Joint/Adjunct Faculty

bar-joseph (2)Lab Website
Ziv Bar-Joseph – Assist Professor, Carnegie Mellon University, Dept. of Computer Science
Ph.D., Computer Science, Massachusetts Institute of Technology
Our group develops computational methods for understanding the dynamics, interactions and conservation of complex biological systems. As new high-throughput biological data sources become available, they hold the promise of revolutionizing molecular biology by providing a large-scale view of cellular activity. However, each type of data is noisy, contains many missing values and only measures a single aspect of cellular activity. Our computational focus is on methods for large scale data integration. We primarily rely on machine learning and statistical methods. Most of our work is carried out in close collaboration with experimentalists. Many computational tools we develop are available and widely used.

Navlakha and Z. Bar-Joseph. “Distributed information processing in biological and computational systems.” Communications of the ACM (CACM), 58 (1), Pages 94-102, 2015.

Navlakha, C. Faloutsos and Z. Bar-Joseph. “MASSEXODUS: Modeling evolving networks in adversarial environments.” Data Mining and Knowledge Discovery (DAMI),” to appear, 2015

Lab Website
Jaime Carbonell – Professor, Carnegie Mellon University Dept. of Computer Science
PhD, MPhil, MS, Computer Science, Yale University
Context-Based Machine Translation, Example-Based Machine Translation, Machine Learning in Computational Proteomics, Active and Proactive Machine Learning, Machine Learning and Language Technologies in Biomedicine (e.g. Optimizing HIV Therapy), Wind Energy Optimization.

Wei-Yu, A. Kılınç-Karzan, F., and Carbonell, J.,
“Saddle Points and Accelerated Perceptron Algorithms”, of International Conference on Machine Learning (ICML), Beijing, 2014.

Flanigan, J., Thomson, S., Carbonell, J., Dyer, C., and Smith, N.,
“A Discriminative Graph-Based Parser for the Abstract Meaning Representation” In  Proc, of the Association for Computational Linguistics Conference (ACL), Baltimore, 2014. (Best paper honorable mention).

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Lillian T. Chong – Assistant Professor, University of Pittsburgh, Dept. of Chemistry
Ph.D., University of California at San Francisco
Development of weighted ensemble approaches for sampling “rare”, but fast events (e.g. protein folding, binding, or switching) with rigorous kinetics. Simulation of protein binding pathways and kinetics. Development of simulation approaches with various levels of coarse-graining to aid the design of protein conformational switches.

Debiec, K. T.; Gronenborn, A. M; and Chong, L. T. “Evaluating the strength of salt bridges – a comparison of current bimolecular force fields.” Phys. Chem. B, Vol. 118, Pages 6561-6569, 2014.

Suarez, E.; Lettieri, S.; Zwier, M. C.; Stringer, C. A.; Subramanian, S. R.; Chong, L. T and Zuckerman, D. M. “Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories,” Chem. Theory Comput., Vol. 10, Pages 2658-2667, 2014.

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Gregory F. Cooper – Associate Professor of Medicine and of Intelligent Systems
PhD, Medical Information Science, MD, Medicine, Stanford University
His research interest is in the application of decision theory, probability theory, and artificial intelligence to address biomedical informatics research questions, with a focus on causal modeling and discovery in medicine and biology, data mining of medical databases, application of Bayesian statistics in medicine, and biosurveillance.

Villamarin R, Cooper G, Wagner M, Tsui FC, Espino JU., “A method for estimating from thermometer sales the incidence of diseases that are symptomatically similar to influenza,” Journal of Biomedical Informatics 46 (2013) 444-457. PMID: 23501015

Hauskrecht M, Batal I, Valko M, Visweswaran S, Cooper GF, Clermont G., “Outlier-detection for patient monitoring and alerting,” Journal of Biomedical Informatics 46 (2013) 47-55. PMID: 22944172. PMCID: PMC3567774

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Lance Davidson – Associate Professor, Department of Bioengineering, Swanson School of Engineering
Ph.D., Biophysics, University of California at Berkeley
To integrate the biomechanics of morphogenesis across a number of size scales from subcellular generation of forces to the macroscopic forces and bulk tissue properties that guide development of the developing embryo. We want to understand, in mechanical terms, how coordinated polarized cell protrusions generate force, and how these forces are converted into tissue-scale movements.

Zhou J, Pal S, Maiti S, Davidson LA., “Force production and mechanical accommodation during convergent extension,” 2015 Feb 15; 142(4):692-701. Doi: 10.1242/dev.116533. PMID: 25670794

McGreevy EM, Vijayraghavan D, Davidson LA, Hildebrand JD., “Shroom3 functions downstream of planar cell polarity to regulate myosin II distribution and cellular organization during neural tube closure,” Biol Open. 2015 Jan 16;4(2);186-96. Doi:10.1242/bio.20149589. PMID: 25596276

Lab Website
Alexander Dömling – Professor and Chair of Drug Design, University of Groningen, Netherlands
Ph.D., Multicomponent Reaction Chemistry, Technical University of Munich
Our team focusses on issues in computational chemistry and drug discovery. Particularly interesting topics for us are : The study of novel mdm2/mdmx inhibitors; Drug discovery projects on various targets; Method development for new MCR scaffolds; High throughput methods development for drug discovery purpose.

Patil P, Khoury K, Herdtweck E, Domling A., “MCR synthesis of a tetracyclic tetrazole scaffold,” Bioorg Med Chem. 2014 Dec 20. Pii: S0968-0896(14)00869-4. Doi:10.1016/j.bmc.2014.12.021.

Patil P, Khoury K, Herdtweck E, Domling A., “A universal isocyanide for diverse heterocycle syntheses,” Org Lett. 2014 Nov 7;16(21):5736-9.

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G. Bard Ermentrout – Professor, University of Pittsburgh, Dept. of Mathematics
Ph.D., Biophysics, University of Chicago
Dr. Ermentrout’s research program investigates models of neural and muscle physiology. His recent focus has been on the behavior of networks of cortical-like neurons. He is interested in the dynamics of wave propagation in cortical and thalamic slice models, the olfactory lobe of the Limax, and the synchronization of cortical networks, in addition to spatial and temporal patterns in neuronal networks such as those observed during flicker stimulation and localized patterns of working memory. He also studies the effects of various ionic current and synaptic plasticity on the interactions between neural oscillators. He is the author of XPPAUT, a software platform for the simulation and analysis of nonlinear dynamical systems.

Guillermo Gonzalez-Burgos, Takeaki Miyamae, Diego E Pafundo, Hiroki Yoshino, Diana C Rotaru, Gil Hoftman, Dibyadeep Datta, Yun Zhang, Mahjub Hammond, Allan R Sampson, Kenneth N Fish, G Bard Ermentrout, David A Lewis, “Functional maturation of GABA synapses during postnatal development of the monkey dorsolateral prefrontal cortex,” Cerebral Cortex 06/2014; 8.31 Impact Factor.

Kiyoshi Kotani, Ikuhiro Yamaguchi, Lui Yoshida, Yasuhiko Jimbo, G Bard Ermentrout, “Population dynamics of the modified theta model: macroscopic phase reduction and bifurcation analysis link microscopic neuronal interactions to macroscopic gamma oscillation,” Journal of The Royal Society Interface 03/2014; 11(95):20140058. 3.86 Impact Factor.

GhedinLab Website
Elodie Ghedin – Professor of Biology, Public Health, New York University
Ph.D., Molecular Parasitology, McGill University, Canada
Research in our group is multidisciplinary and draws upon the tools of genomics, molecular virology, and computational biology. The questions we pursue relate to pathogen emergence and adaptation. Some of our projects include 1) determining the extent, structure and underlying mechanisms of genetic variation in influenza A viruses sampled across populations and within individual hosts; 2) metagenomics approaches for the characterization from clinical samples of viruses believed to cause chronic diseases; 3) mapping of the interactome between the nematode filaria worm and its endosymbiontic bacteria Wolbachia; 4) microbiome studies of lung diseases.

Lijia Cui, Lorrie Lucht, Laura Tipton, Matthew B Rogers, Adam Fitch, Cathy Kessinger, Danielle Camp, Lawrence Kingsley, Nicolas Leo, Ruth M Greenblatt, Serena Fong, Stephen Stone, John Dermand, Eric Kleerup, Laurence Huang, Alison Morris, Elodie Ghedin, “Topographical diversity of the respiratory tract mycobiome and alteration in HIV and lung disease,” American Journal of Respiratory and Critical Care Medicine 01/2015; 11.04 Impact Factor.

Frederic Bringaud, Matthew Rogers, Elodie Ghedin, “Identification and analysis of ingi-related retroposons in the trypanosomatid genomes,”
Methods in molecular biology (Clifton, N.J.) 01/2015; 1201:109-22. 1.29 Impact Factor.

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Vanathi Gopalakrishnan – Asst Prof., U. of Pittsburgh, Dept of Biomedical Informatics and Intelligent Systems Program
Ph.D., Computer Science, University of Pittsburgh
We develop and test machine learning and pattern recognition methods for increasing scientific knowledge from biomedical data. We specialize in rule learning algorithms and variants that employ probabilistic scoring for model generation and selection.

Rafael Ceschin, Ashok Panigraphy, Vanathi Gopalakrishnan, “Open-source software for temporal analysis and visualization of brain tumor diffusion MR using serial functional diffusion mapping,” Cancer Informatics 2015:Suppl. 2 1-9.

Balasubramanian JB, Cooper GF, Visweswaran S, Gopalakrishnan V.,
“Selective model averaging with Bayesian rule learning for predictive biomedicine,” Proceedings of the AMIA 2014 Joint Summits in Translational Science (In Press); April 2014; San Francisco, CA, USA2014.

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Graham Hatfull – Eberly Family Professor of Biotechnology, HHMI Professor
Ph.D. University of Edinburgh
Current lab studies: Exploring bacteriophage genomics, Exploiting mycobacteriophages, Site-specific recombination, Tools – Genetic and Clinical

Pope, W. H., Jacobs-Sera, D., Russell, D. A., Rubin, D. H. F., Kajee, A., Msibi, Z. N. P., Larsen, M. H., Jacobs, W. R. Jr., Lawrence, J. G., Hendrix, R. W., & Hatfull, G. F. (2014)., “Genomics and proteomics of mycobacteriophage patience: An accidental tourist in the mycobacterium neighborhood,” mBio pii: e02145-14. Doi: 10.1128/mBio.02145-14.

Hatfull, G. F. (2014)., “Molecular genetics of mycobacteriophages,”
Microbiol Spectr. 2, 1-36.

Lab Website
Naftali Kaminski – Yale U, Boehringer Ingelheim Pharmaceuticals, Inc. Prof of Medicine (Pulmonary); Section Chief
Medical School of Hadassah and the Hebrew University in Jerusalem
Genomics; microRNAs; Non-coding RNAs; Biomarkers; Idiopathic Pulmonary Fibrosis and other Interstitial Lung Disease; Advanced Lung Disease; Personalized Medicine; Systems Biology; High-throughput technologies; Matrix Mtealloproteases

Pandit KV, Corcoran D, Yousef H, Yarlagadda M, Tzouvelekis A, Gibson KF, Konishi K, Yousem SA, Singh M, Handley D, Richards T, Selman M, Watkins SC, Pardo A, Ben-Yehudah A, Bouros D, Eickelberg O, Ray P, Benos PV, Kaminski N.,
Inhibition and role of Let-7d in idiopathic pulmonary fibrosis,”
Am J Respir Crit Care Med. 2010 Apr 15. [Epub ahead of print].

Yousem SA, Gibson K, Kaminski N, Oddis CV, Ascherman DP.,
“The pulmonary histopathologic manifestations of the anti-Jo-1 tRNA synthetase syndrome,”
Mod Pathol. 2010 Jun; 23(6):874-80.

kashlanLab Website
Ossama Kashlan – Research Assistant Professor, University of Pittsburgh, Renal-Electrolyte Division
PhD, University of Pennsylvania
Research interests: Allosteric regulation of ion channels; Regulation of ion channels by proteases; Ion channels selectivity.

Ossama B Kashlan, Brandon M Blobner, Zachary Zuzek, Michael Tolino, Thomas R Kleyman (2014) Na + Inhibits the Epithelial Na + Channel by Binding to a Site in an Extracellular Acidic Cleft Journal of Biological Chemistry 11/2014; 290(1).

David Pearce, Rama Soundararajan, Christiane Trimpert, Ossama B Kashlan, Peter M T Deen, Donald E Kohan (2014) Collecting Duct Principal Cell Transport Processes and Their Regulation Clinical Journal of the American Society of Nephrology 05/2014; 10(1).

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Dennis Kostka – Assistant Professor, U. of Pittsburgh Dept. of Developmental Biology
Ph.D,, Computational Biology, Free University Berlin / Max Planck Institute for Molecular Genetics
Research: How do different organs and tissues arise? What are the genetic and epigenetic mechanisms that drive this development? To address these questions we design statistical methods and algorithms and apply them to large-scale, genome-wide data. Ultimately, our goal is to generate, test, and confirm hypotheses that are relevant to human health.

John A Capra, Dennis Kostka, “Modeling DNA methylation dynamics with approaches from phylogenetics,” Bioinformatics 2014 Sep;30(17):i408-14.

AK Marrone, DB Stolz, SI Bastacky, D Kostka, A Bodnar and J Ho (2014) miR-17~92 is Required for Nephrogenesis and Renal Function.  Journal of the American Society of Nephrology (JASN), 25 (3).

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Maria Kurnikova – Associate Professor, Carnegie Mellon University, Department of Chemistry
Ph.D. Physical Chemistry, University of Pittsburgh
Our research is in the area of theoretical/computational chemistry and biophysics. We are especially interested in developing functional models of membrane proteins, such as ion channels, signaling and regulatory proteins.

Jose C Flores-Canales, Mauricio Vargas-Uribe, Alexey S Ladokhin, Maria Kurnikova, “Membrane association of the diphtheria toxin translocation domain studied by coarse-grained simulations and experiment,” Journal of Membrane Biology 2/2015; 2.48 Impact Factor.
Aysegul Ozkan, Jose C Flores-Canales, Meera Sitharam, Maria Kurnikova, “Fast and flexible geometric method for enhancing MC sampling of compact configurations for protein docking problem,”
08/2014;

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Christopher James Langmead – Carnegie Mellon U, Assist Prof of Computer Science.
Ph.D. in Computer Science, Dartmouth College, 2003
My group has developed a number of computational methods, primarily built on probabilistic graphical models for simulating and designing molecules. Our current work focuses on: non-parametric graphical models of protein dynamics; graphical models of allosteric regulation; graphical models for simulating the emergence of drug resistance-causing mutations; graphical models for designing resistance-evading drugs.
Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg, “Learning sequence determinants of protein: protein interaction specificity with sparse graphical models,”
01/2014;8394:129-143.Christopher James Langmead, “Generative models of conformational dynamics,” Advances in Experimental Medicine and Biology 01/2014;805:87-105. 2.01 Impact Factor.
Lab Website
Miler Lee – University of Pittsburgh, Biological Sciences
Ph.D., Genomics and Computational Biology, University of Pennsylvania
My research addresses how gene expression programs change, leading to changes to cellular identity. In multicellular organisms, the genetic instructions that guide the initial stages of embryonic development are inherited from the egg as RNA. When the embryonic genome becomes active, new RNAs are transcribed, while maternally provided RNAs are destroyed. During this “maternal-to-zygotic transition,” the embryo is effectively reprogrammed from an oocyte identity to pluripotency.
Yartseva V, Takacs CM, Vejnar CE, Lee MT‡, Giraldez AG‡. 2016. RESA identifies mRNA regulatory
sequences with high resolution. In review.
Reischauer S, Stone O, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Fiddes I,
Kuo T, Chung WS, Salek S, Lerrigo R, Alsio J, Luo S, Tworus D, Augustine SA, Mucenieks S, Nystedt B,
Giraldez AJ, Schroth GP, Andersson O, Stainier DY. 2016. Cloche is a bHLH-PAS transcription factor that
drives haemato-vascular specification. Nature 535(7611), 294-8.
Miskov-ZivanovLab Website
Natasa Miskov-Zivanov – Assistant Professor, Electrical and Computer Engineering, University of Pittsburgh
Ph.D., Computer Engineering, Carnegie Mellon University
Dr. Miskov-Zivanov’s research focuses on systems medicine, which represents convergence of (i) systems approach that allows for deep disease mechanism insights, (ii) emerging technologies that lead to large-scale data acquisition and provide means for new treatments, and (iii) analytic tools that can handle the complexity of the disease mechanisms, or billions of data points, and can suggest personalized therapies.

N. Miskov-Zivanov, M. S. Turner, L. P. Kane, P. A. Morel, J. R. Faeder, “The duration of T cell stimulation is a critical determinant of cell fate and plasticity,” in Science Signaling, 6, ra97, November 2013 [link].
N. Miskov-Zivanov and D. Marculescu, “Multiple Transient Faults in Combinational and Sequential Circuits: A Systematic Approach,” in IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), pp. 1614-1627, October 2010 [tcad10.pdf].

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Zoltan Nagy Oltvai – Associate Professor of Pathology and Computational Biology, University of Pittsburgh, School of Medicine
M.D., Semmelweiss Medical School, Budapest, Hungary
Dr. Oltvai’s research interest is in the area of systems biology of cell metabolism, including the metabolism of prokaryotic and mammalian cells, including tumor cells.

Cobanoglu, M. C., Oltvai, Z. N., Taylor, D. L., Bahar, I., “BalestraWeb: Efficient, online evaluation of drug-target interactions,” 2014 Sep 07.

Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I. (2013) Predicting drug-target interactions using probabilistic matrix factorization. J Chem Inf Model. 2013 Dec 23;53(12):3399-409. doi: 10.1021/ci400219z. Epub 2013 Dec 10.

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John Rosenberg – Professor, University of Pittsburgh, Department of Biological Sciences
My research philosophy is to bring a physical, problem-ori­ented ap­proach to the acquisition and interpretation of biomolecular structural information.   I view biological molecules as amazing machines that have reached the ultimate miniaturization possible in a universe composed of atoms and molecules; my approach is to pick interesting examples where it appears possible to develop understanding of how they work.

Joshua L Adelman, Ying Sheng, Seungho Choe, Jeff Abramson, Ernest M Wright, John M Rosenberg, “Structural determinants of water permeation through the sodium-galactose transporter vSGLT,”
Biophysical Journal (Impact Factor: 3.83). 03/2014; 106(6):1280-9. DOI: 10.1016/j.bpj.2014.01.006

Seungho Choe, Joshua L. Adelman, John M. Rosenburg, Ernest M. Wright, Michael Grabe, “Understanding substrate unbinding from the sodium galactose co-transporter vSGLT based on 16 microseconds of molecular simulation,” Biophysical Journal (Impact Factor: 3.83). 01/2012; 102(3):661-. DOI: 10.1016/j.bpj.2011.11.3603.

Lab Website
Roni Rosenfeld – Professor, Carnegie Mellon U, School of Computer Science
Ph.D., Computer Science, and M.Sc., Computer Science, Carnegie Mellon University
My research interests are in: (1) Forecasting Epidemics – our long term vision is to make epidemiological forecasting as universally accepted and useful as weather forecasting is today. (2) Information and Communication Technologies for Development – (ICT4D) and specifically Spoken Language Technologies for Development (SLT4D) (3) Modeling the evolution of viral epidemics.

Yibin Lin, Agha Ali Raza, Jay-Yoon Lee, Danai Koutra, Roni Rosenfeld and Christos Faloutsos. Influence Propagation: Patterns, Model and a Case Study. PAKDD2014 (The 18th Pacific-Asia Conference on Knowledge Discovery and Data Mining), May 13-16, 2014, Tainan, Taiwan.

Haohan Wang, Agha Ali Raza, Yibin Lin and Roni Rosenfeld. Behavior Analysis of Low-literate Users of a Viral Speech-based Telephone Service. ACM DEV-4, December 6-7, 2013, Cape Town, South Africa.

Lab Website
Jonathan Rubin – Professor, University of Pittsburgh, Department of Mathematics
Ph.D. in Applied Mathematics from Brown University
Pattern formation in networks of coupled neural oscillators; Waves and localized activity generated through nonlocal interactions; Network dynamics in the basal ganglia, with implications for motor disorders, particularly Parkinson’s disease; Mechanisms and implications of synaptic plasticity, particularly spike-timing-dependent plasticity; Geometric singular perturbation theory and its relation to oscillations and bifurcations; Stability of solutions to parabolic systems of partial differential equations and related equations

Wei W, Rubin JE, Wang XJ. Role of the Indirect Pathway of the Basal Ganglia in Perceptual Decision Making. J Neurosci. 2015 Mar 4;35(9):4052-4064.

R. Rosenbaum, A. Zimnik, F. Zheng, R.S. Turner, C. Alzheimer, B. Doiron, and J.E. Rubin, “Axonal and synaptic failure suppress the transmission of firing rate oscillations, synchrony, and information during high frequency deep brain stimulation”, Neurobiol. Disease, 62:86-99, 2014.

Lab Website
Gordon Rule – Professor, Biological Sciences, Carnegie Mellon University
Ph.D., Biological Sciences, Carnegie Mellon University
My research is directed at understanding inter-molecular interactions in biological systems. Our research efforts have been directed at enzyme-substrate interactions, protein-lipid interactions, antibody-antigen interactions, RNA structure, and protein-nucleic acid interactions.

Sinha K1, Jen-Jacobson L, Rule GS. Divide and conquer is always best: sensitivity of methyl correlation experiments. J Biomol NMR. 2013 Aug;56(4):331-5. doi: 10.1007/s10858-013-9751-9. Epub 2013 Jun 15.

Senutovitch N, Stanfield RL, Bhattacharyya S, Rule GS, Wilson IA, Armitage BA, Waggoner AS, Berget PB. A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red. Biochemistry. 2012 Mar 27;51(12):2471-85. Epub 2012 Mar 14.

Lab Website
Hanna Salman – Assistant Professor, Department of Physics & Astronomy
Ph.D., Weizmann Institute of Science
My research aims to understand the mechanisms of collective behavior and variability in bacterial cultures and their effect on the response of bacteria to changes in the environment. By studying the changes in the behavior of bacteria as a function of their concentration, I am able to detect some of the collective mechanisms that govern the bacterial behavior and allow them to better endure environmental stress (e.g. temperature and chemical). I utilize various optical microscopy techniques to observe the swimming pattern of bacteria under different conditions. As for the expression level of proteins, proteins of interest are labeled with fluorescent markers and the expression level is measured using fluorescence microscopy or flow cytometry.

“Bacterial Thermotaxis by Speed Modulation”, Mahmut Demir, and Hanna Salman, Biophysical Journal, 103, 1683–1690 (2012).

“Universal Protein fluctuation in Populations of Microorganisms”,Hanna Salman, Naama Brenner, Chih-kuan Tung, Noa Elyahu, Elad Stolovicki, Lindsay Moore, Albert Libchaber, and Erez Braun, Phys. Rev. Letters, 108, 238105 (2012).

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Mahadev Satyanarayanan – Carnegie Group Professor, School of Computer Science, Carnegie Mellon University
Ph.D., Computer Science, Carnegie Mellon University
As an experimental computer scientist, I design, implement, and evaluate systems. My research interests span mobile computing, pervasive computing and distributed systems (especially distributed file systems). Performance, availability, security, usability and manageability are some of the key attributes that I pay attention to in my work.

Kiryong Ha, Zhuo Chen, Wenlu Hu, Wolfgang Richter, Padmanabhan Pillai, Mahadev Satyanarayanan .Towards wearable cognitive assistance. 06/2014; DOI: 10.1145/2594368.2594383

Wolfgang Richter, Canturk Isci, Benjamin Gilbert, Jan Harkes, Vasanth Bala, Mahadev Satyanarayanan. Agentless Cloud-wide Streaming of Guest File System Updates. Proceedings of the 2nd IEEE International Conference on Cloud Engineering, IC2E, Boston, Massachussettes; 03/2014

shoemakerLab Website
Jason Shoemaker – Assistant Professor, University of Pittsburgh, Chemical/Petroleum Engineering
DPhil, Chemical Engineering, University of California, Santa Barbara
COMPUTATIONALLY DRIVEN DISCOVERY IN HEALTH
Biological information – from molecular events to personal genomics – has exploded. Our group aims to develop computational approaches to exploit large-scale data to promote disease treatment discovery and optimization.

Zhao D, Fukuyama S, Sakai-Tagawa Y, Takashita E, Shoemaker JE, Kawaoka Y (2015) C646, a novel p300/CREB-binding protein-specific inhibitor of histone acetyltransferase, attenuates influenza A virus infection Antimicrob Agents Chemother

Lopes, T.J.S, Shoemaker, J.E., Matsuoka, Y., Kawaoka, Y., Kitano, H. (2015) Identifying problematic drugs based on the characteristics of their targets Front. Pharmacol.

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Alexander Sorkin – Professor and Chair, University of Pittsburgh, Dept. of Cell Biology and Physiology
Ph.D., Cell Biology, Institute of Cytology,Academy of Sciences of the U.S.S.R.
B.A., Biology and Chemistry, Leningrad Pedagogical Institute, Leningrad, U.S.S.R.
My research focuses on the mechanisms of endocytosis of growth factor receptors and neurotransmitter transporters, and the role of endocytosis in regulation of the function of these proteins. We use systems biology approaches to address basic questions of cell biology. We are also interested in the quantitative image analysis and computational modeling of endocytosis and signaling networks.

Goh, L. K., and Sorkin, A. (2013) Endocytosis of receptor tyrosine kinases. Cold Spring Harb Perspect Biol 2013;5:a017459.

Fortian, A. and Sorkin, A. Live cell fluorescence imaging reveals high stoichiometry of Grb2 binding to the EGF receptor sustained during endocytosis. (2014) J. Cell Sci. 127:432-44. Epub 2013 Nov 20.

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Robert Swendsen – Professor, Physics, Carnegie Mellon University
Ph.D., Physics, University of Pennsylvania
My main area of research is solid state physics and statistical mechanics, with an emphasis on computer simulations. I have worked especially on thermodynamic phase transitions combining computer simulations with a renormalization-group analysis. I have also been involved in the development of new algorithms for more efficient simulations, to enable the study of problems that would otherwise involve prohibitively long computer runs.

Robert H. Swendsen, Unnormalized probability: A different view of statistical mechanics, Am. J. Phys. 82, 941 (2014)

Roberta L. Klatzky, Pnina Gershon, Vikas Shivaprabhu, Randy Lee, Bing Wu, George Stetten, Robert H. Swendsen, A model of motor performance during surface penetration: from physics to voluntary control, Experimental Brain Research 230, 251 (2013)

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David Swigon – Assistant Professor, U of Pittsburgh, Dept. of Mathematics
Ph. D.and M.S., Theoretical Mechanics, Rutgers University, Piscataway, NJ.
Mgr., Applied Mathematics(equivalent of M.S.), Charles University, Prague, Czech Republic
My research interests are in the area of mathematical biology, in particular, construction of mathematical models of biological systems within the framework of theories of continuum mechanics, dynamical systems, and stochastic dynamics. Structure of the Lac Repressor-DNA Complex; Flexible docking of DNA to RNA polymerase; Control of transcription by designed DNA bending drugs; Naturally Discrete Model for DNA; Theory of Elastic Rods and Its Application to DNA

T. Stepien & D. Swigon, Traveling waves in one-dimensional elastic continuum model of cell layer migration with stretch-dependent proliferation, SIADS, 13, 1489–1516 (2014).

E. Mochan, D. Swigon, G.B. Ermentrout, S. Lukens, & G. Clermont, A mathematical model of intrahost pneumococcal pneumonia infection dynamics in murine strains, J. Theor. Biol., 353, 44–54 (2014).

Lab Website
Pei Tang – Professor of Anesthesiology, Pharmacology and Chemical Biology, & Computational Biology
PhD, Physical Chemistry, SUNY at Stony Brook
Determination of high-resolution domain structures of neuronal ion channels, such as nicotinic acetylcholine and glycine receptors. Characterization at the molecular level of how low-affinity drugs, particularly general anesthetics and alcohols, affect the functions of transmembrane ion channels. The approaches used in Dr. Tang’s laboratory include high-resolution NMR and large-scale molecular dynamic simulations.

Tillman T, Seyoum E, Mowrey D, Xu Y, Tang P. ELIC-α7 nAChR Chimeras Reveal a Prominent Role of the Extracellular-Transmembrane Domain Interface in Allosteric Modulation. J Biol Chem. In press (2014)

Mowrey D, Kinde MN, Xu Y, Tang P. Atomistic Insights into Human Cys-loop Receptors by Solution NMR, Biochim Biophys Acta, in press, (2014)

Lab Website
George C. Tseng – Assistant Professor, U of Pittsburgh, Dept. of Biostatistics
ScD, Biostatistics, Harvard University; MS, Mathematics, National Taiwan University
We are a statistical group with major applications on genomics and bioinformatics. Our vision is to develop rigorous, timely and useful statistical and computational methodologies to help understand disease mechanisms and improve disease diagnosis and treatment.

Ying Ding, Shaowu Tang, Serena G. Liao, Jia Jia, Steffi Oesterreich, Yan Lin, George C. Tseng. (2014) Bias correction for selecting the minimal-error classifier from many machine learning models. Bioinformatics. 30(22):3152-8.

Serena G. Liao, Yan Lin, Dongwan D. Kang, Naftali Kaminski, Frank C. Sciurba, George C. Tseng. (2014) Missing value imputation in high-dimensional phenomic data: Imputable or not? And how? BMC Bioinformatics. 15:346.

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Ben Van Houten – Professor, Pharmacology and Chemical Biology
PhD (Biomedical Sciences – Genetics), Oak Ridge Graduate School of Biomedical Sciences/University of Tennessee
The Van Houten laboratory studies the formation and repair of DNA damage in nuclear and mitochondrial genomes. We are particularly interested in the structure and function of proteins that mediate nucleotide excision repair and the role of oxidative stress in human disease. Research interests include: Structure-function Studies of Nucleotide Excision Repair Proteins, Mitochondrial DNA Damage & Repair

Qian W, Salamoun J, Wang J, Roginskaya V, Van Houten B, Wipf P. ”The combination of thioxodihydroquinazolinones and platinum drugs reverses platinum resistance in tumor cells by inducing mitochondrial apoptosis independent of Bax and Bak.” Bioorg Med Chem Lett. 2015 Feb 15;25(4):856-63. doi: 10.1016/j.bmcl.2014.12.072. Epub 2014 Dec 30.

Wang J, Li J, Santana-Santos L, Shuda M, Sobol RW, Van Houten B, Qian W. “A novel strategy for targeted killing of tumor cells: Induction of multipolar acentrosomal mitotic spindles with a quinazolinone derivative mdivi-1.” Mol Oncol. 2015 Feb;9(2):488-502. doi: 10.1016/j.molonc.2014.10.002. Epub 2014 Oct 17.

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Yoram Vodovotz – Director, Center for Inflammation and Regenerative Modeling, Professor of Surgery, Immunology, Communication Sci and Disorders, and Comp Biology U of Pittsburgh
PhD, Immunology, Cornell University Graduate School of Medical Sciences
Dr. Vodovotz’s research interests include the biology of acute inflammation in shock states (e.g. septic and hemorrhagic shock) as well as in chronic diseases and wound healing. He is also interested in the cross-regulation of the inducible nitric oxide synthase and the cytokine transforming growth factor-b1 in various disease states, including malaria infection, cancer, sepsis, and neurodegenerative diseases. His main current area of interest revolves around the use of mathematical modeling to unify and gain insight into the plethora of biological interactions that characterize these inflammatory conditions.

Complex Systems and Computational Biology Approaches to Acute Inflammation. An, G.; Vodovotz, Y., eds. New York, NY: New York, NY: Springer. 2013. http://dx.doi.org/10.1007/978-1-4614-8008-2

Solovyev, A.; Mi, Q.; Tzen, Y-T.; Brienza, D.; Vodovotz, Y. Hybrid equation- / agent-based model of ischemia-induced hyperemia and pressure ulcer formation predicts greater propensity to ulcerate in subjects with spinal cord injury. PLoS Comput. Biol. 2013. 9:e1003070.

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Alan Wells – Thomas J Gill III Professor of Pathology
M.D., Brown University
The Wells’ Lab research program, in close collaboration with its research partners, aims to understand cell migration in terms of how motility processes are regulated, and understand how this regulation of migration plays a role in physiologic and pathologic situations.

Khanna D, Mittoo S, Aggarwal R, Proudman SM, Dalbeth N, Matteson EL, Brown K, Flaherty K, Wells AU, Seibold JR, Strand V. Connective Tissue Disease-associated Interstitial Lung Diseases (CTD-ILD) – Report from OMERACT CTD-ILD Working Group. J Rheumatol. 2015 Mar 1. pii: jrheum.141182.

Furukawa M, Wheeler S, Clark AM, Wells A. Lung epithelial cells induce both phenotype alteration and senescence in breast cancer cells. PLoS One. 2015 Jan 30;10(1):e0118060. doi: 10.1371/journal.pone.0118060. eCollection 2015.

Lab Website
Xiang-Qun (Sean) Xie – Professor, U of Pittsburgh, Dept of Pharmaceutical Sciences and Drug Discovery Institute, Associate Dean of the School of Pharmacy, Director of CDAR and CCGS centers
Ph.D., Medicinal Chemistry, School of Pharmacy, University of Connecticut, CT
Xie’s group focuses on development of diseases-specific chemogenomics knowledgebase, an integrated platform of “Big Data to Knowledge” target identification and system pharmacology for drug discovery translational research. The innovation includes GPU-accelerated cloud computing machine-learning TargetHunter programs for drug target identification and system pharmacology. His lab was the first discovered/patented INK4C-targeting small molecule inhibitors for hematopoietic stem cell expansion (Nature Comm 2015), and was the first discovered/patented p62ZZ chemical inhibitors for multiple myeloma (Nature Leukemia 2015) .

Liu, HB, Wang, L, Su, WW and Xie* X-Q, “ALzPlatform: An Alzheimer’s Disease Domain-Specific Chemogenomics Knowledgebase for Polypharmacology and Target Identification Research.” J Comput Info Modeling. 2014, 54(4):1050-60. (cover page story)

Wang L, Ma C, Wipf P, Liu H, Su W and Xie* X-Q. “TargetHunter: An In Silico Target Identification Tool for Predicting Therapeutic Potential of Small Organic Molecules Based on Chemogenomic Database”. AAPS J. 2013, 15, 395-406 PMID:23292636 (AAPS Special Theme Issue)

Lab Website
Eric Xing – Professor, Carnegie Mellon University, Department of Computer Science
PhD,Computer Science, U.C. Berkeley; PhD, Molecular Biology, Rutgers University, NJ
My principal research interests lie in the development of machine learning and statistical methodology, and large-scale computational system and infrastructure, for solving problems involving automated learning, reasoning, and decision-making in high-dimensional, multimodal, and dynamic possible worlds in social and biological systems.

Jinhui Yuan, Fei Gao, Qirong Ho, Wei Dai, Jinliang Wei, Xun Zheng, Eric P. Xing, Tie-Yan Liu, Wei-Ying Ma, LightLDA: Big Topic Models on Modest Compute Clusters , Manuscript, arXiv:1412.1576, communicated 4 Dec 2014.

Xun Zheng, Jin Kyu Kim, Qirong Ho and E. P. Xing, Model-Parallel Inference for Big Topic Models, Manuscript, arXiv:1411.2305, communicated 10 Nov 2014.

yang daLab Website
Da Yang – Assistant Professor, Pharmaceutical Sciences
M.D., Harbin Medical University in China; Ph.D., Pharmacology and Genomics
The research of Dr. Yang’s laboratory is focusing on using integrated genomic and functional studies to identify mechanisms of resistance to cancer therapeutics, and to develop novel approaches/markers to enable personalized cancer medicine.

Comprehensive molecular characterization of human colon and rectal cancer
Cancer Genome Atlas Network, Nature 487 (7407), 330-337

The cancer genome atlas pan-cancer analysis project
JN Weinstein, EA Collisson, GB Mills, KRM Shaw, BA Ozenberger, …, Nature genetics 45 (10), 1113-1120

zuckermanLab Website
Daniel M. Zuckerman – Professor, Oregon Health & Science University, Dept of Biomedical Engineering
Ph.D. in Physics, University of Maryland, College Park
Research: Computational Study of Protein Binding, Allostery, and Molecular Machines. Molecular-level biology is inherently dynamic. The Zuckerman group pursues ensembles of protein structures and pathways of conformational change that play a key role in binding, allostery and molecular machines. The group has been active in developing scale-free “weighted ensemble” (WE) software, which is now in use around the world. Zuckerman and colleagues developed WE methods for sampling steady-state and equilibrium conditions that have been applied to all-atom protein binding and to highly complex systems biology models of cell signaling.

Accurate estimation of protein folding and unfolding times: Beyond Markov state models, Suárez, Ernesto; Adelman, Joshua; Zuckerman, Daniel*, Journal of Chemical Theory and Computation, 12:3473–3481 (2016).

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process, Ramu Anandakrishnan, Zining Zhang, Rory M. Donovan, and Daniel M. Zuckerman*, Proceedings of the National Academy of Sciences, 113: 11220–11225 (2016).