Daniel Tranchina

Daniel Tranchina

Professor of Biology, Mathematics, Neural Science

Ph.D. 1981 (neurobiology), Rockefeller; B.A. 1975 (neurobiology), SUNY (Binghamton).

Office Address: 

New York University
Department of Biology
1009 Silver Center
100 Washington Square East
New York, NY 10003-6688

Phone: 

(212) 998-3109

Fax: 

(212) 995-4015

Areas of Research/Interest: 

Computational Neuroscience, Phototransduction, Stochastic Problems in Cellular and Molecular Biology, Statistical Analysis and Modeling of Genome-Scale Data

List of Publications from Pubmed

List of citations from Google Scholar

Research

My research in computational biology and neuroscience integrates data from experimental studies, theoretical analysis, mathematical modeling, and computer simulation.

One of my ongoing projects, in vertebrate phototransduction, focuses on light adaptation in rods and cones, and on the reproducibility of rod responses to single photons.  Electrophysiological and biochemical data provide a basis for developing mathematical models that account for light adaptation and statistical properties of the singe-photon response in terms of the molecular mechanisms underlying phototransduction.

Another ongoing project involves the development of "statistical mechanical" methods for modeling large neural networks.  These methods employ the theory of the probability (population) density function. Factors that make conventional methods unwieldy or intractable - thousands of neurons and millions of synapses ¬are used to great advantage in these methods. Similar neurons are lumped together into populations, and one tracks the distribution of neurons over state space in each population.  The state of a neuron is determined by the dynamic variables in the underlying single-neuron model.  The population-firing rate is given by the flux of probability across a particular surface in state space. Neurons are coupled via stochastic synapses; the rate of excitatory/inhibitory input events for a target neuron is determined by the rate of action potentials in each of the presynaptic populations and by the average number of synapses the postsynaptic neuron receives from each of these populations.

In an ongoing collaboration with Arjun Raj at the University of Pennsylvania, I am analyzing and modeling stochastic gene expression. The models include gene switching, synthesis and degradation of mRNA and proteins, and cell divisions. A goal is to understand sources of large fluctuations in the number of transcripts from genes that are expressed at low levels, the consequences for protein levels, and the implications for cell fate and cell physiology in general. Future modeling will focus on gene networks.

Finally, I am collaborating with Professor Gloria Coruzzi and her lab on projects involving the identification and modeling of gene regulatory networks underlying nitrogen assimilation and metabolism in Arabidopsis. Statistical analysis of microarray, RNA-Seq and ChIP-Seq data plays a central role in these projects.

Teaching

I teach both in the Department of Biology and the Department of Mathematics.

Graduate Biology courses include:

  1. Statistics in Biology
  2. Mathematics in Medicine and Biology
  3. Computers in Medicine and Biology

Graduate Mathematics courses include:

  1. Mathematical Aspects of Neurophysiology
  2. Stochastic Problems in Cellular, Molecular and Neural Science

Biosketch

I received my Ph.D. in 1981 from the Rockefeller University, where I studied physical chemistry, membrane biophysics, neurophysiology, and mathematics. My dissertation was an analysis of information processing in the outer retina of the turtle. My postdoctoral research was a combined experimental and theoretical study of light adaptation -- a process by which the retina adjusts its sensitivity according to lighting conditions. In 1984, I joined the faculty of New York University with a joint appointment in the Courant Institute of Mathematical Sciences and the Department of Biology.

Fellowships/Honors:

Whitehead Fellowship, New York University, 1986.

Selected Works:

Ekanadham, C., Tranchina, D., and Simoncelli, E.P. (2011) Recovery of sparse transformation-invariant signalswith continuous basis pursuit. IEEE Transactions on Signal Processing, 59, 4735—4744.

Recent Pubmed search results
Modulation of mouse rod response decay by rhodopsin kinase and recoverin.
J Neurosci   (2012 Nov 7)
Chen CK, Woodruff ML, Chen FS, Chen Y, Cilluffo MC, Tranchina D, Fain GL
Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression.
Phys Rev E Stat Nonlin Soft Matter Phys   (2012 Jun)
Stinchcombe AR, Peskin CS, Tranchina D
Channel modulation and the mechanism of light adaptation in mouse rods.
J Neurosci   (2010 Dec 1)
Chen J, Woodruff ML, Wang T, Concepcion FA, Tranchina D, Fain GL
In silico evaluation of predicted regulatory interactions in Arabidopsis thaliana.
BMC Bioinformatics   (2009)
Nero D, Katari MS, Kelfer J, Tranchina D, Coruzzi GM
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule".
BMC Syst Biol   (2009)
Nero D, Krouk G, Tranchina D, Coruzzi GM
Spike train statistics and dynamics with synaptic input from any renewal process: a population density approach.
Neural Comput   (2009 Feb)
Ly C, Tranchina D
A systems approach uncovers restrictions for signal interactions regulating genome-wide responses to nutritional cues in Arabidopsis.
PLoS Comput Biol   (2009 Mar)
Krouk G, Tranchina D, Lejay L, Cruikshank AA, Shasha D, Coruzzi GM, Gutierrez RA
Critical analysis of dimension reduction by a moment closure method in a population density approach to neural network modeling.
Neural Comput   (2007 Aug)
Ly C, Tranchina D
Population density methods for stochastic neurons with realistic synaptic kinetics: firing rate dynamics and fast computational methods.
Network   (2006 Dec)
Apfaltrer F, Ly C, Tranchina D
Stochastic mRNA synthesis in mammalian cells.
PLoS Biol   (2006 Oct)
Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S
A comparison of release kinetics and glutamate receptor properties in shaping rod-cone differences in EPSC kinetics in the salamander retina.
J Physiol   (2005 Dec 15)
Cadetti L, Tranchina D, Thoreson WB
Toward a unified model of vertebrate rod phototransduction.
Vis Neurosci   (2005 Jul-Aug)
Hamer RD, Nicholas SC, Tranchina D, Lamb TD, Jarvinen JL
Kinetics of synaptic transfer from rods and cones to horizontal cells in the salamander retina.
Neuroscience   (2003)
Thoreson WB, Tranchina D, Witkovsky P
Multiple steps of phosphorylation of activated rhodopsin can account for the reproducibility of vertebrate rod single-photon responses.
J Gen Physiol   (2003 Oct)
Hamer RD, Nicholas SC, Tranchina D, Liebman PA, Lamb TD
Modeling corticofugal feedback and the sensitivity of lateral geniculate neurons to orientation discontinuity.
Vis Neurosci   (2001 Nov-Dec)
Hayot F, Tranchina D
Hypermutation in shark immunoglobulin light chain genes results in contiguous substitutions.
Immunity   (2002 Apr)
Lee SS, Tranchina D, Ohta Y, Flajnik MF, Hsu E
Transmission at the photoreceptor synapse.
Prog Brain Res   (2001)
Witkovsky P, Thoreson W, Tranchina D
Population density methods for large-scale modelling of neuronal networks with realistic synaptic kinetics: cutting the dimension down to size.
Network   (2001 May)
Haskell E, Nykamp DQ, Tranchina D
A population density approach that facilitates large-scale modeling of neural networks: extension to slow inhibitory synapses.
Neural Comput   (2001 Mar)
Nykamp DQ, Tranchina D
A population density approach that facilitates large-scale modeling of neural networks: analysis and an application to orientation tuning.
J Comput Neurosci   (2000 Jan-Feb)
Nykamp DQ, Tranchina D
Recovery of cable properties through active and passive modeling of subthreshold membrane responses from laterodorsal tegmental neurons.
J Neurophysiol   (1998 Nov)
Surkis A, Peskin CS, Tranchina D, Leonard CS
The calculus of rod phototransduction.
J Gen Physiol   (1998 Jan)
Tranchina D
Gain of rod to horizontal cell synaptic transfer: relation to glutamate release and a dihydropyridine-sensitive calcium current.
J Neurosci   (1997 Oct 1)
Witkovsky P, Schmitz Y, Akopian A, Krizaj D, Tranchina D
Background contrast modulates kinetics and lateral spread of responses to superimposed stimuli in outer retina.
Vis Neurosci   (1995 Nov-Dec)
Reifsnider ES, Tranchina D
Modulation of synaptic transfer between retinal cones and horizontal cells by spatial contrast.
J Gen Physiol   (1994 Sep)
Cadenas ID, Reifsnider ES, Tranchina D
Origin of the apparent tissue conductivity in the molecular and granular layers of the in vitro turtle cerebellum and the interpretation of current source-density analysis.
J Neurophysiol   (1994 Aug)
Okada YC, Huang JC, Rice ME, Tranchina D, Nicholson C
Membrane currents of horizontal cells isolated from turtle retina.
J Neurophysiol   (1992 Aug)
Golard A, Witkovsky P, Tranchina D
Light adaptation in turtle cones. Testing and analysis of a model for phototransduction.
Biophys J   (1991 Jul)
Tranchina D, Sneyd J, Cadenas ID
Light adaptation in the primate retina: analysis of changes in gain and dynamics of monkey retinal ganglion cells.
Vis Neurosci   (1990 Jan)
Purpura K, Tranchina D, Kaplan E, Shapley RM
Photoreceptor to horizontal cell synaptic transfer in the Xenopus retina: modulation by dopamine ligands and a circuit model for interactions of rod and cone inputs.
J Neurophysiol   (1989 Oct)
Witkovsky P, Stone S, Tranchina D
Phototransduction in cones: an inverse problem in enzyme kinetics.
Bull Math Biol   (1989)
Sneyd J, Tranchina D
Light adaptation in the turtle retina: embedding a parametric family of linear models in a single nonlinear model.
Vis Neurosci   (1988)
Tranchina D, Peskin CS
A model for the polarization of neurons by extrinsically applied electric fields.
Biophys J   (1986 Dec)
Tranchina D, Nicholson C
Retinal light adaptation--evidence for a feedback mechanism.
Nature   (1984 Jul 26-Aug 1)
Tranchina D, Gordon J, Shapley RM
The receptive field organization of X-cells in the cat: spatiotemporal coupling and asymmetry.
Vision Res   (1984)
Dawis S, Shapley R, Kaplan E, Tranchina D
How to see in the dark: photon noise in vision and nuclear medicine.
Ann N Y Acad Sci   (1984)
Peskin CS, Tranchina D, Hull DM
Spatial and temporal properties of luminosity horizontal cells in the turtle retina.
J Gen Physiol   (1983 Nov)
Tranchina D, Gordon J, Shapley R

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Updated on 05/02/2013