Latino Studies at New York University

Computational Biology


Fall 2014

The Fall 2014 Biomathematics/Computational Biology Colloquium will begin on Tuesday, September 9.

   September 9         Antoni Luque, Postdoc, Schlick Lab, Chemistry Department, New York University

                               Role of linker histones in the structure and dynamics of chromatin fibers

   September 16       Adriana Compagnoni, Stevens Institute of Technology

   September 23       To be announced

   September 30       To be announced

   October 7             Alexander Alekseyenko, NYU School of Medicine

                              Bayesian phylogenetics with BEAST

   October 14           Fall Break: No colloquium scheduled

   October 21           Michele Insanally, New York University

   October 28           To be announced

   November 4         Laura Miller, Associate Professor of Mathematics and Biology, University of North Carolina

   November 11       James Sneyd

   November 18       Maurizio Porfiri, Department of Mechanical and Aerospace Engineering, Polytechnic School of Engineering, NYU

   November 25       To be announced

   December 2         To be announced

   December 9         To be announced

Spring 2014

   January 28           Dáibhid Ó Maoiléidigh, Laboratory of Sensory Neuroscience, The Rockefeller University

                              The Babel Fish: Active Signal Detection in the Ear

   February 4           Colloquium Rescheduled

   February 11          Aviv Bergman, Department of Systems and Computational Biology, Albert Einstein College of Medicine

                              Evolution is Pleased with Simplicity

   February 18          No Colloquium Scheduled

   February 25          No Colloquium Scheduled

   March 4                Ilya Korsunsky, Computational Biology PhD Student, New York University

                              Novel Causal Score for Learning Conjunctive Bayesian Networks

   March 11              Leon Axel, Departments of Radiology, NYU School of Medicine

                              Sparsity-based Cardiovascular Magnetic Resonance Imaging (MRI) of Physiologic Dimensions

   March 18              No Colloquium Scheduled: Spring Break

   March 25              Samuel Kou, Department of Statistics, Harvard University

   April 1                  Ben Ovryn, Department of Anatomy and Structural Biology, Albert Einstein College of Medicine

                              Tracking surface glycans on live cancer cells with single molecule sensitivity

   April 8                 Joshua Goldwyn, Center for Neural Science, New York University

                              A model of the medial superior olive explains spatio-temporal features of local field potentials

   April 15                POSTPONED - The new date will be posted here

                              Antoni Luque, Biomath Group, Department of Chemistry, New York University

                              Role of linker histones in the structure and dynamics of chromatin fibers

   April 22                POSTPONED - The new date will be posted here

                              Alexander Alekseyenko, NYU School of Medicine

                              Bayesian phylogenetics with BEAST

   April 29                Constantin Aliferis, NYU Center for Health Informatics and Bioinformatics

                              Frontier problems in feature selection for Big Data analytics

   May 6                   Marc Birtwistle, Mount Sinai School of Medicine

                              Noise and Signaling in Cancer Systems Pharmacology

Fall 2013 SCHEDULE

   Please note the Fall 2013 colloquium will take place in a new location, WWH 1314.

   October 1               Victor Barranca, Courant Institute of Mathematical Sciences and Abu Dhabi, NYU

                                Sparsity and Compressed Coding in Sensory Systems

   October 8               Rodica Curtu, University of Iowa

The unfolded protein response in mammalian cells under stress: a modeling approach

   October 15             No Colloquium Scheduled: Fall Recess

   October 22             Xiaoyu Luo, University of Glasgow

                                The Optimal Fibre Orientation in an Iliac Bifurcation Model

   October 29             Calvin Zhang, Courant Institute of Mathematical Sciences, NYU

Phase response properties of half-center oscillators (joint work with Tim Lewis)

   November 5            Karen Alim, Harvard University

                                Organization of fluid flow in the vein networks of the slime mold Physarum polycephalum

   November 12          Bin Min, New York University

                                Stochastic energetics and adiabatic elimination for non-Gaussian processes:
                                Insight from Marcus stochastic calculus

   November 19          Samuel Isaacson, Boston University

                                The Influence of Spatial Variation in Chromatin Density on the Time to Find DNA Binding Sites

   November 26          Rachel Hodos, Computational Biology PhD Student, NYU

Encoding evidence of independence into Bayesian network structure learning                          

   December 3           Brian Kidd, Icahn Institute for Genomics and Multiscale Biology and Icahn School of Medicine at Mount Sinai

                                Connecting High-throughput Data to Build Better Models of the Immune System in Health and Disease

   December 10          Daniel Fisher, Stanford University

                                 Making sense --- or not --- of deep DNA sequencing data


   January 29             Jay Humphrey, Biomedical Engineering, Yale University

                                Computational Modeling of Vascular Adaptation - Applications from Aneurysms and Tissue Engineering

   February 5             No Colloquium Scheduled

   February 12            Jonathan Fisher, Laboratory of Sensory Neuroscience, Rockefeller University

                                Shedding light on the elusive mechanics of hearing in the mammalian cochlea

   February 19            David Sontag, Computer Science, NYU

                                Extracting structure from data

   February 26            Rolf Ryham, Mathematics, Fordham University

                                Variational Approaches to Membrane Modeling: Pore Dynamics in Liposomes

   March 5                  No Colloquium Scheduled

   March 12                 Justin Jee, Computational Biology PhD Student, NYU

                                 What can signaling games tell us about evolution, from the RNA world to the present?

   March 19                 Spring Break: No Colloquium Scheduled

   March 26                 Dana Pe'er, Biological Sciences, Columbia University

                                 Mapping tumor heterogeneity and developmental trajectories using 40 markers at single cell resolution

   April 2                     No Colloquium Scheduled

   April 9                     Nathaniel Hupert, MD, MPH, Weill Cornell Medical College

                                 Finding math in unlikely places: public health preparedness

   April 16                   Karen Lam, Computational Biology PhD Student, NYU

                                 Using global network alignment for multi-species network alignment

                                 Karen Ong, Computational Biology PhD Student, NYU

                                 Computational modeling of the horizontal transmission of Klebsiella in the ICU

   April 23                   Andrew Matteson, Computational Biology, NYU

                                 Doctoral Dissertation Defense

                                 Computational Methods in Model Merging with Applications to Pharmaceutical Development

   April 30                   Ramya Raviram, Computational Biology PhD Student, NYU

                                 The effect of enhancers on the transcriptome and chromosomal interactome in developing lymphocytes

                                 Mingzhi Lin, Computational Biology PhD Student, NYU

                                 Horizontal gene transfer in bacterial populations: modeling, simulation and bioinformatics analysis

   May 7                     Joel Dudley, Mount Sinai School of Medicine

                                Connecting the universe of biomedical data to build predictive models of drugs and disease

   May 14                   Stephen Keeley, Computational Biology PhD Student, NYU

                                Modeling Fast and Slow Gamma Bands in the Rat Hippocampus


   September 4          Aditya V. Rangan, Courant Institute of Mathematical Sciences, NYU

                                Efficient methods for detecting low-rank substructure

   September 11         No colloquium scheduled

   September 18         Long Qian, PhD Candidate, Center for Genomics and Systems Biology, NYU

                                Evolutionary dynamics of restriction site avoidance

   September 25         Marcelo Magnasco, Mathematical Physics Lab, The Rockefeller University

                                The architecture and plasticity of vascular systems: plant leaves, slime molds and the mammalian cortex

   October 2               Marco Bacci, Engineering Division, University of Florence, Italy

                                Macromolecule Dynamics - from a Coarse Grained Approach to Continuum Modeling

   October 9               Joao Xavier, Computational Biology, Memorial Sloan-Kettering Cancer Center

                                Robustness in cell-cell interactions

   October 16             Fall Recess: No colloquium scheduled

   October 23             Kenneth Ho, Courant Institute of Mathematical Sciences, NYU

                                Parameter-free statistical model invalidation for biochemical reaction networks

   October 30             No colloquium scheduled

   November 6           Robert Froemke, Skirball Institute and NYU Neuroscience Institute, NYU School of Medicine

                                Long-term cortical synaptic plasticity improves sensory perception

   November 13         Alejandra Leo-Macias, Postdoc, Stokes Lab, Skirball Institute, NYU School of Medicine

                               Structural characterization of the Red Blood Cell skeleton by Cryoelectron Tomography

   November 20         Thomas Fai, Doctoral Candidate, Courant Institute of Mathematical Sciences

                               A discrete model of the red blood cell cytoskeleton and its use in Immersed Boundary method simulations

   November 27         Jay Bardhan, Department of Electrical and Computer Engineering, Northeastern University

                               Future-proof modeling tools for protein electrostatics: extending physical insights with boundary-integral methods

   December 4           Ron Elber, Department of Chemistry and Biochemistry and
                                Institute for Computational Engineering and Sciences, University of Texas at Austin

                               Molecular Machines

   December 11         Chengcheng Huang, Computational Biology Program, Mathematics Department, NYU

                               Computational Biology PhD Student Presentation: Frequency Shift Detector Model for Shepard Tone Comparison


 January 30

Cristina Turner, Universidad Nacional Cordoba

Shape Optimization for Tumor Location

 January 31

No Colloquium Scheduled

COB Student Luncheon, Courant Institute Lounge, 13th Floor Warren Weaver Hall

 February 7
No Colloquium Scheduled

 February 14
Bud Mishra, Computer Science and Mathematics, Courant Institute, NYU

The Genome Question: Moore vs. Jevons

 February 21
Adam Stinchcombe, Courant Institute of Mathematical Sciences, New York University

The Role of Randomness in the Expression of Genes

 February 28
Eric Schadt, Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine

Reverse Engineering Biological Systems to Construct Disease Networks

 March 6
No Colloquium Scheduled

 March 13
No Colloquium Scheduled: Spring Break

 March 20
Ravi Iyengar, Experimental Therapeutics Institute and Systems Biology Center New York, Mount Sinai School of Medicine

Shape and Signal Flow in Mammalian Cells

 March 27
Ignacio Rodriguez, University of California, Irvine

Evolutionary Dynamics of Feedback Escape in Stem-cell-driven Cancers

 April 3
Sanford M. Simon, Rockefeller University

The search for the Holey Grail: Transport Mechanism(s) of the nuclear pore

 April 10
Edo Kussell, NYU Biology and Physics

Optimal lineage principle for age-structured populations

 April 17
Lisa Fauci, Tulane University, Mathematics Department

Calcium-driven dynamics of undulatory swimmers: a tale of two Reynolds numbers

 April 24
Stuart Sealfon, Mount Sinai School of Medicine, Neurology

Do we know how drugs work? A systems biology perspective.

 May 1
Kenneth Ho, Computational Biology Program, NYU

Doctoral Dissertation Public Defense: Fast direct methods for molecular electrostatics

SPECIAL DAY, TIME, and LOCATION: Monday, May 14 at 3:45pm, WWH room 1314

Jun Yan, Functional Genomics Group, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences 

Network Reconstruction of Inter-organ Metabolic Transport in Mammals

 May 15
Laura Miller, Mathematical Physiology Group, UNC-Chapel Hill

Scaling effects in biological pumping: Tubular and growing hearts


September 13

Terry Krulwich, Mount Sinai School of Medicine

Are Anomalous effects of genetically deleting a sodium/proton antiporter of Staphylococcus aureaus due to loss of cell-wide stress response?

September 20  

Demian Szyld, MD, NYU Langone Medical Center

Healthcare Simulation at NYU Langone Medical Center: Where are we and where are we going?

September 27

David Wootton, Cooper Union

Image-based modeling of the upper airway in Obstructive Sleep Apnea Syndrome

October 4

Alexander Alekseyenko, NYU School of Medicine

Estimating multiple haplotypes and their frequencies from next-generation sequencing data

October 11

Fall Break

October 18

David Gresham, NYU, Center for Genomics and Systems Biology

Global Analysis of Cell Growth Programs in Saccharomyces cerevisiae

October 25

Timothee Lionnet, Albert Einstein College of Medicine

Probing transcription regulation in live cells, one mRNA at a time

November 1

No Colloquium Scheduled

November 8 

Harold Scheraga, Cornell University, Chemistry Department

Advances in Protein Biophysics

November 15

Themis Lazaridis, City College of New York, Chemistry Department

Modeling membrane binding and permeabilization by antimicrobial peptides

November 22

Ben Ovryn, Albert Einstein College of Medicine

Forward and inverse methods applied to imaging the topography and reflectivity of the ventral surface of fixed and live cells using confocal interference microscopy

November 29

No Colloquium Scheduled

December 6

K. Melissa Hallow, Novartis Pharmaceuticals

The Cardiovascular-Renal Simulator (CVR-sim): a large-scale mechanistic model for evaluating the effects of antihypertensive agents on chronic heart failure

December 13

COB Student Public Presentations

Christoph Hafemeister, NYU, Biology Department

Incorporating Prior Knowledge Into Network Inference

Francis Kirigin, NYU, Sackler Institute

Integrative Biclustering of DNAse hypersensitivity and binding site information for learning conserved co-regulated groups active during hematopoietic stem cells differentiation




January 25

Cheng Ly, University of Pittsburgh

Coupling Regularizes Individual Units in Noisy Populations

(Joint work w/Bard Ermentrout)

February 8 

Enkeleida Lushi, Courant Institute

The coupling of chemotaxis and hydrodynamics in suspensions of micro-swimmers

February 15

Denis Pelli, Psychology & CNS NYU and Jeremy Freeman, CNS NYU

Compulsory pooling of crowded objects. A mixture model

February 22

Frank Hoppensteadt, NYU

Mathematical Models of Malaria: A nonlinear systems analysis of a complex disease

March 1

Timothy Cardozo, Sackler

Computational Biology of Antigenic Variation

March 8

Larry Sirovich, Mount Sinai School of Medicine/Rockefeller

Behavior of Spiking Neurons:  Analyzes & Speculations

March 22

Abba Leffler, D.E. Shaw Research

Applications of long-timescale molecular dynamics simulation to protein function and folding

April 5

David Beveridge, Wesleyan

Dynamical Allosterism in a DNA Mismatch Repair Protein, MutS

April 12

Brian Harms, Merrimack Pharmaceuticals

Systems-guided development of a bispecific antibody against the ErbB receptor network

April 19

Stephen Small, NYU, Biology Department

Experimental tests of the Bicoid morphogen hypothesis

April 26

Arjun Raj, University of Pennsylvania

How does DNA know what time it is?

May 3

COB Student Public Presentations

Chaya Levovitz - Exploring the Association btwn Genetic Variations in Immune-Related Genes and Susceptibility to HNSCC

Leif Halvorsen - Enhancing protein binding with non-canonical amino acids: Building an HIV-1 envelope glycoprotein binding molecule

May 10

COB Student Public Presentation

Irina Nudelman - Reduction and fragility in biological networks



Venue:  Warren Weaver Hall, Fridays at 4 p.m. Room 102WWH

September 17

Michael Shelley, Courant Institute

Complex Fluids in Biology

October 1

Chris Wiggins, Columbia University

Form, function, and information processing in small biological networks

October 22

COB Student Public Presentations

Evgeny Shmelkov (COB/Sackler student) - Statistical Detection of an Epitope-Specific Response to HIV-1 gp120 Immunization in Human Subjects

Ruth Griswold (COB/MSSM student) - Mathematical modeling of metastatic growth in the lymphatic vessels

October 29

Meihua Tu, Pfizer

Computer Assisted Design of ACC Inhibitors

November 12

COB Student Public Presentations

Katherine Mantzaris (COB/MSSM student) - Regression Analysis for Parameter estimation and Model Selection in Electrophysiological Models of Cardiac Cells

Andrew Sundstrom (COB/CS Student) - Analysis of Atomic Force Micrographs to Measure RNA and DNA with High Precision

November 19

Harel Weinstein, Cornell University

Combining Computational and Experimental Biophysics to reveal molecular mechanisms of membrane proteins involved in cell signaling

December 3




Venue:  Warren Weaver Hall, Fridays at 4 p.m. Room 102WWH

January 29

Cameron Abrams, Drexel University

Large-scale conformational sampling in all-atom protein models using temperature-accelerated molecular dynamics

February 12

Stuart Sealfon, Mount Sinai School of Medicine

Systems Biology and Therapeutics

February 26 CANCELLED
March 12

Ravi Sachidanandam, Mount Sinai School of Medicine

Gene Expression: what does it say about you?

April 2

Eric Siggia, Rockefeller

Geometry, Genetics and Evolution

April 16 

COB Student Public Presentations

Yun Lu (NYU - CS) - Functional Annotation, Statistic Analysis, and Integrated Discovery of high throughput datasets

Andrew Matteson (NYU - Math) - Kinetic Model Identification of Hepatocyte Growth Factor Signaling in Cancer

April 30

Sam Burns, NYU

There is no clock in the gamma-band activity of the local field potential



Venue:  Warren Weaver Hall, Fridays at 4 p.m. Room 102WWH

September 25

Bud Mishra, NYU

Expedition in Systems Biology

October 16

Avi Ma'ayan, Mount Sinai School of Medicine

Data Mining in Systems Biology

October 23

COB Student Public Presentations

Mariann Micsinai (NYU, Sackler) - Co-profiling of copy number events and DNA marks in Cancer

David Braun (MSSM) - STAT3 Activation Dynamics in Response to IL-6 and IL-10

October 30

Luca Maragliano, University of Chicago

Mapping the network of pathways of CO diffusion in myoglobin

November 6


November 20

Eric Sobie, Mount Sinai School of Medicine

Models in cardiac cellular physiology: molecular details versus simplicity

December 11

Ruth Lehmann, Skirball

Understanding regulation of a special stem cell



Venue:  Warren Weaver Hall, Fridays at 4 p.m. Room 102WWH

January 30

Mark Siegal, NYU, Biology Department

Testing Models of Phenotypic Robustness and Network Centrality

February 13

Roman Osman, Mount Sinai School of Medicine

The Role of Water in Recognition of Acetylated Lysine by Bromodomains

February 27

John Rinzel, NYU, Center for Neural Science

Precise Temporal Processing in the Auditory Brain Stem

March 13

Mark Tuckerman, NYU, Chemistry Department

Enhancing conformational sampling in complex systems via novel spatial-warping transformations

April 3

Bob Shapley, NYU, Center for Neural Science

Analyses of neuronal populations in the primary visual cortex, V1: Dynamics and spatial summation

April 24

COB Student Public Presentations

Sarah Sirin (NYU, Sackler) - Modelling of lipids and proteins: a Coarse-Grained approach to studying membrane protein dynamics

Segun Jung (NYU, Chemistry) - RNA Structure Analysis and Modelling

May 1

Bruce Tidor, MIT

Molecular and Network Modeling in Synthetic and Systems Biology



Venue: Warren Weaver Hall,  Fridays at 4 p.m. Room 102

September 26

Michael Shelley, NYU Courant Institute, Math Faculty

Living Suspensions

October 10

Alex Greenfield (Sackler)

Towards discovering Cancer pathways

October 17

Charles Peskin, NYU Courant Institute, Math Faculty

The Look-Ahead Model for the Transcriptional Dynamics of RNA Polymerase

October 31

Eric Vanden-Eijnden, NYU Courant Institute, Math Faculty

Transition Pathways of Rare Ractive Events in Molecular Simulations

November 14


COB Student Public Presentations

Hong Wang (Sackler) - Rational Design of Modulators of the Unfolded Protein Response

Kenneth Ho (NYU) - Simple Model Reduction Techniques Applied to Apoptosis


There will be no more COB colloquiums this term.  However, please note, COB Day attendance will be required in lieu of any further COB colloquiums.    Please plan to attend COB Day, scheduled for Saturday, December 6th.



Venue: Warren Weaver Hall,  Fridays at 4 p.m. Room 102

February 1

Kris Gunsalus, NYU, Biology Department

C. elegans embryogenesis as a model for developmental systems biology

Download paper

February 15

COB Student Public Presentations

Mainak Patel (Sackler) - Odor Discrimination in a Hodgkin-Huxley type Model of the Locust Antenna Lobe

Kevin Jarret (NYU) - A Generalized Linear Model for Contrast Gain Control in Retinal Ganglion Cells

February 29

Souheil Inati, NYU, Center for Neural Science

Some Computational Problems in Structural and Functional Magnetic Resonance Imaging of the Brain

March 14

J. Brandon Laflen, Sackler

Common aspects of temporal and spatial processing across normal hearing and cochlear implant listening

March 28

COB Student Public Presentations

Amrita Sarkar (MSSM) - Prediction and Analysis of Cardiac Action Potential Properties Using Partial Least Squares (PLS) Regression

Juan Mobarec (MSSM) - Computational Modeling of GPCRs

April 11

COB Student Public Presentations

Tom Weingarten (NYU) - Coarse Grained Molecular Dynamics Simulations of Biomolecular Systems

David Rooklin (NYU) - PTP1B:  Resolving the Wild-type Mechanism

April 25

Alex Mogilner, UC Davis

Multi-scale modeling of motile cell mechanics and prediction of cell shape