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
 

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

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, Field, C. (1999). Estimation of single generation sibling relationships based on DNA markers. Journal of Agricultural, Biological and Environmental statistics, 4, 136-165.
  • Almudevar, A (2000). Exact confidence regions for species assignment based on DNA markers. The Canadian Journal of Statistics, 28, 81-95.
  • Almudevar, A, Field, C, Robinson, J (2000). The density of multivariate M-estimates. Annals of Statistics, 28, 275-297.
  • Almudevar, A, Bhattacharya, R.N., Sastri, C.C.A. (2000). Estimating the probability mass of unobserved support in random sampling. Journal of Statistical Planning and Inference, 91, 91-105.
  • Almudevar, A, (2001). A dynamic programming algorithm for the optimal control of piecewise deterministic Markov processes. SIAM Journal on Control and Optimization, 40, 525-539.
  • Almudevar, A., (2001). A bootstrap assessment of variability in pedigree reconstruction based on DNA markers. Biometrics, 57, 757-763.
  • Almudevar, A., (2001) Most powerful permutation invariant tests for relatedness hypotheses based on genotypic data. Biometrics, 57, 1080-1088.
  • Le Blanc, J.C., Almudevar, A., Brooks, S.J., Kutcher, S., (2002) Screening for Adolescent Depression: comparison of the Kutcher Adolescent Depression Scale with the Beck Depression Inventory, Journal of Child and Adolescent Psychopharmacology, 12, 113-126.
  • Langley, J.M., Marrie, T., LeBlanc, J., Almudevar, A., Resch, L., Raoult, D., (2003) Coxiella burnetii seropositivity in parturient women is associated with adverse pregnancy outcomes. American Journal of Obstetrics and Gynecology, 189, 228-232.
  • Almudevar, A. (2003) A simulated annealing algorithm for maximum likelihood pedigree reconstruction. Theoretical Population Biology, 63, 63-75.
  • Arruda, E, Do Val, J.B.R, Almudevar, A. (2004) Stability and optimality of a discrete production and storage model with uncertain demand. Proceedings of the 43rd IEEE Conference on Decision and Control, 2004.
  • Arruda, E,, Almudevar, A., Do Val, J.B.R. (2005) Function approximation for a production and storage model under uncertainty. Proceedings of the IEEE International Conference on Mechatronics and Automation (ICMA), 2005.
  • Pianosi, P.,  LeBlanc, J., Almudevar, A. (2005) Peak oxygen uptake and mortality in children with cystic fibrosis. Thorax, 60, 50-54.
  • Pianosi, P.,  LeBlanc, J., Almudevar, A. (2005)  Relationship between FEV1 and peak oxygen uptake in children with cystic fibrosis. Pediatric Pulmonology. 40, 324-329.
  • 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.
  • Hislop SJ, Hsu JH, Narins C, Gillespie B, Jain R, Schippert D, Almudevar A, Illig KA. (2006) Simulator assessment of innate endovascular aptitude vs. empirically correct performance.  Journal of Vascular Surgery, 43, 47-55.
  • Almudevar A, Klebanov LB, Qiu X, Salzman P, Yakovlev AY (2006) Utility of correlation measures in analysis of gene expression. NeuroRx, 3, 384-395.
  • Pianosi P,  Smith CP,  Almudevar A, McGrath PJ (2006)  Dalhousie Dyspnea scales: pictorial scales to measure dyspnea during induced bronchoconstriction. Pediatric Pulmonology 41, 1182-1187.
  • Brouxhon S, Konger RL, VanBuskirk J, Sheu T, Ryan J, Erdle B, Almudevar A, Breyer RM, Scott G, Pentland AP (2006). Deletion of prostaglandin E2 EP2 receptor protects against ultraviolet (UV) induced carcinogenesis, but increases tumor aggressiveness. Journal of Investigative Dermatology.  September2006; doi: 10.1038/sj.jid.5700547.
  • 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 (2006) Using artificial neural networks to predict claim duration in a work injury compensation environment, Proceedings 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
  • 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, Arruda E (2007) Optimal approximation schedules for iterative algorithms with application to dynamic programming. Proceedings of the 46th IEEE Conference on Decision and Control, 4087-4094.
  • Anolik JH, Ravikumar R, Barnard J, Owen T, Almudevar A, Milner ECB, Miller CH, Dutcher PO, Hadley JA, Sanz I (2008) Anti-tumor necrosis factor therapy in rheumatoid arthritis inhibits memory B lymphocytes via effects on lymphoid GCs and FDC networks. The Journal of Immunology,  180, 688-692.
  • 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 (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 (2008) Validation of a home monitoring system based on calibration-free wireless tracking.  Proceedings of the 4th IET International Conference on Intelligent Environments.
  • Bimber BN, Chugh P, Giorgi EE, Kim B, Almudevar AL, Dewhurst S, O'Connor DH, Lee HY (2009)  Nef gene evolution from a single transmitted strain in acute SIV infection. Retrovirology 6, 57.
  • Almudevar A (2009) A note on the calculation of  N-statistics. Journal of Bioinformatics and Computational Biology, 7, 895-903.
  • 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
  • Chen L, Almudevar A, Klebanov L (2010) Multilayer Correlation Structure of Microarray Gene Expression Data, in Statistical Methods for Microarray Data Analysis (eds A. Yakovlev, L. Klebanov, D. Gaile). Humana Press (in press)
  • 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. 2010 Aug 26. [Epub ahead of print] PubMed PMID: 20800701.
  • Arruda E, Ourique F, Almudevar A (2010) Toward an optimized value iteration algorithm for average cost Markov decision processes. Proceedings of the 49th IEEE Conference on Decision and Control.
  • Almudevar A (2011) A commentary on some recent methods in sibling group reconstruction based on set coverings. Optimization Methods and Software. Volume 26, Issue 6, December 2011, pages 993-1003.
  • Casey JR, Block S, Puthoor P, Hedrick J, Almudevar A, Pichichero ME (2011) A Simple Scoring System to Improve Clinical Assessment of Acute Otitis Media. Clinical Pediatr. 50(7):623-9. PMID:21471024
  • Almudevar A, Anderson EC (2011) A new version of PRT software for sibling groups reconstruction with comments regarding several issues in the sibling reconstruction problem. Mol Ecol Resour. PMID: 21883980.
  • Barry CT, D'Souza M, McCall M, Safadjou S, Ryan C, Kashyap R, Marroquin C, Orloff M, Almudevar A, Godfrey TE. (2011) Micro RNA Expression Profiles as Adjunctive Data to Assess the Risk of Hepatocellular Carcinoma Recurrence After Liver Transplantation. Am J Transplant. PMID: 22008552.
  • 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.

  • Xu Z, Almudevar A, Mathews D (2011) Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Research. doi: 10.1093/nar/gkr1081. [Epub ahead of print] PubMed PMID: 22139940.

  • McCall M, Almudevar A (2011) Affymetrix GeneChip microarray preprocessing for multivariate analyses. Briefings in Bioinformatics (In Press).

  • Almudevar A, Lacombe J (2011) On the choice of prior density for the Bayesian analysis of pedigree structure. Theoretical Population Biology (In Press).