Invited Talks

MMBios researchers and lab members present seminars and numerous talks at national and international meetings, such as symposia, workshops and conferences.

 

2021     2020     2019     2018     2017     2016     2015     2014     2013      2012


2021

Ivet Bahar, University of Pittsburgh

April 12, 2021: University of Texas (UT) Southwestern Medical Center Computational and Systems Biology Seminar Series. Dallas, TX. Invited Lecturer.

March 2021: “Chromatin Modeling: Integrating Mathematics, Physics, and Computation for Advances in Biology and Medicine”. Research Centre Erwin Schrodinger International Institute for Mathematics and Physics (ESI), Vienna, Austria, Invited Speaker. (Moved from 2020 due to COVID-19)

May 2021: The Biophysical Society Meeting, “Biophysics at the Dawn of Exascale Computers”. Hamburg, Germany. Invited Speaker. (Moved from 2020 due to COVID-19)

June 8-11, 2021: European Research Council (ERC) PE5 Starting Grant Panel Meeting. Brussels, Belgium. Panel Member.

October 11-15, 2021: European Research Council (ERC) PE5 Starting Grant Panel Meeting. Brussels, Belgium. Panel Member.  

2020

Ivet Bahar, University of Pittsburgh

February 10, 2020: National Institutes of Health (NIH) National Institute of General Medicine Sciences (NIGMS) Seminar Series. Invited Speaker.

February 20, 2020: University of Connecticut Richard D. Berlin Center for Cell Analysis & Modeling CCAM Seminar Series. Invited Speaker.

March 4-6, 2020: U.S. National Library of Medicine. Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Meeting. National Institute of Health, Bethesda, Maryland. Committee Member. (mail in)

2020: Hacettepe University School of Medicine and the University of Pittsburgh School of Medicine Joint Symposium. Ankara, Turkey. Co-organizer and Invited Speaker. (Postponed due to COVID-19)

July 2-3, 2020: The Heidelberg Institute for Theoretical Studies (HITS) HITS gGmbH Scientific Advisory Board “Molecular and Cellular Modeling (MCM)” Research Group Review Board. Heidelberg, Germany. Invited Reviewer.

July 5-6, 2020: Austrian Biophysical Society Annual Meeting. Strobl am Wolfgangsee, Austria. Invited Speaker.

July 19-24, 2020: 2020 Gordon Research Conference (GRC), 33rd Anniversary of the GRC in Computational Chemistry, “Multiscale Modeling of Complex Systems: Methods and Applications”, Castelldefels, Spain. Invited Speaker.

October 22-23, 2020: IUPAB Congress “Workshop on Modular Modeling in Biophysics”, University of Rio de Janeiro, Brazil. Invited Speaker.

October 26-30, 2020: 20th International Congress of IUPAB (International Union for Pure and Applied Biophysics), the 45th Annual SBBf (Brazilian Biophysical Society), and the 49th Annual SBBq (Brazilian Biochemistry and Molecular Biology Society) Meetings. Foz do Iguaco, Brazil. Invited Lecturer.

Phillip Compeau, Carnegie Mellon University

2020: The 28th Conference on Intelligent Systems for Molecular Biology (ISMB). Program Committee. Montreal, Canada.

Robert Murphy, Carnegie Mellon University

July 12-16, 2020: Intelligent Systems for Molecular Biology. Member, Program Committee Montreal, Canada.

Min Xu, Carnegie Mellon University

July 11-17, 2020: 2020 International Joint Conference on Artificial Intelligence (IJCAI-2020). Yokohama, Japan. Member, Program Committee.

2020: 24th International Conference on Research in Computational Molecular Biology (RECOMB). Padova, Italy. Member, Program Committee. (Rescheduled due to COVID-19, more details to follow)

August 18-20, 2020: The 18th Asia Pacific Bioinformatics Conference (APBC-2020). Seoul, Korea. Program Committee. (Rescheduled from February 2020 to August 2020 due to COVID-19)

Xiangrui Zeng, Xu Lab, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

June 16-18, 2020: Oral presentation, “Gum-Net: Unsupervised Geometric Matching for Fast and Accurate 3D -Subtomogram Image Alignment and Averaging”, in Proceedings of the Institute of Electrical and Electronics Engineers (IEEE) Conference on Computer Vision and Pattern Recognition (CVPR 2020). Seattle, WA.

Fen Pei, Bahar/Taylor Labs, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

February 18-20, 2020: Oral presentation and poster, “QuartataWeb: Integrated Chemical-protein-pathway Mapping for Polypharmacology and Chemogenomics”, The Eighth Annual Winter Q-Bio Conference, Quantitative Biology on the Hawaiian Islands. Hawaii, USA.

2019

Ivet Bahar, University of Pittsburgh

March 2-4, 2019: 63rd Annual Meeting of the Biophysical Society, Symposium on Glutamate Receptors. Baltimore, MD. Invited Speaker.

March 5-8, 2019: European Research Council (ERC) Starting Grant Panel Meeting. Brussels, Belgium. Panel Member.

March 20-26, 2019: The 2019 Kadir Has Outstanding Achievement Award, Kadir Has University. Istanbul, Turkey. Award Recipient.

March 31-April 5, 2019: Multiscale Modeling of Chromatin: Bridging Experiment with Theory. (Biophysical Society (BPS) Thematic Meeting). Les Houches, France. Invited Speaker.

May 14, 2019: National Institute of Health (NIH) National Institute on Drug Abuse (NIDA) Intramural Research Program (IRP) Seminar Series. Baltimore, MD, USA, Invited Speaker. https://irp.drugabuse.gov/about-irp/irp-seminar-schedule/

May 13-17, 2019: Hands-on Workshop on Computational Biophysics, Pittsburgh Supercomputing Center. Pittsburgh, PA. Instructor.

May 20-24, 2019: Jacques Monod Conference, Sciences biologiques Ecologie et Environnement, Ligand-gated ion channels from atomic structure to synaptic transmission. Roscoff, France. Invited Speaker.

June 3-7, 2019: European Research Council (ERC) Starting Grant Panel Meeting. Brussels, Belgium. Panel Member.

June 13-14, 2019: U.S. National Library of Medicine. Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Meeting. National Institute of Health, Bethesda, Maryland. Committee Member.

June 27-29, 2019: Izmir Statistical Physics Days Conference, Izmir University of Technology, Izmir, Turkey. Keynote Speaker.

September 4-6, 2019: Biological Physics Mexico City 2019 Scientific International Conference, Mexico City, Mexico. Keynote Speaker.

November 7-8, 2019: The Cleveland Clinic Lerner Research Institute of Genomic Medicine Seminar Series; Cleveland, OH. Invited Lecturer.

November 13-15, 2019: U.S. National Library of Medicine. Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Meeting. National Institutes of Health, Bethesda, Maryland. Committee Member.

December 4, 2019: University of Pittsburgh School of Medicine, Senior Vice Chancellors Laureate Lecture Series. Pittsburgh, PA. Invited Lecturer. http://www.svc-laureate.pitt.edu/

Phillip Compeau, Carnegie Mellon University

2019: Program Committee. 27th Conference on Intelligent Systems for Molecular Biology (ISMB). Basel, Switzerland.

2019: “The Pre-College Program in Computational Biology at CMU”. Annual Meeting of Bioinformatics Education for STudents (BEST) Teachers at the Pittsburgh Supercomputing Center. Pittsburgh, PA.

James Faeder, University of Pittsburgh

April 9-12, 2019: Co-organizer, Cellular Dynamics and Models, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

May 8-10, 2019: Organizer and presenter, MMBioS Cell Modeling Workshop, Pittsburgh Supercomputing Center, Pittsburgh, PA.

July 2019: Invited lecturer, “Introduction to modeling signal transduction using rules”, 13th q-bio Summer School, Houston, TX.

July 22-26, 2019: Invited talk, “Identifying Biochemical Mechanisms that Give Rise to Heterogeneity in Single-Cell Responses”, Mini-symposium on Models and simulations of cellular systems: From single-cells to population dynamics, SciCade 2019, Innsbruck, Austria.

September 16-17, 2019: Invited talk and workshop participant, “Rule-based modeling of biochemical systems”, Los Alamos National Laboratory. Washington, DC.

Carleton Kingsford, Carnegie Mellon University

September 8-10, 2019: Workshop on Algorithms in Bioinformatics (WABI 2019) together with ACM-BCB 2019 Niagara Falls, NY.

December 3, 2019: Speaker at Distinguished Seminar Series at Institute for Computational Medicine at Johns Hopkins University.

Robert Murphy, Carnegie Mellon University

April 8-11, 2019: Associate Editor, Institute for Electrical and Electronics Engineers, (IEEE), International Symposium on Biomedical Imaging, Prague, Czech Republic.

July 21-25, 2019: Member, Program Committee, Intelligent Systems for Molecular Biology, Basel, Switzerland.

Terrence Sejnowksi, Salk Institute for Biological Studies

2019: Lethbridge University, Brenda Milner Lecture, Distinguished Lecturer. Lethbridge, Alberta, Canada.

2019: University of California at Los Angeles (UCLA), Arman Lecutrer. Distinguished Lecturer. Los Angeles, CA.

December 8-14, 2019: Thirty-fourth Conference on Neural Information Processing Systems, NeurIPS. Vancouver, British Colombia, Canada. Invited Speaker.

Min Xu, Carnegie Mellon University

August 10-16, 2019: 2019 International Joint Conference on Artificial Intelligence (IJCAI-2019). Macao, China. Member, Program Committee

January 14-16, 2019: The 18th Asia Pacific Bioinformatics Conference, (APBC-2019). Wuhan, China. Member, Program Committee.

December 2019: “3D Macromolecule Localization in Cryo-electrontomography with Deep Reinforcement Learning”. Conference on Neural Information Processing Systems, (NeurIPS-2019), Deep Reinforcement Learning Workshop. Vancouver, British Colombia, Canada.

Jiyoung Lee, Research Scientist, Bahar Lab, University of Pittsburgh

March 2-6, 2019: Poster, “A Ligand-binding Site in the GluA3 AMPA Receptor N-terminal Domain Observed in Druggability Simulations and X-ray Crystallography”. The 63rd Annual Meeting of the Biophysical Society, Symposium on Glutamate Receptors. Baltimore, MD.

May 20-24, 2019: Poster, “A Mechanism of Pore Opening in AMPA Receptor Coupled to Extracellular Domain Dynamics”. Jacques Monod Conference, Sciences biologiques Ecologie et Environnement, Ligand-gated ion channels from atomic structure to synaptic transmission. Roscoff, France.

James Krieger, Postdoctoral Associate, Bahar Lab, University of Pittsburgh

March 2-6, 2019: Poster, “SignDy: A Pipeline Revealing Shared Signature Dynamics Tempered by Local Fluctuations”. The 63rd Annual Meeting of the Biophysical Society, Symposium on Glutamate Receptors. Baltimore, MD.

May 20-24, 2019: Poster, “GluA3 NTD dimer dynamics from experiments and simulations”. Jacques Monod Conference, Sciences biologiques Ecologie et Environnement, Ligand-gated ion channels from atomic structure to synaptic transmission. Roscoff, France.

Natalie Sauerwald, Kingsford Lab, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

September 8-10, 2019: Oral Presentation, ‘Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation’ Workshop on Algorithms in Bioinformatics (WABI 2019) together with ACM-BCB 2019 Niagara Falls, NY.

Fen Pei, Bahar/Taylor Labs, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

2019: Poster, “Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1”, The Sixth Cold Spring Harbor Laboratory Meeting on Network Biology, NY.

Yan Zhang, Bahar/Xing Labs, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

2019: “Modeling Stochastic Dynamics of Cell Fate”, Multiscale Cell Fate Symposium. University of Calirfornia at Irvine. Irvine, CA.

2019: “CCT Conformational Space Elucidated by Elastic Network Model Analysis of Cryo-EM Data”, MMBioS. University of Pittsburgh. Pittsburgh, PA.

She “John” Zhang, Bahar Lab, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

2019: Oral presentation, “Differences in the Intrinsic Spatial Dynamics of the Chromatin Contribute to Cell Differentiation”, MMBioS, University of Pittsburgh. Pittsburgh, PA.

2018

Ivet Bahar, University of Pittsburgh

February 17-21, 2018: Biophysical Society 62nd Annual Meeting. San Francisco, CA. Attendee.

February 27, 2018: NIMH Intramural Research Program (IRP). National Institute of Health. Bethesda, MD. Invited Speaker.

March 8-9, 2018: U.S. National Library of Medicine. Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Meeting. National Institute of Health, Bethesda, Maryland. Committee Member.

May 3, 2018: Department of Physics, Drexel University. Philadelphia, PA. Invited Colloquium.

May 21-25, 2018: Hands-on Workshop on Computational Biophysics. Pittsburgh Supercomputing Center. Pittsburgh, PA. Instructor.

June 7-8, 2018: U.S. National Library of Medicine. Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Meeting. National Institute of Health, Bethesda, Maryland. Committee Member.

June 21-22, 2018: NIH Biomedical Imaging and Bioengineering 2018 Training Grantees Meeting. National Institute of Health Main Campus. Bethesda, MD. Attendee.

June 25-27, 2018: "CONES2018: Frontiers of Non-Equilibrium Science" Conference, London, UK. Invited Speaker.

July 31-August 2, 2018: 6th Annual iGluRetreat, jointly held with the Department of Chemistry of Carnegie Mellon University and the Department of Neuroscience of the University of Pittsburgh. Pittsburgh, PA. Invited Speaker.

September 8-12, 2018: 17th European Conference in Computational Biology (ECCB) 2018, Athens, Greece. Symposium Chair, Session Organizer, and Invited Speaker.

September 12-14, 2018: CECAM (Centre European pour le Calcul Atomique et Moléculaire) Workshop, "Normal modes of biological macromolecules: methods and applications," Paris, France. Invited Speaker.

September 18-21, 2018: Inaugural International Transmembrane Transporter Society (ITTS) Symposium. Vienna, Austria. Session Organizer and Speaker.

October 6-8, 2018: Computational Biology Workshop, Arizona State University. Phoenix, Arizona. Invited participant.

October 10, 2018: MMBioS National Center for Multiscale Modeling of Biological Systems. External Advisory Board Meeting. Pittsburgh, PA. Principal Investigator.

October 15-17, 2018: CECAM (Centre European pour le Calcul Atomique et Moléculaire) Workshop, "Multiscale simulations of allosteric regulatory mechanisms in cancer-associated proteins and signaling protein networks," Lugano, Switzerland. Invited Speaker.

November 8-10, 2018: Conference on Modeling of Protein Interactions (MPI). Lawrence, Kansas. Invited Speaker.

November 15-16, 2018: U.S. National Library of Medicine. Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Meeting. National Institutes of Health, Bethesda, Maryland. Committee Member.

Phillip Compeau, Carnegie Mellon University

2018: “Establishing a Computational Biology Flipped Classroom”. Education Community of Special Interest (COSI) meeting at the 26th Conference on Intelligent Systems for Molecular Biology (ISMB). Chicago, Illinois.

James Faeder, University of Pittsburgh

March 7-9, 2018: Organizer and presenter, MMBioS Cell Modeling Workshop, Allen Institute for Cell Science, Seattle, WA.

June 4-7,2018: Invited talk, “Rule-based modeling of biochemical systems”, The Annual Meeting of the Canadian Society of Applied and Industrial Mathematics (CAIMS 2018), Ryerson University, Toronto, Canada.

September 6-7, 2018: Invited talk, “Computational modeling of cell decision processes”, CMU Biophysics Workshop 2018, Carnegie Mellon University, Pittsburgh, PA.

November 1, 2018: Invited talk, “Cell Individuality: Identifying the factors that give rise to heterogeneity in cellular responses,” OHSU special seminar, Portland, OR.

Robert Murphy, Carnegie Mellon University

March 7-9, 2018: Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Seattle, Washington.

April 14-18, 2018: Member, Scientific Program Committee, 2018 Annual Meeting, American Association for Cancer Research, Chicago, Illinois.

July 6-10, 2018: Member, Program Committee, Intelligent Systems for Molecular Biology, Chicago, Illinois.

Terrence Sejnowksi, Salk Institute for Biological Studies

April 8-13, 2018: Ernst Strüngmann Forum, Cerebral Cortex 3.0, Complexity and Computation, Frankfurt am Main, Germany

May 5, 2018: 25th Joint Symposium on Neural Computation, The Beckman Institute at Caltech, California Institute of Technology. Pasadena, CA. Invited Speaker.

July 8-13, 2018: Thirty-fourth Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

July 7-12, 2018: Thirty-fifth Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

Min Xu, Carnegie Mellon University

August 18-21, 2018: The 12th International Conference on Computational Systems Biology (ISB-2018), Asia-Pacific Operations Research Center (APORC) Guiyang, China. Member, Program Committee.

December 2018: “Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms”. Institute of Electrical and Electronics Engineers (IEEE) International Conference on Bioinformatics & Biomedicine, Workshop on Machine Learning in High Resolution Microscopy.

Jiyoung Lee, Research Scientist, Bahar Lab, University of Pittsburgh

February 17-21, 2018: Poster, “Molecular Basis for the Functionality of G-secretase Inferred from Structure-based Modeling and Druggability Simulations”, Biophysical Society 62nd Annual Meeting. San Francisco, California.

James Krieger, Postdoctoral Associate, Bahar Lab, University of Pittsburgh

July 31-August 2, 2018: Poster, “GluA3 NTD Dimer Dynamics from Experiments and Simulations”. 6th Annual iGluRetreat. Pittsburgh, PA.

November 6-8, 2018: 2018 Purdue Cryo-EM Symposium. Purdue University, West Lafayette, IN.

Yan Zhang, Bahar/Xing Labs, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

2018: ‘CCT Conformational Space Elucidated by Elastic Network Model Analysis of Cryo-EM Data’, Purdue CryoEM Symposium, Purdue University. West Lafayette, IN.

2018: ‘Multiscale Modeling of the Chromatin Structure’, MMBioS, University of Pittsburgh. Pittsburgh, PA.

She “John” Zhang, Bahar Lab, CPCB Student, University of Pittsburgh/Carnegie Mellon University Joint PhD Program in Computational Biology

2018: ‘Multiscale Modeling of the Chromatin Structure’, MMBioS, University of Pittsburgh. Pittsburgh, PA.

2018: ‘Cell-to-Cell Heterogeneities at Genome Scale Investigated by the Gaussian Network Model’, PittDay in the capital of Pennsylvania., Harrisburg, PA. (chosen to represent the University of Pittsburgh)

2017

Ivet Bahar, University of Pittsburgh

March 30, 2017: UCLA, Cedars Sinai Medical Center, Los Angeles, CA. Invited Speaker.

April 2-6, 2017: Long-range Correlated Motions in Proteins at the 253rd National Meeting, American Chemical Society, San Francisco, CA. Invited Symposium Speaker.

May 10, 2017: Greater Boston Theoretical Chemistry Lectures, Boston University, Boston, MA. Invited Lecturer (series of three talks, at Boston U, MIT and Harvard U, one at each institution).

May 18-20, 2017: 2017 Workshop on Computational Biophysics and Systems Biology (CBSB2017), Cincinnati, OH. Keynote Speaker.

June 11-14, 2017: Gordon Research Conference (GRC) Computational Aspects - Biomolecular NMR, Grand Summit Hotel, Newry, ME. Invited Speaker.

August 7-11, 2017: 5th Edition of the Brazilian Molecular Modelling School, Sao Paolo, Brazil. Invited Speaker and Lecturer.

August 20-25, 2017: The IV International Interdisciplinary Applied Mathematics, Modeling and Computational Science (AMMCS) Conference, Waterloo, Canada. Plenary Speaker.

October 19-21, 2017: "5th International BAU Drug Design Conference", Istanbul, Turkey. Invited Speaker.

October 30-November 1, 2017: CECAM (Centre European pour le Calcul Atomique et Moléculaire) Workshop, "Computational Approaches to Investigating Allostery", Lausanne, Switzerland. Invited Speaker.

December 3-7, 2017: Molecular Perspectives on Protein-Protein Interactions (PPI2017), Eilat, Israel. Invited Speaker.

Joseph Ayoob, University of Pittsburgh

September 2017: “How to Win Graduate School”, CPCB MetaSchool (Professional Development Series) University of Pittsburgh School of Medicine, Pittsburgh, PA.

Thomas Bartol, Salk Institute for Biological Studies

June 30, 2017: "Cell Modeling with MCell" PSC Symposium. Invited Speaker. Pittsburgh, PA.

Phillip Compeau, Carnegie Mellon University

2017: “Life after MOOCs”. NIH Informatics Technology for Cancer Research PI Meeting. Bethesda, MD

James Faeder, University of Pittsburgh

March 27-29, 2017: Co-organizer and presenter, NIMBioS Working Group for Spatial Cell Simulation, Knoxville, TN.

April 12, 2017: Contributed tutorial, “Introduction to rule-based modeling with BioNetGen,” Cell Dynamics and Modeling, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

May 12-16, 2017: Contributed talk, Annual Meeting of the American Association of Immunologists, Washington, DC.

June 9-10, 2017: Invited lecturer, “Introduction to stochastic spatial modeling”, The 11th q-bio Summer School on Cellular Information Processing, Colorado State University, Fort Collins, CO.

June 12, 2017: Invited seminar, “Computational modeling of cell decision processes,” Applied/Computational Math Seminar, University of California at Irvine, Irvine, CA.

June 15, 2017: Invited seminar, “Computational modeling of cell decision processes,” BME Seminar Series, Oregon Health Sciences University, Portland, OR.

July 25, 2017: Contributed tutorial, “Introduction to rule-based modeling with BioNetGen,” 11th International q-bio Conference on Cellular Information Processing, Rutgers University, New Brunswick, NJ.

August 10, 2017: Keynote speaker, “Rule-based modeling of cellular processes”, 9th International Workshop on Bio-Design Automation (IWBDA), Pittsburgh, PA.

October 5-6, 2017: Invited speaker, “Computational models as vehicles for understanding in systems biology,” Bridging the gap: scientific imagination meets aesthetic imagination, London School of Economics, London, UK.

October 9-13, 2017: Invited speaker, “Toward integrated models of cell behavior: How rule-based modeling can contribute,” COMBINE 2017, Milan, Italy.

October 11-12, 2017: Invited speaker, “Computational modeling of cell decision processes in the immune system,” Workshop on Physical Concepts and Computational Models, MIT, Cambridge, MA.

October 19-20, 2017: Invited speaker, “Multiscale modeling of DAT function in dopamine neurons,” Computational Neuroscience Spotlight Session at Science 2017, University of Pittsburgh, Pittsburgh, PA.

October 27, 2017: Invited seminar, “Computational modeling of cell decision processes,” Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA.

Carleton Kingsford, Carnegie Mellon University

February 1, 2017: The Experiment Discovery Problem: Methods for Searching Large Databases of Sequencing Experiments. Univ of California, San Diego, CA.

February 10, 2017: The Experiment Discovery Problem: Methods for Searching Large Databases of Sequencing Experiments. Department of Biomedical Informatics, University of Pittsburgh. Pittsburgh, PA.

Robert Murphy, Carnegie Mellon University

2016-2017: Organizing Committee member, Symposium on Clinical and Pharmaceutical Solutions through Analysis.

June 26-28, 2017: Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh.

Terrence Sejnowksi, Salk Institute for Biological Studies

October 19, 2017: "Neuroscience in the Age of Information" Science 2017. University of Pittsburgh. Pittsburgh, PA. Plenary Speaker

Jiyoung Lee, Research Scientist, Bahar Lab, University of Pittsburgh

April 2-6, 2017: Oral Presentation, “Allosteric Dynamics of AMPA Receptors and Coupling to Membrane”, 253rd National Meeting, American Chemical Society. San Francisco, CA.

Greg Hood, Pittsburgh Supercomputing Center, Carnegie Mellon University

August 17, 2017: "Infrastructure: MPI." NeuroComp17. "Infrastructure: GPU and many-core processors Invited Speaker. Madison, WI.

2016

Ivet Bahar, University of Pittsburgh

January 19-20, 2016: Structural and Computational Biology and Molecular Biophysics (SCBMB) program, Baylor College of Medicine, Houston, TX. Review Board Member.

January 25-27, 2016: The International Human Frontier Science Program Selection Committee, Strasbourg, FR. Selection Committee Member.

February 9, 2016: External Advisory Board Meeting for P41 NIGMS Center for Biomolecular NMR Processing and Analysis, UConn Health, Farmington, CT. Invited EAB Member.

February 10, 2016: Arizona State University in the Center for Biological Physics Seminar Series, Tempe, AZ. Invited Speaker.

March 13-15, 2016: NIH BTRR P41 Directors Meeting, Bethesda, MD. Invited Speaker.

March 15-17, 2016: "Landscapes, Pathways, and Kinetics in Biomolecular Simulations" Symposium, 251st ACS National Meeting & Exposition. San Diego, California. Invited Speaker.

May 26-27, 2016: Big Data Bioinformatics Conference. Boston, MA Invited Distinguished Speaker.

June 6-10, 2016: Hands-on Workshop on Computational Biophysics. Pittsburgh Supercomputing Center, Pennsylvania. Instructor.

June 13-16, 2016: The Center for Causal Discovery from Biomedical Data, Summer Short Course. Instructor.

June 21, 2016: ProDy Webinar hosted by Harvard University (Software Applications, ProDy) Presenter.

July 11-12, 2016: NIBIB Training Grantees Meeting. Natcher Conference Center, NIH Main Campus, Bethesda, MD. Invited NIBIB Training Program Director.

July 18-20, 2016: 4th International Conference on Integrative Biology, "Innovation, Insight and Integration of Future Science". Courtyard Berlin City Centre, Germany. Invited Speaker.

July 28-29, 2016: National Strategic Computing Initiative Anniversary Workshop. The White House, Washington, D.C. Invited Speaker.

August 31- September 2, 2016: 9th SFB35 Symposium, "Transmembrane Transporters in Health and Disease". Vienna, Austria. Invited Chairperson.

September 20, 2016: Academia Sinica, Seminar Series. Taiwan. Taiwan International Graduate Program Distinguished Lecturer.

September 22, 2016: Institute of Bioinformatics and Structural Biology, National Tsing Hua University. Taiwan. Invited Lecturer.

December 4-6, 2016: Review of the Computational Biology Program, The College of Liberal Arts & Sciences, University of Kansas. External Reviewer.

Phillip Compeau, Carnegie Mellon University

2016: Bioinformatics flipped class (with P. Pevzner). Research in Computational Molecular Biology (RECOMB). Santa Monica, CA.

James Faeder, University of Pittsburgh

March 21-23, 2016: Co-organizer and presenter, NIMBioS Working Group for Spatial Cell Simulation, Knoxville, TN.

April 1, 2016: Tutorial, “Introduction to Rule-Based Modeling with BioNetGen” William Dunn School of Pharmacy, Oxford University, Oxford, United Kingdom.

April 1, 2016: Invited seminar, “Computational modeling of cell decision processes”, William Dunn School of Pharmacy, Oxford University, Oxford, United Kingdom.

April 4-8, 2016: Invited talk, “Towards large scale models of biochemical networks”, Advances in numerical and analytic approaches for the study of non-spatial stochastic dynamical systems in molecular biology, Isaac Newton Institute for Mathematical Sciences, Cambridge, United Kingdom.

April 6, 2016: Invited lecturer and tutorial presenter, “Introduction to Rule-Based Modeling”, “Introduction to rule-based modeling with BioNetGen,” Whole Cell Modeling Course, Center for Regulatory Genomics, Barcelona, Spain.

May 16-18, 2016: Invited talk, “Determining the role of T cell antigen receptor signaling strength in T cell differentiation”, Third International Mathematical and Computational Medicine Conference, Columbus, OH.

June 1-3, 2016: Workshop organizer and presenter, Computational Methods for Spatially Realistic Microphysiological Simulations 2015, Pittsburgh Supercomputing Center, Pittsburgh, PA.

June 10-11, 2016: Invited speaker, “Computational modeling of cell decision processes”, Fifth Annual University of Pittsburgh – Tsinghua University Joint Symposium, Tsinghua University, Beijing, China.

July 11-14, 2016: Invited lecturer, “Methods for Simulating Rule-Based Models”, The 10th q-bio Summer School on Cellular Information Processing, University of New Mexico, Albuquerque, NM.

July 27, 2016: Contributed tutorial, “Modeling Complex Biochemical Systems in Time and Space Using BioNetGen and MCell,” 10th International q-bio Conference on Cellular Information Processing, Vanderbilt, TN.

August 28-31, 2016: Invited talk, “Determining the role of T cell antigen receptor signaling strength in T cell differentiation”, A Symposium on Cell Signaling, Santa Fe, New Mexico.

September 23, 2016: Invited seminar, “Rule-based modeling for everyone: Recent developments and adventures in modeling cell decision processes,” Department of Genetics and Genomic Sciences Seminar, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine.

October 19-21, 2016: Co-organizer and presenter, NIMBioS Working Group for Spatial Cell Simulation, Knoxville, TN.

December 15-18, 2016: Keynote speaker, “Energy-based modeling in BioNetGen,” Workshop on Formal Methods for Biological and Biomedical Systems (FMBBS), held at the 2016 Institute of Electrical and Electronics Engineers (IEEE) International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China.

Carleton Kingsford, Carnegie Mellon University

March 2016: Accurate, fast, and model-aware transcript expression quantification with Salmon. Simons Institute; Workshop on Regulatory Genomics and Epigenomics.

October 2016: Featured speaker at CMU President’s Global Advisory Council annual meeting. Pittsburgh, PA.

Robert Murphy, Carnegie Mellon University

April 13-16, 2016: Associate Editor, IEEE International Symposium on Biomedical Imaging, Prague, Czech Republic.

June 1-3, 2016: Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh.

June 11-15, 2016: Member, Organizing Committee, CYTO 2016, Seattle, Washington.

July 8-12, 2016: Area Chair for Bioimaging and Visualization, Intelligent Systems for Molecular Biology, Orlando, Florida.

July 24-27, 2016: Instructor, Bioinformatics Course, University of Freiburg. Breisgau, Germany.

Terrence Sejnowksi, Salk Institute for Biological Studies

May 22-26, 2016: Keystone Symposium on The State of the Brain, Alpbach, Austria.

July 3-8, 2016: Thirty-second Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

July 4-9, 2016: Thirty-third Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

2016: Queensland University, Merson Lecture, Distinguished Lecturer. St. Lucia, Brisbane, Australia.

Jiyoung Lee, Research Scientist, Bahar Lab, University of Pittsburgh

February 27-March 2, 2016: Poster, “Global Dynamics of Intact AMPA and NMDA Receptors Using Elastic Network Models”, The 60th Annual Meeting of the Biophysical Society. Los Angeles, CA.

James Krieger, Postdoctoral Associate, Bahar Lab, University of Pittsburgh

April 3-8, 2016: Oral presentation and poster, “Dynamics of Ionotropic Glutamate Receptors and Allosteric Potential of their N-Terminal Domains”. Les Houches-TSRC Workshop on Protein Dynamics. Les Houches, France.

2015

Ivet Bahar, University of Pittsburgh

January 26-28, 2015: The International Human Frontier Science Program Research Grant Review Committee. Strasbourg, France. Review Committee Member.

February 5, 2015: Inaugural Lecture for your appointment as Distinguished Professor of Computational and Systems Biology in the School of Medicine, University of Pittsburgh. Pittsburgh, PA.

February 7-11, 2015: In Vivo Biophysics Subgroup Symposium in conjunction with the Bridging the Sciences: Computation and Experiment, Biophysical Society 59th Annual Meeting. Baltimore, Maryland. Invited Speaker.

February 15-20, 2015: 22nd International Molecular Medicine Tri-Conference.. San Francisco, CA. Featured Speaker.

March 9-11, 2015: CUP XV OpenEye Scientific Software's Annual Meeting, Santa Fe, CA. Levinthal Lecturer.

March 22-26, 2015: ACS National Meeting Symposium, "Progress and Challenges in Molecular Simulations of Biomolecules". Denver, Colorado. Invited Presenter and Speaker.

March 30-31, 2015: Chair of the NIH IMST-R, Pilot Centers for Precision Disease Modeling (U54) study section meeting. Washington, DC. Chair.

April 16, 2015: Bioengineering Department Seminar Series, University of Pittsburgh, PA. Invited Seminar Speaker.

April 23-24, 2015: NIH Director's New Innovator Award Review, Bethesda, Maryland. Editorial Review Panel Member.

June 1-5, 2015: Hands-on Workshop on Computational Biophysics. Pittsburgh Supercomputing Center, Pittsburgh, PA. Instructor.

June 29- July 1, 2015: The International Human Frontier Science Program Selection Committee, Strasbourg, France. Selection Committee Member.

August 9-10, 2015: P01-DK096990 External Advisory Board Meeting, Pittsburgh, PA. Computational Pharmacology Core PI.

September 7-9, 2015: 8th SFB35 Transmembrane Transporters in Health and Disease Symposium Vienna, Austria. Invited Speaker.

September 17-18, 2015: MMBioS National Center for Multiscale Modeling of Biological Systems External Advisory Board Meeting. Pittsburgh, PA. Principal Investigator.

September 20-22, 2015: NINDS Board of Scientific Counselors meeting. Bethesda, MD. Ad Hoc Reviewer.

October 1-2, 2015: Center for Causal Discovery (CCD) External Advisory Board Meeting. University of Pittsburgh, PA. Principal Investigator.

November 11, 2015: University of Pittsburgh Drug Discovery Institute (UPDDI) External Advisory Board (EAB) meeting. Speaker.

November 17-18, 2015: NIH P01 Program Project application "Molecular structure, dynamics, and mechanism of key membrane transporters and enzymes in cellular metabolism". Online Review Panel Chair.

December 4, 2015: CATER Seminar Series Invited Seminar Speaker.

December 7, 2015: University of Maryland Biophysics Program, Seminar Series. Invited Seminar Speaker.

Joseph Ayoob, University of Pittsburgh

March 2015: “Scientists are Made…not Born”, SciTech Days, Carnegie Science Center, Pittsburgh, PA.

July 2015: “Scientists are Made…not Born”, Discover your Future: STEM Career Tour, Grow a Generation. Robert Morris University Engineering Department. Pittsburgh, PA.

September 2015: “Tiered Mentoring and Training in Computational Biology Research”, Academically Based Community Engagement: An Idea Exchange. University of Pittsburgh Honors College, Pittsburgh, PA.

Phillip Compeau, Carnegie Mellon University

2015: Program Committee, Organizing Committee (chair). RECOMB Satellite Conference on Bioinformatics Education. Howard Hughes Medical Institute, Chevy Chase, USA.

2015: “Life after MOOCs.” ELIXIR-GOBLET workshop: defining an e-learning lingua franca. Ljubljana, Slovenia.

James Faeder, University of Pittsburgh

January 22, 2015: Invited seminar, Computational Modeling of Cell Decision Processes,” Department of Cancer Biology, Vanderbilt University Medical School, Nashville, TN.

March 2, 2015: Invited tutorial, “Rule-Based Modeling with BioNetGen and RuleBender,” Cellular Dynamics and Modeling Meeting, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

March 18-21, 2015: Invited speaker, “Systems approach to understanding T cell differentiation,” World Immune Regulation Meeting-IX, Davos, Switzerland.

April 15, 2015: Invited speaker, “Energy Lasso: Combining Rule-Based Modeling and Bayesian Parameter Estimation to Infer Biochemical Mechanisms,” Biophysical Theory Club, University of Pittsburgh, Pittsburgh, PA.

April 27-29, 2015: Workshop organizer and presenter, Computational Methods for Spatially Realistic Microphysiological Simulations 2015, Pittsburgh Supercomputing Center, Pittsburgh, PA.

May 18-19, 2015: Invited speaker, “Rule-based Modeling of Biochemical Systems: Capabilities and Outlook,” 3rd QCBnetwork Workshop: Modeling Cell Biology: Scale and Granularity, San Francisco, CA.

July 13-16, 2015: Invited lecturer, “Methods for Simulating Rule-Based Models”, The 9th q-bio Summer School on Cellular Information Processing, University of New Mexico, Albuquerque, NM.

December 1-3, 2015: Co-organizer and presenter, NIMBioS Working Group for Spatial Cell Simulation, Knoxville, TN.

Carleton Kingsford, Carnegie Mellon University

2015: Detection of Alternative Domains in Chromosome Conformation Capture Data. Highlights talk at ACM-BCB.

November 2015: How fast do ribosomes move? RECOMB Satellite Conference on Bioinformatics Education, HHMI Chevy Chase campus. Chevy Chase, MD.

Robert Murphy, Carnegie Mellon University

June 26-30, 2015: Member, Organizing Committee, CYTO 2015, Glasgow, Scotland.

February 9, 2015: Session Organizer and Chair, Machine-Learning Advances in the Life Sciences, Society for Laboratory Automation and Screening Annual Meeting, Washington, DC.

April 27-29, 2015: Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh, PA.

July 11-15, 2015: Area Chair for Bioimaging and Visualization, Intelligent Systems for Molecular Biology, Dublin, Ireland.

July 20-24, 2015: Instructor, Bioinformatics Course, University of Freiburg. Breisgau, Germany.

December 1-3, 2015: Organizer (with James Faeder), National Institute for Mathematical and Biological Synthesis Working Group on “Spatial Cell Simulations, Knoxville, Tennessee.

Terrence Sejnowksi, Salk Institute for Biological Studies

January 19, 2015: Crick-Jacobs Workshop on Function and Failure of Calcium at Synapses, La Jolla, CA

July 5-9, 2015: Thirty-first Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

2015: Institute of Electrical and Electronics Engineers (IEEE) International Society for Information Theory (ISIT). Plenary Lecture. Hong Kong, People’s Republic of China.

2014

Ivet Bahar, University of Pittsburgh

January 14, 2014: Laufer Center Seminar Series. Stony Brook University, New York. Invited Seminar Speaker.

January 20-22, 2014: The International Human Frontier Science Program Research Grant Review Committee. Strasbourg, France. Review Committee Member.

February 15-19, 2014: Biophysical Society 58th Annual Meeting on "Bridging the Sciences to Explore Biology". Moscone Center in San Francisco, California. Invited Speaker at the Mid-Career Luncheon.

February 19, 2014: Biophysical Society Publications Committee Meeting. San Francisco, California. Publications Committee Member.

March 5-7, 2014: NIH Review Panel for National Biomedical Computation Resource (P41-BTRC) Program. UCSD, San Diego, CA. Review Panel Member.

March 24-25, 2014: National Institute of Biomedical Imaging and Bioengineering (NIBB) and National Institute for General Medicine Sciences (NIGMS) Biomedical Technology Research (P41) Centers Principal Investigator Meeting. Rockville, Maryland. P41 Principal Investigator.

April 4, 2014: Saint Francis University Seminar Series.. Invited Seminar Speaker.

April 7, 2014: NIH Library of Integrated Network-Based Cellular Signatures (LINCS): Perturbation-Induced Data and Signature Generation Centers (U54) Area Review. Washington, DC. Review Panel Chair.

May 7-9, 2014: Membrane Protein Structural Dynamics Consortium Frontiers in Membrane Protein Structural Dynamics. Chicago, IL. Invited Speaker.

May 19-23, 2014: Hands-on Workshop on Computational Biophysics. Pittsburgh Supercomputing Center, Pennsylvania. Instructor.

June 2-6, 2014: Gordon Research Conference on Biopolymers. Salva Regina, Chair of the Conference.

June 15-19, 2014: Coarse-graining as a Frontier of Statistical Mechanics Conference. Santa Fe, New Mexico, Invited Speaker.

July 16-19, 2014: Zing Conference on Protein Folding. Punta Cana, Dominican Republic, Invited Speaker.

August 11-14, 2014: IUPAP Conference for Computational Physics (CCP 2014). Boston, MA, Invited Speaker.

September 10-14, 2014: Biophysical Society Thematic Meeting "Modeling of Biomolecular Systems Dynamics, Allostery and Regulation: Bridging Experiments and Computations." Istanbul, Turkey. Organizing Committee Member.

September 30, 2014: Children's Hospital of Pittsburgh of UPMC, Molecular Medicine Research Seminar Series. Pittsburgh, PA. Seminar Speaker.

October 20-21, 2014: Biophysical Publications Committee Meeting. Rockville, Maryland. Committee Member.

October 30-31, 2014: MMBioS National Center for Multiscale Modeling of Biological Systems External Advisory Board Meeting. Pittsburgh, PA. Principal Investigator.

November 11, 2014: Seminar Series, Department of Chemistry and Biochemistry, University of Maryland, Baltimore, Maryland. Invited Speaker.

December 4, 2014: Israeli Biochemistry Society Meeting on "Molecular Machines in Action" Weizmann Institute of Science, Rehovot, Israel. Keynote Lecturer.

Joseph Ayoob, University of Pittsburgh

April 2014: “Tiered Mentoring & Training in a Medical School REU (Research Experience for Undergraduates) in Computational Biology”, 2014 National Science Foundation BIO REU (Research Experience for Undergraduates) Workshop, Arlington, VA.

September 2014: “How to Prepare Yourself for Success in Graduate School and Beyond- or -How to Avoid Saying, ‘I wish I would’ve done that during graduate school…’”. CPCB MetaSchool (Professional Development Series), University of Pittsburgh School of Medicine, Pittsburgh, PA.

Phillip Compeau, Carnegie Mellon University

2014: “The First (English-language) Bioinformatics MOOC: Lessons Learned.” RECOMB Satellite Conference on Bioinformatics Education. Pittsburgh, PA.

James Faeder, University of Pittsburgh

April 25-27, 2014: Session co-chair, “Systems & Synthetic Biology Session,” Northeast Biomedical Engineering Conference (NEBEC), Northeastern University, Boston, Massachusetts.

April 28-30, 2014: Workshop organizer and presenter, Computational Methods for Spatially Realistic Microphysiological Simulations 2014, Pittsburgh Supercomputing Center, Pittsburgh, PA.

July 28-31, 2014: Invited lecturer, “Methods for Simulating Rule-Based Models Parts I and II”, The 8th q-bio Summer School on Cellular Information Processing, University of New Mexico, Albuquerque, NM.

August 13, 2014: Contributed tutorial, “Modeling Complex Biochemical Systems in Time and Space Using BioNetGen and MCell,” 8th International q-bio Conference on Cellular Information Processing, Santa Fe, NM.

September 1, 2014: Invited seminar, “Computational Modeling of Cell Decision Processes,” Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA.

September 20, 2014: Invited speaker, “Modeling Cell Decision Processes”, Symposium in Honor of Edmund M. Clarke, School of Computer Science Carnegie Mellon University, Pittsburgh, PA.

December 1-4, 2014: Invited speaker, “Mathematical modeling of T cell differentiation,” 2nd Zing Mathematical and Computational Medicine Conference, Cancun, Mexico.

Carleton Kingsford, Carnegie Mellon University

October 2014: “RNA-seq expression estimates need not take longer than a cup of coffee”. Texas Tech University. Lubbock, TX.

Robert Murphy, Carnegie Mellon University

April 28-30, 2014: Instructor and Co-Organizer, MMBioS Workshop on “Computational Methods for Spatially Realistic Microphysiological Simulations”, Pittsburgh, PA.

May 17-21, 2014: Member, Organizing Committee, CYTO 2014, Ft. Lauderdale, FL.

July 11-15, 2014: Area Chair for Bioimaging and Visualization, Intelligent Systems for Molecular Biology, Boston, MA.

Terrence Sejnowksi, Salk Institute for Biological Studies

May 28-June 2, 2014: 79th Cold Spring Harbor Symposium on Quantitative Biology: Cognition, Cold Spring Harbor, NY.

July 5-9, 2014: Thirtieth Woods Hole Workshop on Computational Neuroscience, Telluride, CO

July 6-11, 2014: Twenty-ninth Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

November 7, 2014: Crick-Jacobs Workshop on Regulation of Global Cortical States, Salk Institute, La Jolla, CA.

2014: National Institutes of Health (NIH), National Library of Medicine, Joseph Leiter Lecture Distinguished Lecturer. Bethesda, MD.

Christopher James Langmead, Carnegie Mellon University

April 4, 2014: "Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models", RECOMB14, Pittsburgh PA.

Troy Wymore, Oak Ridge National Laboratory

March 11, 2014: “Computational Enzyme Design", MNPC Seminar series, University of Iowa, Iowa City, Iowa.

Daniel Zuckerman, University of Pittsburgh

March 2014: "Progress and Challenges in Weighted Ensemble Simulation", American Chemical Society Annual Meeting, Dallas, TX.

2013

Ivet Bahar, University of Pittsburgh

January 13-18, 2013: Gordon Research Conference (GRC) on Stochastic Physics in Biology. Ventura, CA. Invited Session Chair.

January 21-23, 2013: Review Committee Meeting for The International Human Frontier Science Program Organization. Strasbourg, France, Committee Member.

March 7-8, 2013: Tetralateral Symposium Tsinghua University, Hong Kong University of Science and Technology, and the Chinese University of Hong Kong. Hong Kong, People’s Republic of China. Invited Speaker.

March 18-19, 2013: NIH Biomedical Technology & Research Centers (P41) Directors Meeting, Bethesda, MD. Invited Speaker.

April 4, 2013: Women in Medicine & Science Forum, "Advancing in a Male-Dominated Academic Culture" Panel. University of Pittsburgh. Pittsburgh, PA. Panel Member.

April 15-19, 2013: Conference on "Protein Dynamics and Function" Collingwood College, Durham University, UK, and workshop on Protein Dynamics and Function at the Durham Institute of Advanced Study organized jointly between Durham Biophysics Sciences Institute and the EU Network SoftComp. Invited Speaker.

May 6-9, 2013: Symposium on "Computational Biology: Then and Today". Weizmann Institute of Science, Rehovot, Israel, Keynote Speaker.

May 14-16, 2013: GLBIO (Great Lakes Bioinformatics, a conference of the International Society for Computational Biology). Carnegie Mellon University, Pittsburgh, PA, Keynote Speaker.

May 21, 2013: UPCI Basic and Translational Seminar Series.. University of Pittsburgh Cancer Institute, PA. Invited Seminar Speaker.

June 3-6, 2013: "In-silico Drug Design and In-silico Screening" track in Drug Discovery & Therapy World Congress 2013 International Conference. International Conference. Boston, MA, Invited Speaker.

June 10-14, 2013: Theoretical and Computational Biophysics Group Computational Biophysics Workshop. Pittsburgh, PA, Lecturer.

July 1-3, 2013: NIH-Interdisciplinary Molecular Science and Training (IMST) Program Review Panel-Site Visit for P41 Application. University of Wisconsin, Madison. Review Panel.

July 21-26, 2013: 7th International Discussion Meeting on Relaxations in Complex Systems (7th IDMRCS). Session: Amorphous pharmaceuticals and biopharmaceuticals - physical and chemical stability. Barcelona Spain. Invited Speaker.

October 1-2, 2013: MMBioS National Center for Multiscale Modeling of Biological Systems External Advisory Board Meeting. Pittsburgh, PA. Principal Investigator.

October 2-3, 2013: MMBioS National Center for Multiscale Modeling of Biological Systems Workshop: Critical Challenges for Spatially temporally-realistic Cell Modeling Packages. Pittsburgh, PA. Workshop Participant.

October 4, 2013: Science 2013 Symposium. Pittsburgh, PA. Invited Speaker.

October 20-22, 2013: NIH Advisory Board Meeting. University of Illinois Urbana-Champaign, IL. Advisory Board Member.

October 25, 2013: Publications Committee Meeting. Rockville, MD. Committee Member.

December 9-10, 2013: NIH R15 Area Review. Washington, DC. Review Panel (Study Section) Member.

Joseph Ayoob, University of Pittsburgh

July 2013: “The Importance of Finding Mentors and Getting Involved”, Find Your Path to a Career in the Health Professions: The Path to Walk Symposium, University of Pittsburgh School of Medicine, Pittsburgh, PA.

Phillip Compeau, Carnegie Mellon University

2013: “Rosalind: Free Bioinformatics Education via Online Introductory Programming.” Joint Mathematics Meetings. San Diego, CA.

James Faeder, University of Pittsburgh

March 19-22, 2013: Contributed talk, “Heterogeneity, signal integration, and synergy in Bacillus subtilis spore germination,” Computational Cell Biology Meeting, 4th Cold Spring Harbor meeting on Computational Cell Biology, Cold Spring Harbor, New York.

April 3, 2013: Invited seminar, “Rule-Based Modeling of Biochemical Signaling,” Van Andel Research Institute Seminar, Grand Rapids, MI.

April 14, 2013: Tutorial presenter, “Spatial Rule-based Modeling of Cellular Biochemistry with MCell/BioNetGen/CellBlender,” Great Lakes Bioinformatics Conference, Pittsburgh, PA.

April 20-22, 2013: Workshop organizer and presenter, Computational Methods for Spatially Realistic Microphysiological Simulations 2013, Pittsburgh Supercomputing Center, Pittsburgh, PA.

May 26-31, 2013: Invited participant, Workshop on Mathematical tools for evolutionary systems biology, Banff International Research Station for Mathematical Innovation and Discovery, Banff, Canada.

July 30, 2013: Invited lecture, “Methods for Simulating Rule-Based Models”, The 7th q-bio Summer School on Cellular Information Processing, Los Alamos National Laboratory.

August 5, 2013: Invited talk, “Rule-Based Modeling of Cell Signaling and Decision-Making in the Immune System,” 2013 NIAID Future of Computational Immunology Workshop, Bethesda, Maryland.

August 7, 2013: Contributed tutorial, “Rule-Based Modeling of Biochemical Systems with BioNetGen,” The 7th International q-bio Conference on Cellular Information Processing, Santa Fe, NM.

August 30-September 3, 2013: Invited talk and session chair, “Energy Lasso: Combining Rule-Based Modeling and Bayesian Parameter Estimation to Infer Biochemical Mechanisms” in session “Physiology based modeling of disease states” at the International Conference on Systems Biology 2013, Copenhagen, Denmark.

November 22, 2013: Keynote address, Annual Retreat of the University of Pittsburgh Immunology Department, Twentieth Century Club, Pittsburgh, PA.

Carleton Kingsford, Carnegie Mellon University

May 2013: RNA-seq expression estimates need not take longer than a cup of coffee. University of Maryland.

November 2013: RNA-seq expression estimates need not take longer than a cup of coffee. Penn State University.

2013: Computational Challenges Comprehending Chromosome Conformation Capture Constraints, 13th INFORMS Computing Society Conference.

2013: Modeling the Evolution of Networks. Systems Biology: Networks, Cold Spring Harbor, NY.

Robert Murphy, Carnegie Mellon University

January 8-11, 2013: High Content Analysis, San Francisco, California, Invited Speaker.

February 26, 2013: Biomolecular Signaling and Control Group, ETH (Swiss Federal Institute of Technology) Zurich, Switzerland, Seminar Speaker.

March 12, 2013: 52nd Annual Meeting, Society for Toxicology, San Antonio, Texas, Invited Speaker.

March 19-22, 2013: 2013 Meeting on Computational Cell Biology, Cold Spring Harbor, New York, Invited Speaker and Session Chair.

April 7-11, 2013: Special Sessions Chair, Institute of Electrical and Electronics Engineers (IEEE) International Symposium on Biomedical Imaging, San Francisco, California.

May 13-14, 2013: Advanced Models of Imaging-based Drug Screening, Houston, Texas, Invited Speaker and Session Chair.

May 14-16, 2013: "Estimating Microtubule Distributions from 2D Immunofluorescence Microscopy Images Reveals Differences Among Human Cultured Cell Lines", 2013 Great Lakes Bioinformatics Conference, Pittsburgh.

May 19-22, 2013: Member, Organizing Committee, CYTO 2013, San Diego, California.

June 12, 2013: Wolfson Bioimaging Colloquium, University of Bristol, England.

June 26, 2013: Seminar, Faculty of Biology, University of Freiburg, Breisgau, Germany.

July 8-9, 2013: “Journées Thématiques du GDR” Bioimage Informatics, Institute Curie, Paris, France, Invited Keynote Speaker.

July 7-12, 2013: Invited Faculty Member, EMBO Practical Course on “Intravital Microscopy, Flow Cytometry and Cell Sorting”, Berlin, Germany.

August 30-September 3, 2013: International Conference on Systems Biology, Copenhagen, Denmark, Invited Speaker and Session Chair.

September 10-13, 2013: 17th International Conference on Image Analysis and Processing, 2nd International Workshop on Pattern Recognition in Proteomics, Structural Biology and Bioinformatics, Naples, Italy, Invited Speaker and Chair.

September 16-17, 2013: The First International Aizu Conference on Biomedical Informatics and Technology, Aizu-Wakamatsu, Japan, Invited Keynote Speaker.

September 23-24, 2013: Cybio Users Group Meeting, Freiburg, Germany, Invited Speaker.

September 27, 2013: Seminar, Novartis, Basel, Switzerland.

September 2013: Track Chair for Bioimage Analysis, ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Washington, DC.

September 29-October 1, 2013: FRIAS LifeNet Meeting on Proteostasis, Breisach, Germany, Invited Speaker.

October 4, 2013: Science 2013, University of Pittsburgh, Invited Speaker.

Terrence Sejnowksi, Salk Institute for Biological Studies

July 7-12, 2013: Twenty-eighth Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

December 19-20, 2013: Crick-Jacobs Symposium on Transgenic Models of the Human Brain, Salk Institute, La Jolla, CA.

Daniel Zuckerman, University of Pittsburgh

July 2013: "The Weighted Ensemble Paradigm for Parallel Sampling of Equilibrium and Non-equilibrium Processes", The Workshop for Free Energy Calculations: Three Decades of Adventure in Chemistry and Biophysics. Snowmass, CO; Organizers: J. Andrew McCammon, Benoit Roux, and Wei Yang.

November 2013: "From the Physics of Trajectories to Simulation Methods for Slow Events at Multiple scales", University of Sao Paolo Workshop on pDynamo and Molecular Simulation. Sao Paolo, Brazil.

November 2013: "Tunable, Mixed-resolution Modeling with Library-based Monte Carlo", University of Sao Paolo Workshop on pDynamo and Molecular Simulation. Sao Paolo, Brazil.

Art Wetzel, Pittsburgh Supercomputing Center

March 26, 2013: "Electron Microscopy Image Registration at the PSC/NRBSC", Seminar, Lichtman Lab, Harvard University, Cambridge, MA.

March 27, 2013: "Electron Microscopy Image Registration at the PSC/NRBSC", Seminar, Emmons Lab, Albert Einstein College of Medicine, Bronx, NY.

Christopher James Langmead, Carnegie Mellon University

March 27, 2013: “Structured probabilistic models of proteins across fitness landscapes", Janelia Farm Research Conference on Biological Sequence Analysis and Probabilistic Models. Ashburn, VA.

Armaghan Naik, Murphy Lab, Carnegie Mellon University

March 20-21, 2013: “Learning and using image-derived cell models with CellOrganizer”, LINCS Data Forum, Harvard Medical School, Boston, Massachusetts.

May 14-16, 2013: "Active Learning of Drug Effects on Subcellular Patterns", 2013 Great Lakes Bioinformatics Conference. Pittsburgh, PA. flash talk.

Devin Sullivan, Murphy Lab, Carnegie Mellon University

May 14-16, 2013: "Predicting subcellular localization of small molecules", 2013 Great Lakes Bioinformatics Conference. Pittsburgh, PA. flash talk.

Taraz Buck, Murphy Lab, Carnegie Mellon University

May 14-16, 2013: “Modeling and simulation of 3D cellular and nuclear shape using a shape space learned from fluorescent microscopic images”, 2013 Great Lakes Bioinformatics Conference. Pittsburgh, PA. flash talk.

Gregory Johnson, Murphy Lab, Carnegie Mellon University

May 14-16, 2013: "Image-derived models of morphological changes associated with neuronal differentiation of PC12 cells", 2013 Great Lakes Bioinformatics Conference. Pittsburgh, PA. flash talk.

Aparna Kumar, Murphy Lab, Carnegie Mellon University

May 14-16, 2013: "Automated Analysis of Immunohistochemical Images Identifies Candidate Location Biomarkers for Cancers", 2013 Great Lakes Bioinformatics Conference. Pittsburgh, PA. flash talk.

2012

Ivet Bahar, University of Pittsburgh

February 25-29, 2012: 56th Biophysical Society Annual Meeting .San Diego, CA. Executive Committee Member, Council Member and Panelist.

March 7-9. 2012: EMBO Workshop VIZBI 2012 on Visualizing Biological Data, Visualization of Proteins & Complexes Session, European Molecular Biology Laboratory. Heidelberg, Germany. Invited Speaker.

April 24, 2012: Seminar at SUNY Buffalo, NY.

May 2-4, 2012: Membrane Protein Structural Dynamics Consortium (MPSDC). Chicago, IL. Invited Speaker and Discussion Panel member.

June 3-8, 2012: Gordon Research Conference on Biopolymers. Salve Regina, Newport, RI. Vice Chair.

July 24-26, 2012: Biodynamics Meeting. Buffalo, NY. Keynote Speaker.

September 6, 2012: Seminar at the Ohio State University, Children's Hospital.

October 8-10, 2012: CECAM Workshop "Signalling pathways: Interplay between microscopic changes and global behavior of biological systems." Ecole Normale Supérieure de Cachan, France. Invited Speaker.

October 28-29, 2012: RiMED symposium on Comparative Effectiveness Research & Personalized Medicine. Sicily, Italy. Invited Speaker and advisory board member for RiMed.

October 31, 2012: University of Pittsburgh School of Medicine and Koc University School of Medicine Joint Symposium. Istanbul, Turkey. Invited Speaker at the symposium and Bogazici University Chemical Engineering Department.

December 3-7, 2012: Zing Conference on Mathematical and Computational Medicine. Mexico. Plenary Speaker.

Joseph Ayoob, University of Pittsburgh

July 2012: “Finding your Summer Experience and Beyond” The Road to Medical School and Professional Opportunities in the Health Sciences: The Path to Walk Symposium, Children’s Hospital of Pittsburgh UPMC, Pittsburgh, PA.

Phillip Compeau, Carnegie Mellon University

2012: RECOMB Satellite Conference on Bioinformatics Education. Program Committee, Organizing Committee. St. Petersburg, Russia.

2012: “Rosalind: Learning Bioinformatics through Programming.” Toward the 3-D Virtual Cell. La Jolla, CA, USA.

James Faeder, University of Pittsburgh

February 21, 2012: Invited talk, “Modeling Bacterial Spore Germination,” MURI Review Meeting, Natick Soldier Systems Center, Natick, MA.

March 28-29, 2012: Invited talk, “A Brief Introduction to Rule-Based Modeling,” CMACS Workshop on Systems Biology and Formals Methods, New York University, New York, NY.

April 27, 2012: Invited seminar, “Rule-Based Modeling of Biochemical Signaling”, Biophysics Seminar, Ohio State University, Columbus, Ohio.

May 7-9, 2012: Workshop organizer and presenter, Computational Methods for Spatially Realistic Microphysiological Simulations 2012, Pittsburgh Supercomputing Center, Pittsburgh, PA.

June 8, 2012: Invited seminar, “Modeling Cell Decisions: Two Case Studies,” Systems Biology Theory Lunch, Harvard Medical School, Boston, MA.

June 29, 2012: Invited talk, “(Some) Frontiers in Rule-Based Modeling,” 4th Workshop on Logic and Systems Biology in association with LICS 2012, Dubrovnik, Croatia.

August 3, 2012: Invited lecture, “Methods for Simulating Rule-Based Models”, The Sixth q-bio Summer School on Cellular Information Processing, Los Alamos National Laboratory.

August 8, 2012: Contributed tutorial, “Rule-Based Modeling of Biochemical Systems with BioNetGen,” Sixth International q-bio Conference on Cellular Information Processing, Santa Fe, NM.

August 28-9, 2012: Invited talk, “Modeling Bacterial Spore Germination,” MURI Spore Germination Workshop, University of Connecticut Health Center, Farmington, CT.

September 14, 2012: Invited talk, “Some Frontiers in Rule-Based Modeling,” CMACS-ARiSE Workshop, Washington, DC.

October 10, 2012: Invited seminar, “Rule-Based Modeling for Systems Biology,” Genetics Colloquium, University of Wisconsin, Madison, WI.

October 18-19, 2012: Invited talk, “Modeling and Analysis of Peripheral T Cell Differentiation,” CMACS PI meeting, Stony Brook University, Stony Brook, NY.

November 6, 2012: Invited talk, “Rule-Based Modeling for Systems Biology,” International Conference on Computer-Aided Design (ICCAD), Special Session on Modeling and Design Automation of Biological Circuits and Systems, San Jose, CA.

December 1-4, 2012: Invited talk, “Rule-Based Modeling for Systems Biology,” Mathematical and Computational Medicine Conference, Cancun, Mexico.

Carleton Kingsford, Carnegie Mellon University

January 2012: Graph-theoretic Approaches for Testing Embeddability and Spatial Functional Enrichment in Chromosome Conformation Data. Pac. Symp. Biocomp., Hawaii.

February 2012: Two computational challenges in evolution: Influenza reassortment detection & Reconstruction of ancestral protein interactions. Campbell & Company, Baltimore, Maryland.

March 2012: Network Archaeology: Uncovering Ancient Networks from Present-day Interactions. IMA workshop Network Links: Connecting Social, Communication, and Biological Network Analysis, University of Minnesota.

2012: Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions, ISMB 2012 highlights track talk.

2012: Network Archaeology: Uncovering Ancient Networks from Present-day Interactions, SIAM Conference on Discrete Mathematics, Halifax, Nova Scotia.

Robert Murphy, Carnegie Mellon University

May 2-5, 2012: Member, Program Committee, International Symposium on Biomedical Imaging, Barcelona, Spain.

May 15-17, 2012: Honorary Conference Chair and member of Organizing Committee, GLBIO 2012, Ann Arbor, Michigan.

June 22-27, 2012: Member, Organizing Committee, CYTO 2012, Leipzig, Germany.

July 15-17, 2012: Area Chair for Bioimaging and Visualization (with Sean O’Donoghue), Intelligent Systems for Molecular Biology, Long Beach, California.

October 7-10, 2012: Track Chair for Bioimage Analysis, ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Orlando, Florida.

September 20-21, 2012: Invited Faculty Member, International Symposium in Applied Bioimaging, Porto, Portugal.

September 24-27, 2012: MipTec 2012, Basel, Switzerland, Invited Speaker.

October 5, 2012: Institute of Electrical and Electronics Engineers (IEEE) Conference on Bioinformatics and Biomedicine (BIBM), 2012, Philadelphia, Pennsylvania, Invited Keynote Speaker.

December 1-5, 2012: Mathematical and Computational Medicine Conference, Invited Speaker, Xcaret, Mexico.

Terrence Sejnowksi, Salk Institute for Biological Studies

July 8-13, 2012: Twenty-seventh Woods Hole Workshop on Computational Neuroscience, Telluride, CO.

2012: York University Ian P. Howard Lecture, Distinguished Lecturer. Toronto, Ontario, Canada.

Christopher James Langmead, Carnegie Mellon University

March 7, 2012: “Probabilistic graphical models for protein sequence, structure, and dynamics”, Rutgers University, Department of Chemistry and Chemical Biology, New Brunswick, NJ.

April 18, 2012: “Probabilistic graphical models for structural biology”, Carnegie Mellon University, Department of Philosophy, Seminar on Causation. Pittsburgh PA.

Narges Sharif Razavian, Langmead Lab, Carnegie Mellon University

December 8, 2012: “Kernels for Protein Structure Prediction”, 2012 NIPS Workshop entitled “Confluence between Kernel Methods and Graphical Models”. Lake Tahoe, NV

Markus Dittrich, Pittsburgh Supercomputing Center

2012: Structure and Function of Synapses: Novel Insights from Spatially Realistic Cell Simulations, Seminar, Theoretical and Computational Biophysics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL.

 

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