Selected Publications

Computational Biology & Bioinformatics

J. Goutsias and S. Kim
A Nonlinear Discrete Dynamical Model for
Transcriptional Regulation: Construction
and Properties
Biophysical Journal
Vol. 86, pp. 1922-1945, April 2004
J. Goutsias
Quasiequilibrium Approximation of Fast Reaction Kinetics in Stochastic Biochemical Systems
The Journal of Chemical Physics
Vol. 122, No. 184102, pp. 1-15, 2005
J. Goutsias
A Hidden Markov Model for Transcriptional Regulation in Single Cells
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Vol. 3, No. 1, pp. 57-71, 2006
J. Goutsias and S. Kim
Stochastic Transcriptional Regulatory Systems with Time Delays:
A Mean-Field Approximation
Journal of Computational Biology
Vol. 13, No. 5, pp. 1049-1076, 2006
J. Goutsias
Classical versus Stochastic Kinetics Modeling of Biochemical Reaction Systems
Biophysical Journal
Vol. 92, pp. 2350-2365, 2007
J. Goutsias and N. H. Lee
Computational and Experimental Approaches for Modeling Gene Regulatory Networks
Current Pharmaceutical Design
Vol. 13, No. 14, pp. 1415-1436, 2007
H. X. Zhang, W. P. Dempsey, Jr., and J. Goutsias
Probabilistic sensitivity analysis of biochemical reaction systems
The Journal of Chemical Physics
Vol. 131, No. 094101, pp. 1-20, 2009
H. X. Zhang and J. Goutsias
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
BMC Bioinformatics
Vol. 11, No. 246, 2010
G. Jenkinson, X. Zhong, and J. Goutsias
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems
BMC Bioinformatics
Vol. 11, No. 547, 2010
H. X. Zhang and J. Goutsias
Reducing experimental variability in variance-based sensitivity analysis of biochemical reaction systems
The Journal of Chemical Physics
Vol. 134, No. 114105, 2011
G. Jenkinson and J. Goutsias
Thermodynamically consistent model calibration in chemical kinetics
BMC Systems Biology
Vol. 5, No. 64, 2011.
G. Jenkinson and J. Goutsias
Numerical integration of the master equation in some models of stochastic epidemiology
PLoS One
Vol. 7, No. 5, e36160, 2012.
J. Goutsias and G. Jenkinson
Markovian dynamics on complex reaction networks
Physics Reports
Vol. 529, No. 2, pp. 199-264, 2013.
G. Jenkinson and J. Goutsias
Statistically testing the validity of analytical and computational approximations to the chemical master equation
The Journal of Chemical Physics
Vol. 138, No. 204108, 2013.
G. Jenkinson and J. Goutsias
Intrinsic noise induces critical behavior in leaky Markovian networks leading to avalanching
PLoS Computational Biology
Vol. 10, No. 1, e1003411, 2014.
A. S. Afshar, J. Xu, and J. Goutsias
Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer
PLoS One
Vol. 9, No. 6, e100806, 2014.
G. Jenkinson, E. Pujadas, J. Goutsias, and A. P. Feinberg
Potential energy landscapes identify the information-theoretic nature of the epigenome
Nature Genetics
Vol. 49, No. 5, pp. 719-729, 2017
H. Nakamura, A. A. Lee, A. S. Afshar, S. Watanabe, E. Rho, S. Razavi, A. Suarez, Y.-C. Lin, M. Tanigawa, B. Huang, R. DeRose, D. Bobb, W. Hong, S. B. Gabelli, J. Goutsias, and T. Inoue
Intracellular production of hydrogels and synthetic RNA granules by multivalent molecular interactions
Nature Materials
Vol. 17, No. 1, pp. 79-89, 2018
G. Jenkinson, J. Abante, A. P. Feinberg, and J. Goutsias
An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
BMC Bioinformatics
Vol. 19, No. 87, 2018
G. Jenkinson, J. Abante, M. A. Koldobskiy, A. P. Feinberg, and J. Goutsias
Ranking genomic features using an information-theoretic measure of epigenetic discordance
BMC Bioinformatics
Vol. 20, No. 175, 2019
F. E. Garrett-Bakelman, et al
The NASA twins study: A multidimensional analysis of a year-long human spaceflight
Science
Vol. 364, No. 6436, 2019
M. A. Koldobskiy, et al
A dysregulated DNA methylation landscape linked to gene expression in MLL-rearranged AML
Epigenetics
Vol. 15, No. 8, pp. 841-858, 2020
J. Abante, Y. Fang, A. P. Feinberg, and J. Goutsias
Detection of haplotype-dependent allele-specific DNA methylation in WGBS data
Nature Communications
Vol. 11, No. 5238, pp. 1-13, 2020
J. Abante and J. Goutsias
CpelTdm.jl: a Julia package for targeted differential DNA methylation analysis
bioRxiv
https://www.biorxiv.org/content/10.1101/2020.10.17.343020v1, 2020.
M. Koldobskiy, et al
Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukemia identified by an information-theoretic analysis
Nature Biomedical Engineering
Vol. 5: 360-376, 2021.
J. Abante, S. Kambhampati, A. P. Feinberg, and J. Goutsias
Estimating DNA methylation potential energy landscapes from nanopore sequencing data
Scientific Reports
Vol. 11, No. 21619, 2021

Signal Processing

J.M. Mendel and J. Goutsias
One-Dimensional Normal-Incidence Inversion: A Solution Procedure for Band-Limited and Noisy Data
Proceedings of the IEEE
Vol. 74, No. 3, pp. 401- 414, March 1986
J. Goutsias and J.M. Mendel
Maximum-Likelihood Deconvolution: An Optimization Theory Perspective
Geophysics
Vol. 51, No. 6, pp. 1206-1220, June 1986
J. Goutsias and J.M. Mendel
Inverse Problems in Two-Dimensional Acoustic Media: A Linear Imaging Model
Journal of the Acoustical Society of America
Vol. 81, No. 5, pp. 1471-1485, May 1987
J. Goutsias and J.M. Mendel
Optimal Simultaneous Detection and Estimation of Filtered Discrete Semi-Markov Chains
IEEE Transactions on Information Theory
Vol. 34, No. 3, pp. 551-568, May 1988
J. Goutsias and H.J.A.M. Heijmans
Multiresolution Signal Decomposition Schemes. Part 1: Linear and Morphological Pyramids
IEEE Transactions on Image Processing
Vol. 9, No. 11, pp. 1862-1876, 2000
H.J.A.M. Heijmans and J. Goutsias
Multiresolution Signal Decomposition Schemes. Part 2: Morphological Wavelets
IEEE Transactions on Image Processing
Vol. 9, No. 11, pp. 1897-1913, 2000
U. Braga-Neto and J. Goutsias
Supremal Multiscale Signal Analysis
SIAM Journal on Mathematical Analysis
Vol. 36, No.1, pp. 94-120, 2004

Image Analysis

J. Goutsias and J.M. Mendel
Simultaneous Optimal Segmentation and Model Estimation of Nonstationary Noisy Images
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 11, No. 9, pp. 990-998, September 1989
J.R. Berry, Jr. and J. Goutsias
A Comparative Study of Matrix Measures for Maximum Likelihood Texture Classification
IEEE Transactions on Systems, Man, and Cybernetics
Vol. 21, No. 1, pp. 252-261, January / February 1991
D. Schonfeld and J. Goutsias
Optimal Morphological Pattern Restoration from Noisy Binary Images
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 13, No. 1, pp. 14-29, January 1991
D. Schonfeld and J. Goutsias
On the Morphological Representation of Binary Images in a Noisy Environment
Journal of Visual Communication and Image Representation
Vol. 2, No. 1, pp. 17-30, March 1991
J. Goutsias and D. Schonfeld
Morphological Representation of Discrete and Binary Images
IEEE Transactions on Signal Processing
Vol. 39, No. 6, pp. 1369-1379, June 1991
J. Goutsias
Morphological Analysis of Discrete Random Shapes
Journal of Mathematical Imaging and Vision
Vol. 2, No. 2-3, pp. 193-215, November 1992
X. Kong and J. Goutsias
A Study of Pyramidal Techniques for Image Representation and Compression
Journal of Visual Communication and Image Representation
Vol. 5, No. 2, pp. 190-203, June 1994
J. Goutsias, H.J.A.M. Heijmans, and K. Sivakumar
Morphological Operators for Image Sequences
Computer Vision and Image Understanding
Vol. 62, No. 3, pp. 326-346, November 1995
K. Sivakumar and J. Goutsias
Binary Random Fields, Random Closed Sets, and Morphological Sampling
IEEE Transactions on Image Processing
Special Issue on Nonlinear Image Processing
Vol. 5, No. 6, pp. 899-912, June 1996
K. Sivakumar and J. Goutsias
Discrete Morphological Size Distributions and Densities:
Estimation Techniques and Applications
Journal of Electronic Imaging
Special Issue on Random Models in Imaging
Vol. 6, No. 1, pp. 31-53, January 1997
K. Sivakumar and J. Goutsias
On the Discretization of Morphological Operators
Journal of Visual Communication and Image Representation
Vol. 8, No. 1, pp. 39-49, March 1997
A. Banerji and J. Goutsias
A Morphological Approach to Automatic Mine Detection Problems
IEEE Transactions on Aerospace and Electronic Systems
Vol. 34, No. 4, pp. 1085-1096, October 1998
J. Goutsias and K. Sivakumar
A Multiresolution Morphological Approach to Stochastic Image Modeling
CWI Quarterly
Vol. 11, No. 4, pp. 347-369, December 1998
K. Sivakumat and J. Goutsias
Morphologically Constrained Gibbs Random Fields: Applications to Texture Synthesis and Analysis
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 21, No. 2, pp. 99-113, 1999
J. Goutsias and H.J.A.M. Heijmans
Fundamenta Morphologicae Mathematicae
Fundamenta Informaticae
Special Issue on Mathematical Morphology
Vol. 41, pp. 1-31, 2000
U. Braga-Neto and J. Goutsias
Connectivity on Complete Lattices: New Results
Computer Vision and Image Understanding
Vol. 85, pp. 22-53, 2002
U. Braga-Neto and J. Goutsias
A Multiscale Approach to Connectivity
Computer Vision and Image Understanding
Vol. 89, pp. 70-107, 2003
S. Batman and J. Goutsias
Unsupervised Iterative Detection of Land Mines in Highly Cluttered Environments
IEEE Transactions on Image Processing
Vol. 12, No. 5, pp. 509-523, 2003
U. Braga-Neto and J. Goutsias
A Theoretical Tour of Connectivity in Image Processing and Analysis
Journal of Mathematical Imaging and Vision
Vol. 19, pp. 5-31, 2003
U. Braga-Neto, M. Choudhary and J. Goutsias
Automatic Target Detection and Tracking in Forward-Looking Infrared Image Sequences Using Morphological Connected Operators
Journal of Electronic Imaging
Vol. 13, No. 4, pp. 802-813, 2004
U. Braga-Neto and J. Goutsias
Grayscale Level Connectivity: Theory and Applications
IEEE Transactions on Image Processing
Vol. 13, No. 12, pp. 1567-1580, 2004
U. Braga-Neto and J. Goutsias
Object-Based Image Analysis Using Multiscale Connectivity
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 27, No. 6, pp. 892-907, 2005
U. Braga-Neto and J. Goutsias
Constructing Multiscale Connectivities
Computer Vision and Image Understanding
Vol. 99, pp. 126-150, 2005

Gibbs/Markov Random Fields

J. Goutsias
Mutually Compatible Gibbs Random Fields
IEEE Transactions on Information Theory
Vol. 35, No. 6, pp. 1233-1249, November 1989
J. Goutsias
Unilateral Approximation of Gibbs Random Field Images
Computer Vision, Graphics, and Image Processing: Graphical Models and Image Processing
Vol. 53, No. 3, pp. 240-257, May 1991
J. Goutsias
A Theoretical Analysis of Monte Carlo Algorithms for the Simulation of Gibbs Random Field Images
IEEE Transactions on Information Theory
Vol. 37, No. 6, pp. 1618-1628, November 1991
G. Potamianos and J. Goutsias
Partition Function Estimation of Gibbs Random Field Images Using Monte Carlo Simulations
IEEE Transactions on Information Theory
Vol. 39, No. 4, pp. 1322-1332, July 1993
G. Potamianos and J. Goutsias
Stochastic Approximation Algorithms for Partition Function Estimation of Gibbs Random Fields
IEEE Transactions on Information Theory
Vol. 43, No.6, pp. 1948-1965, November 1997
K. Sivakumat and J. Goutsias
Morphologically Constrained Gibbs Random Fields: Applications to Texture Synthesis and Analysis
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 21, No. 2, pp. 99-113, 1999
K. Sivakumar and J. Goutsias
A Morphological Estimator for Clique Potentials of Binary Markov Random Fields
IEEE Signal Processing Letters
Vol. 7, No. 5, pp. 120-122, 2000

Selected Publications

Computational Biology & Bioinformatics

J. Goutsias and S. Kim A Nonlinear Discrete Dynamical Model for Transcriptional Regulation: Construction and Properties Biophysical Journal Vol. 86, pp. 1922-1945, April 2004

J. Goutsias Quasiequilibrium Approximation of Fast Reaction Kinetics in Stochastic Biochemical Systems The Journal of Chemical Physics Vol. 122, No. 184102, pp. 1-15, 2005

J. Goutsias A Hidden Markov Model for Transcriptional Regulation in Single Cells IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 3, No. 1, pp. 57-71, 2006

J. Goutsias and S. Kim Stochastic Transcriptional Regulatory Systems with Time Delays: A Mean-Field Approximation Journal of Computational Biology Vol. 13, No. 5, pp. 1049-1076, 2006

J. Goutsias Classical versus Stochastic Kinetics Modeling of Biochemical Reaction Systems Biophysical Journal Vol. 92, pp. 2350-2365, 2007

J. Goutsias and N. H. Lee Computational and Experimental Approaches for Modeling Gene Regulatory Networks Current Pharmaceutical Design Vol. 13, No. 14, pp. 1415-1436, 2007

H. X. Zhang, W. P. Dempsey, Jr., and J. Goutsias Probabilistic sensitivity analysis of biochemical reaction systems The Journal of Chemical Physics Vol. 131, No. 094101, pp. 1-20, 2009

H. X. Zhang and J. Goutsias A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems BMC Bioinformatics Vol. 11, No. 246, 2010

G. Jenkinson, X. Zhong, and J. Goutsias Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems BMC Bioinformatics Vol. 11, No. 547, 2010

H. X. Zhang and J. Goutsias Reducing experimental variability in variance-based sensitivity analysis of biochemical reaction systems The Journal of Chemical Physics Vol. 134, No. 114105, 2011

G. Jenkinson and J. Goutsias Thermodynamically consistent model calibration in chemical kinetics BMC Systems Biology Vol. 5, No. 64, 2011.

G. Jenkinson and J. Goutsias Numerical integration of the master equation in some models of stochastic epidemiology PLoS One Vol. 7, No. 5, e36160, 2012.

J. Goutsias and G. Jenkinson Markovian dynamics on complex reaction networks Physics Reports Vol. 529, No. 2, pp. 199-264, 2013.

G. Jenkinson and J. Goutsias Statistically testing the validity of analytical and computational approximations to the chemical master equation The Journal of Chemical Physics Vol. 138, No. 204108, 2013.

G. Jenkinson and J. Goutsias Intrinsic noise induces critical behavior in leaky Markovian networks leading to avalanching PLoS Computational Biology Vol. 10, No. 1, e1003411, 2014.

A. S. Afshar, J. Xu, and J. Goutsias Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer PLoS One Vol. 9, No. 6, e100806, 2014.

G. Jenkinson, E. Pujadas, J. Goutsias, and A. P. Feinberg Potential energy landscapes identify the information-theoretic nature of the epigenome Nature Genetics Vol. 49, No. 5, pp. 719-729, 2017

G. Jenkinson, J. Abante, A. P. Feinberg, and J. Goutsias An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data BMC Bioinformatics Vol. 19, No. 87, 2018

G. Jenkinson, J. Abante, M. A. Koldobskiy, A. P. Feinberg, and J. Goutsias Ranking genomic features using an information-theoretic measure of epigenetic discordance BMC Bioinformatics Vol. 20, No. 175, 2019

F. E. Garrett-Bakelman, et al The NASA twins study: A multidimensional analysis of a year-long human spaceflight Science Vol. 364, No. 6436, 2019

M. A. Koldobskiy, et al A dysregulated DNA methylation landscape linked to gene expression in MLL-rearranged AML Epigenetics Vol. 15, No. 8, pp. 841-858, 2020

J. Abante, Y. Fang, A. P. Feinberg, and J. Goutsias Detection of haplotype-dependent allele-specific DNA methylation in WGBS data Nature Communications Vol. 11, No. 5238, pp. 1-13, 2020

J. Abante and J. Goutsias CpelTdm.jl: a Julia package for targeted differential DNA methylation analysis bioRxiv https://www.biorxiv.org/content/10.1101/2020.10.17.343020v1, 2020.

M. Koldobskiy, et al Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukemia identified by an information-theoretic analysis Nature Biomedical Engineering Vol. 5: 360-376, 2021.

J. Abante, S. Kambhampati, A. P. Feinberg, and J. Goutsias Estimating DNA methylation potential energy landscapes from nanopore sequencing data Scientific Reports Vol. 11, No. 21619, 2021

Signal Processing

J.M. Mendel and J. Goutsias One-Dimensional Normal-Incidence Inversion: A Solution Procedure for Band-Limited and Noisy Data Proceedings of the IEEE Vol. 74, No. 3, pp. 401- 414, March 1986

J. Goutsias and J.M. Mendel Maximum-Likelihood Deconvolution: An Optimization Theory Perspective Geophysics Vol. 51, No. 6, pp. 1206-1220, June 1986

J. Goutsias and J.M. Mendel Inverse Problems in Two-Dimensional Acoustic Media: A Linear Imaging Model Journal of the Acoustical Society of America Vol. 81, No. 5, pp. 1471-1485, May 1987

J. Goutsias and J.M. Mendel Optimal Simultaneous Detection and Estimation of Filtered Discrete Semi-Markov Chains IEEE Transactions on Information Theory Vol. 34, No. 3, pp. 551-568, May 1988

J. Goutsias and H.J.A.M. Heijmans Multiresolution Signal Decomposition Schemes. Part 1: Linear and Morphological Pyramids IEEE Transactions on Image Processing Vol. 9, No. 11, pp. 1862-1876, 2000

H.J.A.M. Heijmans and J. Goutsias Multiresolution Signal Decomposition Schemes. Part 2: Morphological Wavelets IEEE Transactions on Image Processing Vol. 9, No. 11, pp. 1897-1913, 2000

U. Braga-Neto and J. Goutsias Supremal Multiscale Signal Analysis SIAM Journal on Mathematical Analysis Vol. 36, No.1, pp. 94-120, 2004

Image Analysis

J. Goutsias and J.M. Mendel Simultaneous Optimal Segmentation and Model Estimation of Nonstationary Noisy Images IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 11, No. 9, pp. 990-998, September 1989

J.R. Berry, Jr. and J. Goutsias A Comparative Study of Matrix Measures for Maximum Likelihood Texture Classification IEEE Transactions on Systems, Man, and Cybernetics Vol. 21, No. 1, pp. 252-261, January / February 1991

D. Schonfeld and J. Goutsias Optimal Morphological Pattern Restoration from Noisy Binary Images IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 13, No. 1, pp. 14-29, January 1991

D. Schonfeld and J. Goutsias On the Morphological Representation of Binary Images in a Noisy Environment Journal of Visual Communication and Image Representation Vol. 2, No. 1, pp. 17-30, March 1991

J. Goutsias and D. Schonfeld Morphological Representation of Discrete and Binary Images IEEE Transactions on Signal Processing Vol. 39, No. 6, pp. 1369-1379, June 1991

J. Goutsias Morphological Analysis of Discrete Random Shapes Journal of Mathematical Imaging and Vision Vol. 2, No. 2-3, pp. 193-215, November 1992

X. Kong and J. Goutsias A Study of Pyramidal Techniques for Image Representation and Compression Journal of Visual Communication and Image Representation Vol. 5, No. 2, pp. 190-203, June 1994

J. Goutsias, H.J.A.M. Heijmans, and K. Sivakumar Morphological Operators for Image Sequences Computer Vision and Image Understanding Vol. 62, No. 3, pp. 326-346, November 1995

K. Sivakumar and J. Goutsias Binary Random Fields, Random Closed Sets, and Morphological Sampling IEEE Transactions on Image Processing Special Issue on Nonlinear Image Processing Vol. 5, No. 6, pp. 899-912, June 1996

K. Sivakumar and J. Goutsias Discrete Morphological Size Distributions and Densities: Estimation Techniques and Applications Journal of Electronic Imaging Special Issue on Random Models in Imaging Vol. 6, No. 1, pp. 31-53, January 1997

K. Sivakumar and J. Goutsias On the Discretization of Morphological Operators Journal of Visual Communication and Image Representation Vol. 8, No. 1, pp. 39-49, March 1997

A. Banerji and J. Goutsias A Morphological Approach to Automatic Mine Detection Problems IEEE Transactions on Aerospace and Electronic Systems Vol. 34, No. 4, pp. 1085-1096, October 1998

J. Goutsias and K. Sivakumar A Multiresolution Morphological Approach to Stochastic Image Modeling CWI Quarterly Vol. 11, No. 4, pp. 347-369, December 1998

K. Sivakumat and J. Goutsias Morphologically Constrained Gibbs Random Fields: Applications to Texture Synthesis and Analysis IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 21, No. 2, pp. 99-113, 1999

J. Goutsias and H.J.A.M. Heijmans Fundamenta Morphologicae Mathematicae Fundamenta Informaticae Special Issue on Mathematical Morphology Vol. 41, pp. 1-31, 2000

U. Braga-Neto and J. Goutsias Connectivity on Complete Lattices: New Results Computer Vision and Image Understanding Vol. 85, pp. 22-53, 2002

U. Braga-Neto and J. Goutsias A Multiscale Approach to Connectivity Computer Vision and Image Understanding Vol. 89, pp. 70-107, 2003

S. Batman and J. Goutsias Unsupervised Iterative Detection of Land Mines in Highly Cluttered Environments IEEE Transactions on Image Processing Vol. 12, No. 5, pp. 509-523, 2003

U. Braga-Neto and J. Goutsias A Theoretical Tour of Connectivity in Image Processing and Analysis Journal of Mathematical Imaging and Vision Vol. 19, pp. 5-31, 2003

U. Braga-Neto, M. Choudhary and J. Goutsias Automatic Target Detection and Tracking in Forward-Looking Infrared Image Sequences Using Morphological Connected Operators Journal of Electronic Imaging Vol. 13, No. 4, pp. 802-813, 2004

U. Braga-Neto and J. Goutsias Grayscale Level Connectivity: Theory and Applications IEEE Transactions on Image Processing Vol. 13, No. 12, pp. 1567-1580, 2004

U. Braga-Neto and J. Goutsias Object-Based Image Analysis Using Multiscale Connectivity IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 27, No. 6, pp. 892-907, 2005

U. Braga-Neto and J. Goutsias Constructing Multiscale Connectivities Computer Vision and Image Understanding Vol. 99, pp. 126-150, 2005

Gibbs/Markov Random Fields

J. Goutsias Mutually Compatible Gibbs Random Fields IEEE Transactions on Information Theory Vol. 35, No. 6, pp. 1233-1249, November 1989

J. Goutsias Unilateral Approximation of Gibbs Random Field Images Computer Vision, Graphics, and Image Processing: Graphical Models and Image Processing Vol. 53, No. 3, pp. 240-257, May 1991

J. Goutsias A Theoretical Analysis of Monte Carlo Algorithms for the Simulation of Gibbs Random Field Images IEEE Transactions on Information Theory Vol. 37, No. 6, pp. 1618-1628, November 1991

G. Potamianos and J. Goutsias Partition Function Estimation of Gibbs Random Field Images Using Monte Carlo Simulations IEEE Transactions on Information Theory Vol. 39, No. 4, pp. 1322-1332, July 1993

G. Potamianos and J. Goutsias Stochastic Approximation Algorithms for Partition Function Estimation of Gibbs Random Fields IEEE Transactions on Information Theory Vol. 43, No.6, pp. 1948-1965, November 1997

K. Sivakumat and J. Goutsias Morphologically Constrained Gibbs Random Fields: Applications to Texture Synthesis and Analysis IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 21, No. 2, pp. 99-113, 1999

K. Sivakumar and J. Goutsias A Morphological Estimator for Clique Potentials of Binary Markov Random Fields IEEE Signal Processing Letters Vol. 7, No. 5, pp. 120-122, 2000

J. Goutsias and S. Kim
A Nonlinear Discrete Dynamical Model for
Transcriptional Regulation: Construction
and Properties
Biophysical Journal
Vol. 86, pp. 1922-1945, April 2004

J. Goutsias
Quasiequilibrium Approximation of Fast Reaction Kinetics in Stochastic Biochemical Systems
The Journal of Chemical Physics
Vol. 122, No. 184102, pp. 1-15, 2005

J. Goutsias
A Hidden Markov Model for Transcriptional Regulation in Single Cells
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Vol. 3, No. 1, pp. 57-71, 2006

J. Goutsias and S. Kim
Stochastic Transcriptional Regulatory Systems with Time Delays:
A Mean-Field Approximation
Journal of Computational Biology
Vol. 13, No. 5, pp. 1049-1076, 2006

J. Goutsias
Classical versus Stochastic Kinetics Modeling of Biochemical Reaction Systems
Biophysical Journal
Vol. 92, pp. 2350-2365, 2007

J. Goutsias and N. H. Lee
Computational and Experimental Approaches for Modeling Gene Regulatory Networks
Current Pharmaceutical Design
Vol. 13, No. 14, pp. 1415-1436, 2007

H. X. Zhang, W. P. Dempsey, Jr., and J. Goutsias
Probabilistic sensitivity analysis of biochemical reaction systems
The Journal of Chemical Physics
Vol. 131, No. 094101, pp. 1-20, 2009

H. X. Zhang and J. Goutsias
A comparison of approximation techniques for variance-based sensitivity analysis of biochemical reaction systems
BMC Bioinformatics
Vol. 11, No. 246, 2010

G. Jenkinson, X. Zhong, and J. Goutsias
Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems
BMC Bioinformatics
Vol. 11, No. 547, 2010

H. X. Zhang and J. Goutsias
Reducing experimental variability in variance-based sensitivity analysis of biochemical reaction systems
The Journal of Chemical Physics
Vol. 134, No. 114105, 2011

G. Jenkinson and J. Goutsias
Thermodynamically consistent model calibration in chemical kinetics
BMC Systems Biology
Vol. 5, No. 64, 2011.

G. Jenkinson and J. Goutsias
Numerical integration of the master equation in some models of stochastic epidemiology
PLoS One
Vol. 7, No. 5, e36160, 2012.

J. Goutsias and G. Jenkinson
Markovian dynamics on complex reaction networks
Physics Reports
Vol. 529, No. 2, pp. 199-264, 2013.

G. Jenkinson and J. Goutsias
Statistically testing the validity of analytical and computational approximations to the chemical master equation
The Journal of Chemical Physics
Vol. 138, No. 204108, 2013.

G. Jenkinson and J. Goutsias
Intrinsic noise induces critical behavior in leaky Markovian networks leading to avalanching
PLoS Computational Biology
Vol. 10, No. 1, e1003411, 2014.

A. S. Afshar, J. Xu, and J. Goutsias
Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer
PLoS One
Vol. 9, No. 6, e100806, 2014.

G. Jenkinson, E. Pujadas, J. Goutsias, and A. P. Feinberg
Potential energy landscapes identify the information-theoretic nature of the epigenome
Nature Genetics
Vol. 49, No. 5, pp. 719-729, 2017

G. Jenkinson, J. Abante, A. P. Feinberg, and J. Goutsias
An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
BMC Bioinformatics
Vol. 19, No. 87, 2018

G. Jenkinson, J. Abante, M. A. Koldobskiy, A. P. Feinberg, and J. Goutsias
Ranking genomic features using an information-theoretic measure of epigenetic discordance
BMC Bioinformatics
Vol. 20, No. 175, 2019

F. E. Garrett-Bakelman, et al
The NASA twins study: A multidimensional analysis of a year-long human spaceflight
Science
Vol. 364, No. 6436, 2019

M. A. Koldobskiy, et al
A dysregulated DNA methylation landscape linked to gene expression in MLL-rearranged AML
Epigenetics
Vol. 15, No. 8, pp. 841-858, 2020

J. Abante, Y. Fang, A. P. Feinberg, and J. Goutsias
Detection of haplotype-dependent allele-specific DNA methylation in WGBS data
Nature Communications
Vol. 11, No. 5238, pp. 1-13, 2020

J. Abante and J. Goutsias
CpelTdm.jl: a Julia package for targeted differential DNA methylation analysis
bioRxiv
https://www.biorxiv.org/content/10.1101/2020.10.17.343020v1, 2020.

M. Koldobskiy, et al
Converging genetic and epigenetic drivers of paediatric acute lymphoblastic leukemia identified by an information-theoretic analysis
Nature Biomedical Engineering
Vol. 5: 360-376, 2021.

J. Abante, S. Kambhampati, A. P. Feinberg, and J. Goutsias
Estimating DNA methylation potential energy landscapes from nanopore sequencing data
Scientific Reports
Vol. 11, No. 21619, 2021

J.M. Mendel and J. Goutsias
One-Dimensional Normal-Incidence Inversion: A Solution Procedure for Band-Limited and Noisy Data
Proceedings of the IEEE
Vol. 74, No. 3, pp. 401- 414, March 1986

J. Goutsias and J.M. Mendel
Maximum-Likelihood Deconvolution: An Optimization Theory Perspective
Geophysics
Vol. 51, No. 6, pp. 1206-1220, June 1986

J. Goutsias and J.M. Mendel
Inverse Problems in Two-Dimensional Acoustic Media: A Linear Imaging Model
Journal of the Acoustical Society of America
Vol. 81, No. 5, pp. 1471-1485, May 1987

J. Goutsias and J.M. Mendel
Optimal Simultaneous Detection and Estimation of Filtered Discrete Semi-Markov Chains
IEEE Transactions on Information Theory
Vol. 34, No. 3, pp. 551-568, May 1988

J. Goutsias and H.J.A.M. Heijmans
Multiresolution Signal Decomposition Schemes. Part 1: Linear and Morphological Pyramids
IEEE Transactions on Image Processing
Vol. 9, No. 11, pp. 1862-1876, 2000

H.J.A.M. Heijmans and J. Goutsias
Multiresolution Signal Decomposition Schemes. Part 2: Morphological Wavelets
IEEE Transactions on Image Processing
Vol. 9, No. 11, pp. 1897-1913, 2000

U. Braga-Neto and J. Goutsias
Supremal Multiscale Signal Analysis
SIAM Journal on Mathematical Analysis
Vol. 36, No.1, pp. 94-120, 2004

J. Goutsias and J.M. Mendel
Simultaneous Optimal Segmentation and Model Estimation of Nonstationary Noisy Images
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 11, No. 9, pp. 990-998, September 1989

J.R. Berry, Jr. and J. Goutsias
A Comparative Study of Matrix Measures for Maximum Likelihood Texture Classification
IEEE Transactions on Systems, Man, and Cybernetics
Vol. 21, No. 1, pp. 252-261, January / February 1991

D. Schonfeld and J. Goutsias
Optimal Morphological Pattern Restoration from Noisy Binary Images
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 13, No. 1, pp. 14-29, January 1991

D. Schonfeld and J. Goutsias
On the Morphological Representation of Binary Images in a Noisy Environment
Journal of Visual Communication and Image Representation
Vol. 2, No. 1, pp. 17-30, March 1991

J. Goutsias and D. Schonfeld
Morphological Representation of Discrete and Binary Images
IEEE Transactions on Signal Processing
Vol. 39, No. 6, pp. 1369-1379, June 1991

J. Goutsias
Morphological Analysis of Discrete Random Shapes
Journal of Mathematical Imaging and Vision
Vol. 2, No. 2-3, pp. 193-215, November 1992

X. Kong and J. Goutsias
A Study of Pyramidal Techniques for Image Representation and Compression
Journal of Visual Communication and Image Representation
Vol. 5, No. 2, pp. 190-203, June 1994

J. Goutsias, H.J.A.M. Heijmans, and K. Sivakumar
Morphological Operators for Image Sequences
Computer Vision and Image Understanding
Vol. 62, No. 3, pp. 326-346, November 1995

K. Sivakumar and J. Goutsias
Binary Random Fields, Random Closed Sets, and Morphological Sampling
IEEE Transactions on Image Processing
Special Issue on Nonlinear Image Processing
Vol. 5, No. 6, pp. 899-912, June 1996

K. Sivakumar and J. Goutsias
Discrete Morphological Size Distributions and Densities:
Estimation Techniques and Applications
Journal of Electronic Imaging
Special Issue on Random Models in Imaging
Vol. 6, No. 1, pp. 31-53, January 1997

K. Sivakumar and J. Goutsias
On the Discretization of Morphological Operators
Journal of Visual Communication and Image Representation
Vol. 8, No. 1, pp. 39-49, March 1997

A. Banerji and J. Goutsias
A Morphological Approach to Automatic Mine Detection Problems
IEEE Transactions on Aerospace and Electronic Systems
Vol. 34, No. 4, pp. 1085-1096, October 1998

J. Goutsias and K. Sivakumar
A Multiresolution Morphological Approach to Stochastic Image Modeling
CWI Quarterly
Vol. 11, No. 4, pp. 347-369, December 1998

K. Sivakumat and J. Goutsias
Morphologically Constrained Gibbs Random Fields: Applications to Texture Synthesis and Analysis
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 21, No. 2, pp. 99-113, 1999

J. Goutsias and H.J.A.M. Heijmans
Fundamenta Morphologicae Mathematicae
Fundamenta Informaticae
Special Issue on Mathematical Morphology
Vol. 41, pp. 1-31, 2000

U. Braga-Neto and J. Goutsias
Connectivity on Complete Lattices: New Results
Computer Vision and Image Understanding
Vol. 85, pp. 22-53, 2002

U. Braga-Neto and J. Goutsias
A Multiscale Approach to Connectivity
Computer Vision and Image Understanding
Vol. 89, pp. 70-107, 2003

S. Batman and J. Goutsias
Unsupervised Iterative Detection of Land Mines in Highly Cluttered Environments
IEEE Transactions on Image Processing
Vol. 12, No. 5, pp. 509-523, 2003

U. Braga-Neto and J. Goutsias
A Theoretical Tour of Connectivity in Image Processing and Analysis
Journal of Mathematical Imaging and Vision
Vol. 19, pp. 5-31, 2003

U. Braga-Neto, M. Choudhary and J. Goutsias
Automatic Target Detection and Tracking in Forward-Looking Infrared Image Sequences Using Morphological Connected Operators
Journal of Electronic Imaging
Vol. 13, No. 4, pp. 802-813, 2004

U. Braga-Neto and J. Goutsias
Grayscale Level Connectivity: Theory and Applications
IEEE Transactions on Image Processing
Vol. 13, No. 12, pp. 1567-1580, 2004

U. Braga-Neto and J. Goutsias
Object-Based Image Analysis Using Multiscale Connectivity
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 27, No. 6, pp. 892-907, 2005

U. Braga-Neto and J. Goutsias
Constructing Multiscale Connectivities
Computer Vision and Image Understanding
Vol. 99, pp. 126-150, 2005

J. Goutsias
Mutually Compatible Gibbs Random Fields
IEEE Transactions on Information Theory
Vol. 35, No. 6, pp. 1233-1249, November 1989

J. Goutsias
Unilateral Approximation of Gibbs Random Field Images
Computer Vision, Graphics, and Image Processing: Graphical Models and Image Processing
Vol. 53, No. 3, pp. 240-257, May 1991

J. Goutsias
A Theoretical Analysis of Monte Carlo Algorithms for the Simulation of Gibbs Random Field Images
IEEE Transactions on Information Theory
Vol. 37, No. 6, pp. 1618-1628, November 1991

G. Potamianos and J. Goutsias
Partition Function Estimation of Gibbs Random Field Images Using Monte Carlo Simulations
IEEE Transactions on Information Theory
Vol. 39, No. 4, pp. 1322-1332, July 1993

G. Potamianos and J. Goutsias
Stochastic Approximation Algorithms for Partition Function Estimation of Gibbs Random Fields
IEEE Transactions on Information Theory
Vol. 43, No.6, pp. 1948-1965, November 1997

K. Sivakumat and J. Goutsias
Morphologically Constrained Gibbs Random Fields: Applications to Texture Synthesis and Analysis
IEEE Transactions on Pattern Analysis and Machine Intelligence
Vol. 21, No. 2, pp. 99-113, 1999

K. Sivakumar and J. Goutsias
A Morphological Estimator for Clique Potentials of Binary Markov Random Fields
IEEE Signal Processing Letters
Vol. 7, No. 5, pp. 120-122, 2000