Elsevier. doi: 10.1016/j.gie.2022.01.007.
  • Brand, R.M., Moore, B.A., Zyhowski, A., Siegel, A., Uttam, S., Metter, E.J., Engstrom, J., Brand, R.E., Biswas, N., Whitcomb, D.C., Binion, D.G., Schwartz, M., & McGowan, I. (2021). Tofacitinib inhibits inflammatory cytokines from ulcerative colitis and healthy mucosal explants and is associated with pSTAT1/3 reduction in T-cells. Am J Physiol Gastrointest Liver Physiol, 320(3), G396-G410.American Physiological Society. doi: 10.1152/ajpgi.00383.2020.
  • Furman, S.A., Stern, A.M., Uttam, S., Taylor, D.L., Pullara, F., & Chennubhotla, S.C. (2021). In situ functional cell phenotyping reveals microdomain networks in colorectal cancer recurrence. Cell Rep Methods, 1(5).Elsevier. doi: 10.1016/j.crmeth.2021.100072.
  • Uttam, S., Stern, A.M., Sevinsky, C.J., Furman, S., Pullara, F., Spagnolo, D., Nguyen, L., Gough, A., Ginty, F., Lansing Taylor, D., & Chakra Chennubhotla, S. (2020). Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks. Nat Commun, 11(1), 3515.Springer Nature. doi: 10.1038/s41467-020-17083-x.
  • Fouquerel, E., Barnes, R.P., Uttam, S., Watkins, S.C., Bruchez, M.P., & Opresko, P.L. (2019). Targeted and Persistent 8-Oxoguanine Base Damage at Telomeres Promotes Telomere Loss and Crisis. Mol Cell, 75(1), 117-130.e6.Elsevier. doi: 10.1016/j.molcel.2019.04.024.
  • Uttam, S., Hashash, J.G., LaFace, J., Binion, D., Regueiro, M., Hartman, D.J., Brand, R.E., & Liu, Y. (2019). Three-Dimensional Nanoscale Nuclear Architecture Mapping of Rectal Biopsies Detects Colorectal Neoplasia in Patients with Inflammatory Bowel Disease. Cancer Prev Res (Phila), 12(8), 527-538.American Association for Cancer Research (AACR). doi: 10.1158/1940-6207.CAPR-19-0024.
  • Uttam, S., Stern, A.M., Furman, S., Pullara, F., Spagnolo, D., Nguyen, L., Gough, A., Sevinsky, C.J., Ginty, F., Taylor, D.L., & Chennubhotla, S.C. (2019). Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks. In bioRxiv. doi: 10.1101/635730.
  • Uttam, S., & Liu, Y. (2018). Fourier phase based depth-resolved nanoscale nuclear architecture mapping for cancer detection. Methods, 136, 134-151.Elsevier. doi: 10.1016/j.ymeth.2017.10.011.
  • Xu, J., Ma, H., Jin, J., Uttam, S., Fu, R., Huang, Y., & Liu, Y. (2018). Super-Resolution Imaging of Higher-Order Chromatin Structures at Different Epigenomic States in Single Mammalian Cells. Cell Rep, 24(4), 873-882.Elsevier. doi: 10.1016/j.celrep.2018.06.085.
  • Uttam, S., & Liu, Y. (2015). Fourier phase in Fourier-domain optical coherence tomography. J Opt Soc Am A Opt Image Sci Vis, 32(12), 2286-2306.Optica Publishing Group. doi: 10.1364/JOSAA.32.002286.
  • Uttam, S., Pham, H.V., LaFace, J., Leibowitz, B., Yu, J., Brand, R.E., Hartman, D.J., & Liu, Y. (2015). Early Prediction of Cancer Progression by Depth-Resolved Nanoscale Mapping of Nuclear Architecture from Unstained Tissue Specimens. Cancer Res, 75(22), 4718-4727.American Association for Cancer Research (AACR). doi: 10.1158/0008-5472.CAN-15-1274.
  • Hartman, D.J., Krasinskas, A.M., Uttam, S., Staton, K., Bista, R., I Ilyas, S., Slivka, A., Brand, R., & Liu, Y. (2014). Assessment of nuclear nanomorphology marker to improve the detection of malignancy from bile duct biopsy specimens. Am J Clin Pathol, 141(6), 884-891.Oxford University Press (OUP). doi: 10.1309/AJCPXQD0NSJNK0CX.
  • Liu, Y., Uttam, S., Alexandrov, S., & Bista, R.K. (2014). Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer. BMC Biophys, 7(1), 1.Springer Nature. doi: 10.1186/2046-1682-7-1.
  • Fasanella, K.E., Bista, R.K., Staton, K., Rizvi, S., Uttam, S., Zhao, C., Sepulveda, A., Brand, R.E., McGrath, K., & Liu, Y. (2013). Nuclear Nano-architecture Markers of Gastric Cardia and Upper Squamous Esophagus Detect Esophageal Cancer "Field Effect". J Cancer, 4(8), 626-634.Ivyspring International Publisher. doi: 10.7150/jca.6990.
  • Uttam, S., Alexandrov, S.A., Bista, R.K., & Liu, Y. (2013). Tomographic imaging via spectral encoding of spatial frequency. Opt Express, 21(6), 7488-7504.Optica Publishing Group. doi: 10.1364/OE.21.007488.
  • Uttam, S., Bista, R.K., Staton, K., Alexandrov, S., Choi, S., Bakkenist, C.J., Hartman, D.J., Brand, R.E., & Liu, Y. (2013). Erratum: Investigation of depth-resolved nanoscale structural changes in regulated cell proliferation and chromatin decondensation: erratum. Biomed Opt Express, 4(11), 2491.Optica Publishing Group. doi: 10.1364/BOE.4.002491.
  • Alexandrov, S.A., Uttam, S., Bista, R.K., Staton, K., & Liu, Y. (2012). Spectral encoding of spatial frequency approach for characterization of nanoscale structures. Appl Phys Lett, 101(3), 33702.AIP Publishing. doi: 10.1063/1.4737209.
  • Alexandrov, S.A., Uttam, S., Bista, R.K., Zhao, C., & Liu, Y. (2012). Real-time quantitative visualization of 3D structural information. Opt Express, 20(8), 9203-9214.Optica Publishing Group. doi: 10.1364/OE.20.009203.
  • Bista, R.K., Uttam, S., Hartman, D.J., Qiu, W., Yu, J., Zhang, L., Brand, R.E., & Liu, Y. (2012). Investigation of nuclear nano-morphology marker as a biomarker for cancer risk assessment using a mouse model. J Biomed Opt, 17(6), 066014.SPIE, the international society for optics and photonics. doi: 10.1117/1.JBO.17.6.066014.
  • Bista, R.K., Wang, P., Bhargava, R., Uttam, S., Hartman, D.J., Brand, R.E., & Liu, Y. (2012). Nuclear nano-morphology markers of histologically normal cells detect the "field effect" of breast cancer. Breast Cancer Res Treat, 135(1), 115-124.Springer Nature. doi: 10.1007/s10549-012-2125-2.
  • Uttam, S., Goodman, N.A., & Neifeld, M.A. (2012). Feature-specific difference imaging. IEEE Trans Image Process, 21(2), 638-652.Institute of Electrical and Electronics Engineers (IEEE). doi: 10.1109/TIP.2011.2165549.
  • Alexandrov, S.A., Uttam, S., Bista, R.K., & Liu, Y. (2011). Spectral contrast imaging microscopy. Opt Lett, 36(17), 3323-3325.Optica Publishing Group. doi: 10.1364/OL.36.003323.
  • Bista, R.K., Uttam, S., Wang, P., Staton, K., Choi, S., Bakkenist, C.J., Hartman, D.J., Brand, R.E., & Liu, Y. (2011). Quantification of nanoscale nuclear refractive index changes during the cell cycle. J Biomed Opt, 16(7), 070503.SPIE, the international society for optics and photonics. doi: 10.1117/1.3597723.
  • Uttam, S., Bista, R.K., Hartman, D.J., Brand, R.E., & Liu, Y. (2011). Correction of stain variations in nuclear refractive index of clinical histology specimens. J Biomed Opt, 16(11), 116013.SPIE, the international society for optics and photonics. doi: 10.1117/1.3650306.
  • Wang, P., Bista, R.K., Khalbuss, W.E., Qiu, W., Uttam, S., Staton, K., Zhang, L., Brentnall, T.A., Brand, R.E., & Liu, Y. (2010). Nanoscale nuclear architecture for cancer diagnosis beyond pathology via spatial-domain low-coherence quantitative phase microscopy. J Biomed Opt, 15(6), 066028.SPIE, the international society for optics and photonics. doi: 10.1117/1.3523618.
  • Uttam, S., Goodman, N.A., Neifeld, M.A., Kim, C., John, R., Kim, J., & Brady, D. (2009). Optically multiplexed imaging with superposition space tracking. Opt Express, 17(3), 1691-1713.Optica Publishing Group. doi: 10.1364/oe.17.001691.

  • Jacob, T., Soong, T.R., & Uttam, S. (2026). Graph theoretic spatial heterogeneity analysis of multiplexed immunofluorescence images enables quantitative differentiation of HGSC precursor lesions in the fallopian tube. In CANCER RESEARCH, 86(7).American Association for Cancer Research (AACR). doi: 10.1158/1538-7445.AM2026-4154.
Research Interests
Oncology and carcinogenesis Atomic, molecular and optical physics
headshot of Shikhar Uttam
Contact Shikhar Uttam
Assistant Professor
Bioengineering Department
shf28@pitt.edu