Research Faculty


Research Faculty
Mary H. Cheng
412-648-9614
hoc2@pitt.edu
Office: 3070 BST3
Lab Website
Mary H. Cheng, PhD - Research Assistant Professor
Ph.D. Chemical Engineering, Rensselaer Polytechnic Institute
I have modeling experience in a wide range of ion channels/transporters, including several types of sodium coupled neurotransmitter transporters, neurotransmitter-gated ion channels, voltage-gated ion channels/transporters, and gape junction Claudin-2. My research interest and expertise lie in protein modeling and medicinal chemistry, focusing on molecular mechanisms of i) transporter functions, i.e., transporter cycle; ii) ion transport through membrane protein channels, i.e. channel conductance and charge selectivity; iii) drug modulation of protein receptors, i.e. ligand binding sites and binding affinity; and iv) protein-lipid and lipid-lipid interactions. I am particularly interested in development/implement of multi-scale modeling technology to investigate biological systems at both molecular and cellular levels. I developed a hybrid molecular dynamics/Brownian dynamics methodology that can be applied to investigate ion permeation through membrane protein channels.
Cheng MH, Torres-Salazar D, Gonzalez-Suarez AD, Amara SG, Bahar I (2017) Substrate Transport and Anion Permeation Proceed through Distinct Pathways in Glutamate Transporters. ELife. 6: e25850

Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I (2017) Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization. J Biol Chem. 292: 12471-12482

Albert Gough
412-383-5915
gough@pitt.edu
Office: BST3
Lab Website
Albert Gough, PhD - Research Associate Professor
Ph.D. in Biology/Biophysics, Carnegie Mellon University
My research is focused on relating in vitro cellular systems models to in vivo biological functions. Using automated high content imaging systems we are able to create cellular models with readouts that indicate a wide range of cellular functions. Alterations in function at the tissue, organ and organism level, should be related to alterations in cellular functions. However, the interactions and heterogeneity at the cellular level complicates that relationship. Presently we are building a cellular model in which to analyze cancer pathway interactions and heterogeneity. The goal is to provide an approach to developing therapies that address the heterogeneity of biological systems.
Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes M, Himmelfarb J, Truskey G, Wikswo JP, Taylor DL (2017) Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci Rep. 7: 42296

Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla SC, Schurdak ME, Haney SA, Taylor DL (2017) Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS Discov.. (3): 213-237

Bing Liu
412-648-7775
liubing@pitt.edu
Office: 3085 BST3
Lab Website
Bing Liu, PhD - Research Assistant Professor
Ph.D. in Computational Systems Biology, National U of Singapore
Computational modeling and analysis of the dynamics of biological systems; development of high-performance computing, formal verification, and machine learning techniques for systems biology.
Liu B, Oltvai ZN, Bayir H, Silverman G, Pak S, Perlmutter D, Bahar I (2017) Quantitative Assessment Of Cell Fate Decision Between Autophagy And Apoptosis bioRxiv. 129767: doi:10.1101/129767

Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, Croix CS, Dar H, Liu B, Tyurin VA, Ritov VB, Kapralov OA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli R, Stockwell BR, Tyurina YY, Conrad M, Bayir H (2017) Oxidized Arachidonic and Adrenic PEs Navigate Cells to Ferroptosis Nature Chemical Biology. 13: 81-90

Mark T. Miedel
412-383-9893
mmiedel@pitt.edu
Office: W904 BST
Lab Website
Mark T. Miedel, PhD - Research Assistant Professor
PhD in Cell Biology and Physiology, University of Pittsburgh School of Medicine
Identifying the mechanisms that cause resistance in ER ligand binding domain mutants, and to use this information to develop novel therapeutic strategies for the treatment of endocrine-resistant metastatic breast cancer.
Shanhang J, Miedel MT, Ngo M, Hessenius R, Wang P, Bahreini A, Li Z, Ding Z, Chen N, Shun TY, Zuckerman DM, Taylor DL, Puhalla SL, Lee AV, Oesterreich S, Stern AM (2017) Clinically observed estrogen receptor alpha mutations within the ligand-binding domain confer distinguishable phenotypes indicative of Darwinian-like somatic evolution Oncology.

Shi S, Luke CJ, Miedel MT, Silverman GA, Kleyman TR (2016) Activation of the Caenorhabditis elegans degenerin channel by shear stress requires the MEC-10 subunit. Journal of Biological Chemistry. 291(27): 14012-22

Mark E. Schurdak
412-648-3090
mes234@pitt.edu
Office: 10045 BST3
Lab Website
Mark E. Schurdak, PhD - Visiting Research Associate Professor
Ph.D. in Pharmacology, Baylor College of Medicine
My research interests center on applying a systems biology/pharmacology approach to develop more effective drug discovery strategies that utilize integrated phenotype/function-based analysis (where all targets involved are functioning in a more physiologic relevant environment) and to better understand the molecular mechanisms that cause drugs to succeed or fail in the clinic.
Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla SC, Schurdak ME, Haney SA, Taylor DL (2017) Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS Discov.. (3): 213-237

DAiuto L, Zhi Y, KumarDas D, Wilcox MR, Johnson JW, McClain L, MacDonald ML, DiMaio R, Schurdak ME, Piazza P, Viggiano L, Sweet R, Kinchington PR, Bhattacharjee AG, Yolken R, Nimgaonka VL (2014) Large-scale generation of human iPSC-derived neural stem cells/early neural progenitor cells and their neuronal differentiation ORGANOGENESIS. 10: 365-377

Indira Shrivastava
412-383-5806
ihs2@pitt.edu
Office: 3089 BST3
Lab Website
Indira Shrivastava, PhD - Research Assistant Professor
Ph.D. University of Pune, Chemistry
Research Interests: I am interested in analyzing the functional dynamics of biomolecular complexes, molecular modeling and simulation approaches. The computational models I employ include: elastic network models (ANM/GNM), Molecular Dynamics (MD) simulations, and Quantum chemical (QM) calculations. The aim is to analyze the 3-D structure of the protein and its interactions with ligands and/or environment, as a function of space and time. I am also interested in harnessing allosteric properties of protein in identifying potential binding sites in targets and potential leads for drug-discovery.
Gasanov SE, Shrivastava IH, Israilov FS, Kim AA, Rylova KA, Zhang B, Dagda RK (2015) Naja naja oxiana Cobra Venom Cytotoxins CTI and CTII Disrupt Mitochondrial Membrane Integrity: Implications for Basic Three-Fingered Cytotoxins PLoS One. 10(6): e0129248

Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Wang KZQ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayir H, Kagan VE (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells Nature Cell Biology. 15: 1197-1205

Andrew M. Stern
412-648-9897
Sternam@pitt.edu
Office: 10048 BST3
Lab Website
Andrew M. Stern, PhD - Visiting Research Associate Professor
Ph.D. in Biological Chemistry, University of California at Los Angeles
The overarching goal of our research is to identify mechanisms involved in complex human disease progression and use this knowledge to develop novel therapies for individual patients. We apply a holistic clinically relevant quantitative systems biology and pharmacology approach. This involves the development, implementation, and integration of several high throughput and high content molecular and cell-based technologies and models to comprehensively define fundamental biological processes that are perturbed in particular diseases.
Bahreini A, Li Z, Wang P, Levine KM, Tasdemir N, Cao L, Weir HM, Puhalla SL, Davidson NE, Stern AM, Chu D, Park BH, Lee AV, Oesterreich S (2017) Mutation site and context dependent effects of ESR1 mutation in genome-edited breast cancer cell models. Breast Cancer Res. 19(1): 60

Gough A, Stern AM, Maier J, Lezon T, Shun TY, Chennubhotla SC, Schurdak ME, Haney SA, Taylor DL (2017) Biologically Relevant Heterogeneity: Metrics and Practical Insights. SLAS Discov.. (3): 213-237

Shikhar Uttam
412-383-7475
shf28@pitt.edu
Office: 3071 BST3
Lab Website
Shikhar Uttam, PhD - Research Assistant Professor
Ph.D. Electrical Engineering (Minor: Mathematics) The University of Arizona, Tucson
My research has two broad themes: 1. Cancer prognosis and prediction; 2. Development of new computational imaging, optical, and machine learning approaches. Within cancer research my focus has been on cancer prognosis in colorectal, breast, and esophageal disease models, where I have used computational imaging and physical optics to characterize alterations in precancerous cells with nanoscale sensitivity. Recently, my research scope has expanded to include understanding the tumor micro environment and its role in cancer progression and recurrence. This work focuses on machine learning approaches applied to multiplexed fluorescence imaging of tumor bio-markers to characterize and model the effect of tumor heterogeneity on cancer progression.
Uttam S, Pham HV, LaFace J, Leibowitz B, Yu J, Brand RE, Hartman DJ, Liu Y (2015) Early prediction of cancer progression by depth-resolved nanoscale mapping of nuclear architecture from unstained tissue specimens Cancer Res. 75: 4718-4727

Uttam S, Liu Y (2015) Fourier phase in Fourier-domain optical coherence tomography J. Opt. Soc. Am. A. 32: 2286-2306

Larry Vernetti
412-383-5856
vernetti@pitt.edu
Office: BST3
Lab Website
Larry Vernetti, PhD - Research Associate Professor
Ph.D. in Toxicology, University of Arizona
The focus of my research is developing early in vitro safety assessment and in vitro ADME models to identify risky compound candidates and allowing the drug developer to focus on fewer but more likely to succeed candidates. An important part of this research is the identification of the molecular mechanism of toxicity (MOA) within the cell, and then understanding how this can be used to predict target organ toxicity. The need for such an application is clear just by considering liver toxicity as an example. Despite decades of extensive animal testing, only half of the pharmaceutics which eventually produced clinical liver toxicity showed evidence of liver damage during animal trials. Bridging this gap is a necessary step forward to developing safer and effective drugs.
Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes M, Himmelfarb J, Truskey G, Wikswo JP, Taylor DL (2017) Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci Rep. 7: 42296

Vernetti L, Gough A, Baetz N, Blutt S, Broughman JR, Brown JA, Foulke-Abel J, Hasan N, In J, Kelly E, Kovbasnjuk O, Repper J, Senutovitch N, Stabb J, Yeung C, Zachos NC, Donowitz M, Estes M, Himmelfarb J, Truskey G, Wikswo JP, Taylor DL (2017) Corrigendum: Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci Rep. 7: 44517