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 2.22). 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

Selected Publications

  • 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. Molecular Ecology Resources. 12(1):164-78. PMID: 21883980.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(2):428-37. PMID: 22008552.
  • Xu Z, Almudevar A, Mathews D (2012) Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Res. 40(4):e26. PMID: 22139940; PMCID: PMC3287165.
  • Almudevar A, Lacombe J (2012) On the choice of prior density for the Bayesian analysis of pedigree structure. Theoretical Population Biology. 81(2):131-143. PMID:22200649143
  • 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. 8(6):799-805. PMID: 22495112; PMCID: PMC3679215.
  • 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. 57(12): 3132-3146.
  • Almudevar A, Lacombe J (2012) An extension of a calibration-free trajectory reconstruction method for wireless networks. IEEE Transactions on Signal Processing. 60(10):5588-5592.
  • 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. 25(4):280-1. PMID: 22840940; PMCID: PMC3690189.
  • Casey JR, Block SL, Hedrick J, Almudevar A, Pichichero ME (2012) Comparison of amoxicillin/clavulanic acid high dose with cefdinir in the treatment of acute otitis media. Drugs. 72(15):1991-7. PMID: 23039319. 
  • Xu Q, Almudervar A, Casey JR, Pichichero ME (2012) Nasopharyngeal bacterial interactions in children. Emerg Infect Dis. 18(11):1738-45. PMID: 24447582; PMCID: PMC3901485.
  • 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. 7(20):1282-9. PMID: 22739674.
  • Arruda EF,  Ourique FO,  LaCombe J, Almudevar A (2013) Accelerating the convergence of value iteration by using partial transition functions. European J. Op. Res. 229(1):190-198.
  • Pichichero ME, Casey JR, Almudevar A (2013) Nonprotective responses to pediatric vaccines occur in children who are otitis prone. Pediatr Infect Dis J. 2013 32(11):1163-8. PubMed PMID: 24141796; PMCID: PMC3884640.
  • Sharma SK, Roumanes D, Almudevar A, Mosmann TR, Pichichero ME (2013) CD4+ T-cell responses among adults and young children in response to Streptococcus pneumoniae and Haemophilus influenzae vaccine candidate protein antigens. Vaccine. 31(30):3090-7. PMID: 23632305; PMCID: PMC3777711.
  • Liu K, Kaur R, Almudevar A, Pichichero ME (2013) Higher serum levels of interleukin 10 occur at onset of acute otitis media caused by Streptococcus pneumoniae compared to Haemophilus influenzae and Moraxella catarrhalis. Laryngoscope. 123(6):1500-1505. PMID:23404508; PMCID: PMC3966296.
  • Pichichero ME, Casey JR, Almudevar A (2013) Reducing the frequency of acute otitis media by individualized care. Pediatr Infect Dis J. 32(5):473-8. PMID: 23340550; PMCID:PMC3681924.
  • Arruda E, Ourique F, Almudevar A, Silva R (2013) On cost based algorithm selection for problem solving. American Journal of Operations Research, 3(5):431-438.
  • Chen L, Almudevar A, Klebanov L. (2013) Aggregation effect in microarray data analysis.    Statistical Methods for Microarray Data Analysis (Methods in Molecular Biology), ed Yakovlev A, Klebanov L, Gaile D. Springer, New York. 177-191. PMID: 23385538.
  • Almudevar A (2013) Multiple hypothesis testing: a methodological overview. Statistical Methods for Microarray Data Analysis (Methods in Molecular Biology), ed Yakovlev A, Klebanov L, Gaile D. Springer, New York. 37-55. PMID: 23385530.
  • Tran V, McCall MN, McMurray HR, Almudevar A (2013) On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior. Frontiers in Genetics. 4:263. PMID: 24376454; PMCID: PMC3859184.
  • Almudevar A (2014) Applications of sequential methods in multiple hypothesis testing. Proceedings of Statistical Modeling for Biological Systems: In Memory of Andrei Yakovlev (IMS Collections), ed  Almudevar A, Oakes D, Hall J.  IMS Collections. [in press].
  • Chen L, Klebanov L, Almudevar A,  Proschel C (2014) A study of the correlation structure of microarray gene expression data based on mechanistic modeling of cell population kinetics. Proceedings of Statistical Modeling for Biological Systems: In Memory of Andrei Yakovlev (IMS Collections), ed  Almudevar A, Oakes D, Hall J. Institute of Mathematical Statistics. [in press].
  • Almudevar A (2014) Nasopharyngeal bacterial interactions in children: Response. Emerging Infectious Diseases.20(2):324-325.PMID:24596952; PMCID: PMC3901493.
  • Barry CT, Hah Z, Partin A, Mooney RA, Chuang KH, Augustine A, Almudevar A, Cao W, Rubens DJ, Parker KJ (2014). Mouse liver dispersion for the diagnosis of early-stage fatty liver disease: a 70-sample study. Ultrasound Med Biol. 40(4):704-13. PMID: 24412179.
  • McCall MN, McMurray H, Land H, Almudevar A (2014) On non-detects in qPCR data. Bioinformatics. 2014 Apr 23 [Epub ahead of print]. PMID: 24764462.

Books

  • Almudevar A (2014) Approximate Iterative Algorithms. CRC Press/Balkema. Leiden, The Netherlands.
  • Almudevar A, Oakes D, Hall J (editors) (2014) Proceedings of Statistical Modeling for Biological Systems: In Memory of Andrei Yakovlev (IMS Collections). Institute of Mathematical Statistics. [in press].