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Biostatistics and Computational Biology

URMC / Department of Biostatistics and Computational Biology / People & Research / Faculty / Anthony Almudevar, PhD

 

Anthony Almudevar, PhD

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
265 Crittenden Boulevard, CU 420630 
Rochester, New York 14642-0630

Office: Saunders Research Building 4168
Phone: (585) 275-6992
Fax: (585) 273-1031
E-mail: Anthony_Almudevar@urmc.rochester.edu]

URMC Research Profile

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.

Software

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.
  • 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.
  • Morris, M. C., Almudevar, A. L., Casey, J. R., & Pichichero, M. E. (2015). Familial and microbiological contribution to the otitis–prone condition. International Journal of Pediatric Otorhinolaryngology, 79(12), 2174-2177. PMID:2649078
  • Ren, D., Almudevar, A. L., & Pichichero, M. E. (2015). Synchrony in serum antibody response to conserved proteins of Streptococcus pneumoniae in young children. Human Vaccines & Immunotherapeutics, 11(2), 489-497. PMID: 25692218
  • Ren, D., Almudevar, A. L., Murphy, T. F., Lafontaine, E. R., Campagnari, A. A., Luke-Marshall, N., Casey, J. R., Pichichero, M. E. (2015). Serum antibody response to Moraxella catarrhalis proteins OMP CD, OppA, Msp22, Hag, and PilA2 after nasopharyngeal colonization and acute otitis media in children. Vaccine, 33(43), 5809-5814. PMID: 26392013
  • Sandal, S., Almudevar, A., Parajuli, S., & Bose, A. (2015). Comparing 10-yr renal outcomes in deceased donor and living donor liver transplants. Clinical Transplantation, 29(12), 1140-1147. PMID: 26383173
  • Almudevar, A. (2016). An information theoretic approach to pedigree reconstruction. Theoretical Population Biology, 107, 52-64. PMID: 26453931
  • Almudevar, A. (2016). Higher order density approximations for solutions to estimating equations. Journal of Multivariate Analysis, 143, 424-439.
  • Xie, QY, Almudevar, A, Whitney-Miller, CL, Barry, CT, McCall MN. (2016) A microRNA biomarker of hepatocellular carcinoma recurrence following liver transplantation accounting for within-patient heterogeneity. BMC Med Genomics. 2016 Apr 8;9(1):18.  PMID: 27059462
  • Pichichero ME, Almudevar A. (2016) Serum cytokine biomarkers accurately predict presence of acute otitis media infection and recovery caused by Haemophilus influenzae. Int J Pediatr Otorhinolaryngol. 2016 Apr;83:200-4. PMID: 26968077.
  • Pichichero ME, Casey JR, Almudevar A, Basha S, Surendran N, Kaur R, Morris M, Livingstone AM, Mosmann TR. (2016) Functional immune cell differences associated with low vaccine responses in infants. J Infect Dis. 2016 PMID: 26908730.
  • Chen W, Melamed ML, Hostetter TH, Bauer C, Raff AC, Almudevar AL, Lalonde A, Messing S, Abramowitz MK. (2016) Effect of oral sodium bicarbonate on fibroblast growth factor-23 in patients with chronic kidney disease: a pilot study. BMC Nephrol. 2016 Aug 5;17(1):114. doi: 10.1186/s12882-016-0331-6. PubMed PMID: 27495287; PubMed Central PMCID: PMC4974735.
  • Pichichero ME, Almudevar A. (2016) Inflammation-associated cytokine analysis identifies presence of respiratory bacterial pathogens in the nasopharynx. Pathog Dis. 2016 Aug;74(6). pii: ftw064. doi: 10.1093/femspd/ftw064. PubMed PMID:27493063.
  • Xu Q, Casey JR, Almudevar A, Pichichero ME. (2017) Correlation of Higher Antibody Levels to Pneumococcal Proteins with Protection from Pneumococcal Acute Otitis Media but not Protection from Nasopharyngeal Colonization in Young Children. Clin Microbiol Infect. 2017 Jan 28. pii: S1198-743X(17)30044-7. doi:10.1016/j.cmi.2017.01.011. [Epub ahead of print] PubMed PMID: 28143785.

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].

Book Chapters

  • 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.
  • Almudevar, A (2016). A Functional Analytic Approach to Approximate Iterative Algorithms. in "Modern Trends in Controlled Stochastic Processes: Theory and Applications, Volume II" (ed. A. Piunovskiy), pp 66-85, Luniver Press

Last updated: July 6, 2018