Alfred Hero: Bioinfo

Alfred Hero - Interests in Bioinformatics

My interests are in reliable extraction of differential expression signals from gene microarray data, gene clustering, and genetic networks. My primary collaborators are Gilles Fleury at SupElec in Paris, Dr. Alan Mears at Univ. of Ottawa, and Dr. Anand Swaroop at the UM Kellog Eye Center.

Presentations

"In vitro measurement of gene expression, Part II: Analysis." Slides from a tutorial given at the IEEE Intl. Symposium on Biomedical Imaging (ISBI-04) are here

"Statistical signal processing for gene microarrays." Slides from a plenary talk given at EUSIPCO, Vienna Austria, Sept. 2004 here

Journals

D. Zhu, A.O. Hero, Z.S. Qin, "High throughput screening of co-expressed gene pairs with controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS)," (.pdf) , submitted to Journal of Computational Biology, Nov. 2004. Supplemental tables: (.pdf) .

S. Zareparsi, A.O. Hero, D.J. Zack, R. Williams, A. Swaroop, "Seeing the Unseen: Microarray-based Gene Expression Profiling in Vision," , Journal of Investigative Ophthalmology and Vision Research (IOVS), Oct. 2004.

S. Yoshida, A. J. Mears, J. S. Friedman, T. Carter, S. He, E. Oh, Y. Jing, R. Farjo, G. Fleury, C. Barlow, A. O. Hero, A. Swaroop, "Expression profiling of the developing and mature Nrl-/- mouse retina: Identification of retinal disease candidates and transcriptional regulatory targets of Nrl," (.pdf) , Human Molecular Genetics, vol. 13, no. 14, pp. 1497=1503, 2004. Supplement ,

G. Fleury, A. Hero, S. Zareparsi, and A. Swaroop, "Gene Discovery Using Pareto Depth Sampling Distributions" (.html) , (.pdf) , Special Issue on Genomics, Signal Processing and Statistics, Journ. of Franklin Institute, vol. 341, No. 1-2, pp. 55-75, Jan-Mar 2004.

A. Hero, G. Fleury, A. Mears and A. Swaroop, "Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays," color version with corrections (.pdf) , journal version (.pdf) , Special Issue on Genomic Signal Processing, EURASIP Journ. of Applied Signal Processing (EURASIP JASP), vol. 2004, No. 1, pp. 43-52, 2004. Note: the journal version has some typos: 1) in equation (9) $\hat{\xi}(g)$ is the maximum paired t statistic defined in previous paragraph; 2) above (9) "...>fcmin" should be replaced by "...>f", where f is the standard FDR significance threshold; 3) in equation (10) $\alpha$ should be replaced by $1-(1-\alpha)^{1/3}$ (Thanks to Jing Qiu of Cornell University for picking these typos up). These typos have been corrected in the color version.

A. Hero and G. Fleury, "Pareto-optimal methods for gene ranking" (.pdf) , Journ. of VLSI Signal Processing, Special Issue on Genomic Signal Processing, vol. 38, pp. 259-275, 2004.

Conference Proceedings

D. Zhu and A. O. Hero, "Unsupervised posterior analysis of signaling pathways from gene microarray data," (.pdf), submitted to Proc. of GENSIPS , Newport RI, April 2005.

D. Zhu and A. O. Hero, "Gene co-expression network discovery with controlled statistical and biological significance," (.pdf), Proc. of ICASSP , Philadelphia, March, 2005.

D. Zhu and A. O. Hero, "Network constrained clustering for gene microarray data," (.pdf), Proc. of ICASSP , Philadelphia, March, 2005.

"Pareto Depth Sampling Distributions for Gene Ranking" (.pdf) , G. Fleury, A. Hero, S. Zareparsi, and A. Swaroop, to appear in Proc. of IEEE Intern, Symp. on Biomedical Imaging, April 2004.

Yu J, Mears AJ, Yoshida S, Farjo R, Carter TA, Ghosh D, Hero A, Barlow C, Swaroop A: From disease genes to cellular pathways: A progress report (.pdf) . In "Retinal dystrophies: functional genomics to gene therapy." Wiley, Chichester (Novartis Foundation Sympoium 255) pp 147-164, 2004.

"Gene selection and ranking with microarray data" (.pdf) , A. Hero, paper accompanying plenary talk. Proc. of Intl Conf on Signal Processing and Applications, Paris, July 2003.

"Posterior Pareto front analysis for gene filtering" (.pdf) , A. Hero and G. Fleury, Proc. of Workshop on Genomic Signal Processing and Statistics (GENSIPS), Raleigh NC, Oct 11-13 2002.

"Mathematical Morphology applied to Spot Segmentation and Quantification of Gene Microarray Images", (.pdf) , K.I. Siddiqui, A. Hero, and M. Siddiqui, 2002 Asilomar Conference on Signals and Systems, Nov. 2002.

"Clustering Gene Expression Signals from Retinal Microarray Data," (.pdf) G. Fleury, A. Hero, S. Yoshida, T. Carter, C. Barlow and A. Swaroop, in Proc. IEEE Int. Conf. on Acoust., Speech, and SIg. Process., Orlando FL, May 2002.

"Pareto analysis for gene filtering in microarray experiments," (.pdf) G. Fleury, A. Hero, S. Yoshida, T. Carter, C. Barlow and A. Swaroop, Proc. XI European Signal Processing Conference, Toulouse France, Sept 2002.

Conference Abstracts

Alan J. Mears, Shigeo Yoshida, James S. Friedman, Shirley He, Edwin Oh, Gilles Fleury, Alfred O. Hero and Anand Swaroop, "Identification of the downstream targets of Nrl: the key regulator of rod photoreceptor differentiation," ARVO-2004.

Some bioinformatics links

Thinkquest's basic genetics tutorial Molecular genetics

A newsletter for computational genetics Human Genome News

A peer reviewed electronic journal on bioinformatics In Silico Biology

Y.F. Leung's site with news, glossaries, tutorials etc Functional Genomics

Oligonucleotide chips: Affymetrix

Terry Speed's microarray analysis website

NIH NHGRI site

Carollee Barlow's site
Affymetrix third party software site

Some Bayesian Nets links

Gharamani, Z. Learning Bayesian networks.

Scheines, R. An Introduction to Causal Inference.