Anthony Almudevar, PhD

Associate Professor of Biostatistics and Computational Biology
Ph.D. (1994) University of Toronto


Contact Information:

University of Rochester
Dept of Biostatistics and Computational Biology
601 Elmwood Avenue Box 630
Rochester, New York 14642
 
Office: Saunders Research Building 4168
Phone: (585) 275-6992
Fax: (585) 273-1031
E-mail: Anthony_Almudevar@urmc.rochester.edu
Anthony Almudevar, PhD

Research Interests

I am interested in genetics and bioinformatics, especially in the area of graphical modelling, with applications to cellular networks and population biology. I also have a more general interest in optimization and control theory, particularly in the area of Markov decision processes.

As well, I am interested in the analysis of technological motion data, particularly data collected from home monitoring systems.

I was awarded a Ph.D. from the Department of Statistics at the University of Toronto in 1994.


Software

Graphical Threshold Selection. R library implementation of algorithms described in "Selection of statistical thresholds in graphical models" (Anthony Almudevar 2008).

Pedigree Reconstruction Tools (PRT 2.0). Sibling groups reconstruction (Almudevar and Field 1999, JABES).

Pedigree Application (PedApp). Graphical approaches to pedigree reconstruction (Almudevar 2007, Theoretical Population Biology).

Bayesian Network GSA Library

R Library for Almudevar (2011) Optimization Methods and Software

lognormal_functions.zip


Technical reports

  • Almudevar, A. (2006). Calibration-Free Motion Tracking in a Wireless Network 06/10).
  • Almudevar, A. (2006). A Graphical Approach to Relatedness Inference (Technical Report 06/01).
  • Almudevar, A. and Arruda, E. F. (2004). Using Partial Information to Improve the Convergence of DP Algorithms (Technical Report 04/05).
  • Almudevar, A. (2004). Approximate Fixed Point Iteration With an Application to Markov Decision Processes (Technical Report 04/02.)

Selected Publications

  • Almudevar, A, Salzman, P (2005) Using a Bayesian posterior density in the design of perturbation experiments, in Proceedings 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 216-222.
  • Salzman P, Almudevar A (2006) Using complexity for the estimation of Bayesian networks. Statistical Applications in Genetics and Molecular Biology. 5/1, Article 21.
  • Almudevar A (2007) A graphical approach to relatedness inference. Theoretical Population Biology. 71, 213-229.
  • Almudevar A (2007) Efficient coding of labeled graphs. Proceedings of 2007 IEEE Information Theory Workshop. 523-528.
  • Almudevar A (2008) Approximate fixed point iteration with an application to infinite-horizon Markov decision processes. SIAM Journal on Control and Optimization. 47, 2303-2347.
  • Almudevar A, Leibovici A, Tentler A (2008) Home monitoring using wearable radio frequency transmitters. Artificial Intelligence in Medicine. 42, 109-120.
  • Almudevar A (2008) Approximate calibration-free trajectory reconstruction in a wireless network. IEEE Transactions on Signal Processing. 56, 3081-3088.
  • Almudevar A (2009) Selection of statistical thresholds in graphical models. EURASIP Journal on Bioinformatics and Systems Biology. 2009:878013. Epub 2010 Mar 4.
  • Almudevar A (2010) A hypothesis test for equality of Bayesian network models. EURASIP Journal on Bioinformatics and Systems Biology. 2010, Article ID 947564.
  • Pichichero ME, Kaur R, Casey JR, Sabirov A, Khan N, Almudevar A (2010) Antibody response to Haemophilus influenzae outer membrane protein D, P6, and OMP26 after nasopharyngeal colonization and acute otitis media in children. Vaccine. 28, 7184-92.
  • Almudevar A (2011) A commentary on some recent methods in sibling group reconstruction based on set coverings. Optimization Methods and Software. 26, 993-1003.
  • Almudevar A, McCall M, McMurray H, Land H (2011) Fitting Boolean networks from steady state perturbation data. Statistical Applications in Genetics and Molecular Biology. Vol. 10: Iss. 1, Article 47.
  • McCall M, Almudevar A (2011) Affymetrix GeneChip microarray preprocessing for multivariate analyses. Briefings in Bioinformatics. 2011 Dec 30. [Epub ahead of print].
  • Barry CT, D'Souza M, McCall M, Safadjou S, Ryan C, Kashyap R, Marroquin C, Orloff M, Almudevar A, Godfrey TE (2012) Micro RNA Expression Profiles as Adjunctive Data to Assess the Risk of Hepatocellular Carcinoma Recurrence After Liver Transplantation. Am J Transplant. 12, 428-37.
  • Almudevar A, Lacombe J (2012) On the choice of prior density for the Bayesian analysis of pedigree structure. Theoretical Population Biology. 81, 131-43.
  • Xu Z, Almudevar A, Mathews D (2012) Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Research. 40(4):e26.
  • Almudevar A, Anderson EC (2012) A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem. Mol Ecol Resour. 12, 164-78.
  • Pichichero ME, Kaur R, Casey JR, Xu Q, Almudevar A, Ochs M (2012) Antibody response to Streptococcus pneumoniae proteins PhtD, LytB, PcpA, PhtE and Ply after nasopharyngeal colonization and acute otitis media in children. Hum Vaccin Immunother. 2012 Jun 1;8(6).
  • Almudevar A, Arruda EF (2012) Optimal Approximation Schedules for a Class of Iterative Algorithms, with an Application to Multigrid Value Iteration. IEEE Transactions on Automatic Control. [Early Access] doi: 10.1109/TAC.2012.2203053
  • Almudevar A, Lacombe J (2012) An extension of a calibration-free trajectory reconstruction method for wireless networks. IEEE Transactions on Signal Processing. [Early Access] doi: 10.1109/TSP.2012.2203817
  • Adler DH, Almudevar A, Gray GE, Allan B, Williamson AL (2012) High Level of Agreement between Clinician-Collected and Self-Collected Samples for HPV Detection among South African Adolescents. J Pediatr Adolesc Gynecol. 2012 Aug;25(4):280-1. PubMed PMID: 22840940.
  • Vora RN, Barron BA, Almudevar A, Utell MJ (2012) Work-Related Chronic Low Back Pain-Return-to-work outcomes after referral to Interventional Pain and Spine Clinics. Spine 2012 Jun 26. [Epub ahead of print] PubMed PMID: 22739674.
  • Xu Q, Almudevar A, Casey JR, Pichichero ME (2012) Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis Interactions in the Nasopharynx Differ during Health and at Onset of Acute Otitis Media in Young Children. Emerging Infectious Diseases [in press].