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Perry Ridge Jr

Associate Professor
Biology

4126 LSB
Provo, UT 84602

Biography

Teaching Interests

  • Bioinformatics
  • Genetics
  • Genomics

Research Interests

  • Bioinformatics
  • Computational Biology
  • Genetics

Memberships

  • International Society for Computational Biology, 2013-Present
  • Alzheimer's Association, 2012-Present
  • American Society of Human Genetics, 2010-Present

Courses Taught

Winter 2019

  • BIO 494R: Mentored Research Section 015
  • BIO 799R: Dissertation Section 013

Fall 2018

  • BIO 165: Introduction to Bioinformatics Section 001, 002
  • BIO 494R: Mentored Research Section 015
  • BIO 664: Bioinf & Data Analysis 1 Section 001
  • BIO 799R: Dissertation Section 014

Summer 2018

  • BIO 799R: Dissertation Section 013

Spring 2018

  • BIO 194: Intro to Mentored Research Section 001
  • BIO 799R: Dissertation Section 012

Research Interests

Bioinformatics, Computational Biology, Genetics, Genome Biology

Teaching Interests

Bioinformatics, Genetics, Genomics

Memberships

  • International Society for Computational Biology: ( - Present)
  • Alzheimer's Association: ( - Present)
  • American Society of Human Genetics: ( - Present)

Professional Citizenship

  • Committee/Council Chair, Provo High School Community Council, 2020-09-01 - 2020-09-30 - Present
  • Reviewer, Ad Hoc Reviewer, Applications in Plant Science, 2020-08-01 - 2020-08-31 - Present
  • Reviewer, Ad Hoc Reviewer, Nature Communications, 2020-07-01 - 2020-07-31 - Present
  • Reviewer, Ad Hoc Reviewer, Frontiers in Neuroscience, 2020-06-01 - 2020-06-30 - Present
  • Reviewer, Ad Hoc Reviewer, Heliyon, 2020-06-01 - 2020-06-30 - Present
  • Reviewer, Ad Hoc Reviewer, Neurobiology of Disease, 2020-06-01 - 2020-06-30 - Present
  • Committee/Council Member, Provo School District Sex Education Committee, 2019-10-01 - 2019-10-31 - Present
  • Reviewer, Ad Hoc Reviewer, Algorithms, 2019-03-01 - 2019-03-31 - Present
  • Reviewer, Ad Hoc Reviewer, Mitochondrion, 2019-03-01 - 2019-03-31 - Present
  • Reviewer, Ad Hoc Reviewer, Pharmaceuticals, 2019-03-01 - 2019-03-31 - Present
  • Editor, Associate Editor, Genes, Special Issue: Genetics and Genomics of Alzheimer's Disease, 2019-02-01 - 2019-02-28 - Present
  • Reviewer, Ad Hoc Reviewer, Advances in Medical Science, 2019-01-01 - 2019-01-31 - Present
  • Reviewer, Ad Hoc Reviewer, Alzheimer's Association, 2018-01-01 - 2018-12-31 - Present
  • Reviewer, Ad Hoc Reviewer, BMC Genomics, 2018-01-01 - 2018-12-31 - Present
  • Reviewer, Ad Hoc Reviewer, BMC Neurology, 2018-01-01 - 2018-12-31 - Present
  • Grant Proposal Reviewer, External, Fight for Sight Foundation, 2018-01-01 - 2018-12-31 - Present
  • Reviewer, Ad Hoc Reviewer, Journal of Alzheimer's Disease, 2018-01-01 - 2018-12-31 - Present
  • Reviewer, Ad Hoc Reviewer, Molecular Ecology Resources, 2018-01-01 - 2018-12-31 - Present
  • Reviewer, Ad Hoc Reviewer, Neurobiology of Aging, 2018-01-01 - 2018-12-31 - Present
  • Committee/Council Chair, Westridge Elementary Community Council, 2018-01-01 - 2018-12-31 - Present
  • Reviewer, Ad Hoc Reviewer, Neuroscience Letters, 2017-11-01 - 2017-11-30 - Present
  • Reviewer, Ad Hoc Reviewer, Rejuvenation Research, 2017-11-01 - 2017-11-30 - Present
  • Committee/Council Member, International Society for Computational Biology, ISMB Function Sig, 2017-04-01 - 2017-04-30 - Present
  • Reviewer, Ad Hoc Reviewer, BMC Bioinformatics, 2017-03-01 - 2017-03-31 - Present
  • Reviewer, Ad Hoc Reviewer, PeerJ, 2017-01-01 - 2017-01-31 - Present
  • Reviewer, Ad Hoc Reviewer, Scientific Reports, 2017-01-01 - 2017-01-31 - Present
  • Other, Westridge PTO, 2016-04-01 - 2016-04-30 - Present
  • Reviewer, Ad Hoc Reviewer, Giga Science, 2015-05-01 - 2015-05-31 - Present
  • Reviewer, Ad Hoc Reviewer, Bioinformatics, 2014-09-01 - 2014-09-30 - Present
  • Other, Letters of Recommendation, 2014-01-01 - 2014-01-31 - Present
  • Reviewer, Ad Hoc Reviewer, PLoS One, 2013-04-01 - 2013-04-30 - Present
  • Reviewer, Ad Hoc Reviewer, Alzheimer's & Dementia, 2012-12-01 - 2012-12-31 - Present
  • Other, Biotechnology and Bioinformatics Symposium, 2016-08-01 - 2016-08-31 - 2017-03-01 - 2017-03-31
  • Other, BMC Bioinformatics, 2016-10-01 - 2016-10-31 - 2017-02-01 - 2017-02-28
  • Other, BMC Genomics, 2016-10-01 - 2016-10-31 - 2017-02-01 - 2017-02-28
  • Reviewer, Ad Hoc Reviewer, Biotechnology and Bioinformatics Symposium, 2013-08-01 - 2013-08-31 - 2017-01-01 - 2017-01-31
  • Other, BMC Bioinformatics, 2015-10-01 - 2015-10-31 - 2016-06-01 - 2016-06-30
  • Other, BMC Genomics, 2015-10-01 - 2015-10-31 - 2016-06-01 - 2016-06-30
  • Other, Biotechnology and Bioinformatics Symposium, 2015-08-01 - 2015-08-31 - 2016-06-01 - 2016-06-30
  • Other, BMC Bioinformatics, 2014-10-01 - 2014-10-31 - 2015-04-01 - 2015-04-30
  • Other, BMC Genetics, 2014-10-01 - 2014-10-31 - 2015-04-01 - 2015-04-30
  • Other, Biotechnology and Bioinformatics Symposium, 2014-08-01 - 2014-08-31 - 2015-04-01 - 2015-04-30
  • Guest Speaker, Workshop for High School Science Teachers, 2014-06-01 - 2014-06-30 - 2014-06-01 - 2014-06-30
  • Other, BMC Bioinformatics, 2013-11-01 - 2013-11-30 - 2014-05-01 - 2014-05-31
  • Other, Biotechnology and Bioinformatics Symposium, 2013-09-01 - 2013-09-30 - 2014-05-01 - 2014-05-31

Courses Taught

2020

  • BIO 664 : Section 001
  • BIO 799R: Section 020
  • BIO 165 : Section 001
  • BIO 165 : Section 002
  • BIO 494R: Section 020
  • BIO 799R: Section 011
  • BIO 799R: Section 010
  • BIO 494R: Section 018
  • PWS 598R: Section 010
  • BIO 799R: Section 013
  • BIO 494R: Section 015

2019

  • BIO 559R: Section 002
  • BIO 799R: Section 012
  • BIO 165 : Section 001
  • BIO 165 : Section 002
  • BIO 165 : Section 004
  • BIO 494R: Section 015
  • BIO 799R: Section 013
  • BIO 494R: Section 001
  • BIO 799R: Section 012
  • BIO 194 : Section 001
  • BIO 799R: Section 013
  • BIO 494R: Section 015

2018

  • BIO 664 : Section 001
  • BIO 799R: Section 014
  • BIO 165 : Section 001
  • BIO 165 : Section 002
  • BIO 494R: Section 015
  • BIO 799R: Section 013
  • BIO 799R: Section 012
  • BIO 194 : Section 001
  • BIO 559R: Section 003
  • BIO 799R: Section 013
  • BIO 494R: Section 016

2017

  • BIO 559R: Section 003
  • C S 418 : Section 001
  • BIO 365 : Section 001
  • BIO 799R: Section 014
  • BIO 165 : Section 001
  • BIO 165 : Section 002
  • BIO 494R: Section 016
  • BIO 494R: Section 031
  • BIO 799R: Section 013
  • BIO 799R: Section 012
  • BIO 559R: Section 003
  • BIO 494R: Section 016

2016

  • BIO 559R: Section 003
  • BIO 165 : Section 001
  • BIO 165 : Section 002
  • BIO 494R: Section 16
  • BIO 559R: Section 004
  • BIO 494R: Section 20
  • BIO 559R: Section 003
  • BIO 165 : Section 001
  • BIO 165 : Section 002
  • BIO 494R: Section 017

2015

  • BIO 559R: Section 003
  • BIO 494R: Section 016
  • BIO 494R: Section 023
  • BIO 165 : Section 001
  • BIO 494R: Section 020
  • BIO 559R: Section 003
  • BIO 165 : Section 001
  • BIO 494R: Section 017

2014

  • BIO 559R: Section 003
  • C S 418 : Section 001
  • BIO 365 : Section 001
  • BIO 165 : Section 001
  • BIO 494R: Section 016
  • BIO 494R: Section 025
  • BIO 494R: Section 023
  • BIO 494R: Section 020
  • BIO 559R: Section 004
  • BIO 465 : Section 002
  • BIO 165 : Section 001
  • BIO 494R: Section 017

2013

  • BIO 494R: Section 010

Publications

  • Pickett BD, Wallace EM, Ridge PG, Kauwe JSK. April (2nd Quarter/Spring), 2020. Lingering Taxonomic Challenges Hinder Conservation and Management of Global Bonefishes.
  • Morley S, Peralta-Castro A, Brieba LG, Miller J, Ong K, Ridge PG, Oliphant A, Aldous S, Nielsen B. June 6, 2019. Arabidopsis thaliana organelles mimic the T7 phage DNA replisome with specific interactions between Twinkle protein and DNA polymerases Pol1A and Pol1B.
  • Ridge PG, Karch CM, Hsu S, Arano I, Teerlink CC, Ebbert MTW, Murcia JDG, Farnham JM, Damato AR, Allen M, et alNovember 29, 2017. Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience.
  • Lythgoe C, Perkes A, Peterson M, Schmutz C, Leary M, Ebbert MT, Ridge PG, Norton MC, Tschanz JT, Munger RG, et al2015. Population-based analysis of cholesteryl ester transfer protein identifies association between I405V and cognitive decline: the Cache County Study. 1st ed.
  • Gardner SG, Miller JB, Dean T, Robinson T, Erickson M, Ridge PG, McCleary WR. April (2nd Quarter/Spring) 23, 2015. Genetic analysis, structural modeling, and direct couple analysis suggest a mechanism for phosphate signaling in Escherichia coli . Suppl 2nd ed.
  • Seeley M, Clement MJ, Giraud-Carrier CG, Snell QO, Bodily P, Fujimoto S, Kauwe JSK, Ridge PG. 2014. A Structured Approach to Ensemble Learning for Alzheimer’s Disease Prediction. New York, NY, USA: ACM.
  • Bodily PM, Clement MJ, Snell QO, Fujimoto S, Ridge PG. 2014. Haplotype-centered Mapping for Improved Alignments and Genetic Association Studies. New York, NY, USA: ACM.
  • Ebbert MT, Ridge PG, Wilson AR, Sharp AR, Bailey M, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JSK. 2014. Population-based Analysis of Alzheimer’s Disease Risk Alleles Implicates Genetic Interactions. 9th ed.
  • Kauwe JSK, Bailey MH, Ridge PG, Perry R, Wadsworth ME, Hoyt KL, Staley LA, Karch CM, Harari O, Cruchaga C, et alOctober (4th Quarter/Autumn) 1, 2014. Genome-wide association study of CSF levels of 59 alzheimer's disease candidate proteins: significant associations with proteins involved in amyloid processing and inflammation. 10th ed.
  • Cruchaga C, Karch CM, Jin SC, Benitez BA, Cai Y, Guerreiro R, Harari O, Norton J, Budde J, Bertelsen S, et alJanuary (1st Quarter/Winter) 23, 2014. Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. 7484th ed.
  • Ridge PG, Maxwell TJ, Foutz SJ, Bailey MH, Corcoran CD, Tschanz JT, Norton MC, Munger RG, O'Brien E, Kerber RA, et alJanuary (1st Quarter/Winter) 1, 2014. Mitochondrial genomic variation associated with higher mitochondrial copy number: the Cache County Study on Memory Health and Aging. Suppl 7th ed.
  • Sharp AR, Ridge PG, Bailey MH, Boehme KL, Norton MC, Tschanz JT, Munger RG, Corcoran CD, Kauwe JSK. January (1st Quarter/Winter) 1, 2014. Population substructure in Cache County, Utah: the Cache County study. Suppl 7th ed.
  • Ebbert MT, Wadsworth ME, Boehme KL, Hoyt KL, Sharp AR, O'Fallon BD, Kauwe JSK, Ridge PG. January (1st Quarter/Winter) 1, 2014. Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files. Suppl 7th ed.
  • Ridge PG, Mukherjee S, Crane PK, Kauwe JSK, ADGC. November 7, 2013. Alzheimer's disease: analyzing the missing heritability. 11th ed.
  • Chen K, Coonrod EM, Kumanovics A, Franks ZF, Durtschi JD, Margraf RL, Wu W, Heikal NM, Augustine NH, Ridge PG, et alOctober (4th Quarter/Autumn), 2013. Germline Mutations in NFKB2 Implicate the Noncanonical NF-ë¼B Pathway in the Pathogenesis of Common Variable Immunodeficiency.
  • Kauwe JSK, Ridge PG, Foster NL, Cannon-Albright LA. October (4th Quarter/Autumn), 2013. Strong evidence for a genetic contribution to late-onset Alzheimer’s disease mortality: a population-based study. 10th ed.
  • Ridge PG, Koop A, Maxwell TJ, Bailey MH, Swerdlow RH, Kauwe JSK, Honea RA. September 11, 2013. Mitochondrial haplotypes associated with biomarkers for Alzheimer’s disease. 9th ed.
  • Ridge PG, Ebbert MT, Kauwe JSK. July (3rd Quarter/Summer), 2013. Genetics of Alzheimer’s disease. 254954th ed.

Presentations

  • Nelson A, Murcia JG, Dearden L, Weinert A, Freitas C, Ferrel M, Grose JH, Ridge PG, Wilson E, Kauwe JSK, et alThe CCRL2 atypical chemokine receptor variant V180M alters CCL4 secretion in leukocytes . American Society of Microbiology Intermountain Branch Meeting . December, 2020.
  • Dearden L, Murcia JG, Nelson A, Weinert A, Freitas C, Ferrel M, Grose JH, Ridge PG, Wilson E, Kauwe JSK, et alThe CCRL2 atypical chemokine receptor variant V180M has a higher binding affinity for chemerin . American Society of Microbiology Intermountain Branch Meeting . December, 2020.
  • Miller J, McKinnon LM, Murcia J, Black G, Ward E, Webster J, Kauwe JSK, Ridge PG. Synonymous variant rs2405442 in PILRA is associated with Alzheimer's disease and affects RNA expression by destroying a ramp sequence. Alzheimer's Association International Conference. July, 2020.
  • McKinnon LM, Miller J, Whiting MF, Kauwe JSK, Ridge PG. A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates. Intelligent Systems for Molecular Biology. July, 2020.
  • Cutler L, Hunt J, McKinnon L, Miller J, Ridge PG. A comprehensive analysis of orthologous genes across all domains. International Society of Computational Biology Rocky Mountain Bioinformatics Conference. December, 2019.
  • Pickett B, Kauwe JSK, Ridge PG. Assessing long-read correction and polishing strategies for genome assembly. International Society of Computational Biology Rocky Mountain Bioinformatics Conference. December, 2019.
  • McKinnon L, Miller J, Ridge PG. Using Ramp Sequences to Identify Causes of Disease Association. International Society of Computational Biology Rocky Mountain Bioinformatics Conference. December, 2019.
  • Ebbert M, Jensen T, Jansen-West K, Sens J, Ridge PG, Kauwe JSK, al. e. ‘Dark’ and ‘camouflaged’ genes may harbor disease-relevant variants that long-read sequencing can resolve. ASHG Annual Meeting. October, 2019.
  • Pickett BD, Miller J, Ridge PG. A Case Study on the Effects of Noisy, Long-read Correction Approaches on Assembly Contiguity. ISCB Rocky Mountain Bioinformatics Conference. 2018.
  • McKinnon L, Miller J, Ridge PG. Codon Pairs are Phylogenetically Conserved: Codon Pairing as a Novel Phylogenetic Character State for Parsimony and Alignment-Free Methods. ISCB Rocky Mountain Bioinformatics Conference. 2018.
  • Miller J, Brase L, Ridge PG. ExtRamp: A novel algorithm for extracting the ramp sequences based on the tRNA adaptation index or relative codon adaptiveness. ISCB Rocky Mountain Bioinformatics Conference. 2018.
  • Maltba H, Beecroft S, Smith S, Ridge PG. Select: A SQL-based, high-resolution selection scanning tool to identify genomic selection signals using next-generation sequencing data. ISCB Rocky Mountain Bioinformatics Conference. 2018.
  • Miller JB, McKinnon LM, Whiting MF, Ridge PG. Codon Aversion Motifs: An alignment-free method to recover phylogenies. ISCB Rocky Mountain Bioinformatics Conference. December, 2017.
  • Pickett B, Smith S, Ridge PG. Detecting Selective Sweeps in Genetic Variants in Model and Non-Model Organisms. Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology. July, 2017.
  • Miller J, Pickett B, Ridge PG. JustOrthologs: A Fast, Accurate, and User-Friendly Ortholog Identification Algorithm. Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology. July, 2017.
  • Morley S, Miller J, Ridge PG, Nielsen B. Assembling the Arabidopsis Mitochondrial DNA Replisome. 28th International Conference on Arabidopsis Research. June, 2017.
  • Ridge PG, Wadsworth ME, Miller JB, Saykin AJ, Green RC, ADNI, Kauwe JSK. Assembly of 809 whole mitochondrial genomes with clinical, imaging, and fluid biomarker phenotyping: the Alzheimer’s Disease Neuroimaging Initiative. Biotechnology and Bioinformatics Symposium. December, 2016.
  • Cormier M, Wright S, Miller J, Ridge PG. Determining the effects variants have on gene splicing. Biotechnology and Bioinformatics Symposium. December, 2016.
  • Miller JB, Hippen AA, Wright SM, Morris C, Ridge PG. Human viruses have codon usage biases that match highly expressed proteins in the tissues they infect. Biotechnology and Bioinformatics Symposium. December, 2016.
  • Picket BD, Miller JB, Ridge PG. Kmer-SSR: A fast and exhaustive SSR search algorithm. Biotechnology and Bioinformatics Symposium. December, 2016.
  • Pickett BD, Miller JB, Ridge PG. Kmer-SSR: An efficient tool for perfect SSR detection in genetic sequences. American Society of Human Genetics annual meeting. October, 2016.
  • Pickett BD, Shiozawa DK, Whiting MF, Davis N, Ridge PG. Congruence of plecopteran transcriptomes and Sanger-generated molecular markers with emphasis on resolution of the perloidea. Society for Freshwater Science annual meeting. May, 2016.
  • Bodily P, Fujimoto S, Page J, Clement MJ, Ridge PG. A Novel Approach for Multi-SNP GWAS and its Application in Alzheimer's Disease. Biotechnology and Bioinformatics Symposium. December, 2015.
  • Ebbert M, Wadsworth M, Staley L, Pickett B, Initiative ADN, Kauwe JSK, Ridge PG. An Evaluation of the Necessity of PCR Duplicate Removal From Next-Generation Sequencing Data and a Comparison of Approaches. Biotechnology and Bioinformatics Symposium. December, 2015.
  • Miller J, Hippen A, Belyeu J, Whiting MF, Ridge PG. Missing something?: Codon non-usage as a character in phylogenetic inference in tetrapods. Biotechnology and Bioinformatics Symposium. December, 2015.
  • Shiozawa DK, Oh SY, Ridge PG, Pickett B, Evans RP. Phylogeography of Cottids in the Lost River Streams of Idaho. Annual Meeting, American Fisheries Society. August, 2015.
  • Shiozawa DK, Ridge PG, Unmack PJ, Houston DD, Evans RP. Refining Phylogenetic Relationships Among Cutthroat Trout . Annual Meeting, American Fisheries Society. August, 2015.
  • Pickett B, Karlinsey S, Shiozawa DK, Whipple CJ, Ridge PG. A Novel Algorithm for Finding SSRs in Genetic Sequences. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Karlinsey S, Ridge PG. A Novel Approach to Finding SSRs Using Suffix Arrays. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Pickett B, Ridge PG. Comparison of next-generation sequencing alignment programs using 15 whole genomes from the Cache County Study on Memory Health. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Smith H, Ridge PG. Composite of Multiple Signals: Finding Patterns of Natural Selection in Whole Genome Data. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Law J, Clawson N, Ridge PG. Kinship Coefficient Calculator. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Nielsen D, Ridge PG. Splice Variant Classification Tool: Analysis of Splice Region Variants and Potential Rescue Mechanisms. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Miller J, Duce J, Ridge PG. The Alignable Portion. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Wadsworth M, Ridge PG. The Variant Characterization of 211 Whole Genome Sequences: The Cache County Study on Memory Health and Aging. Biotechnology and Bioinformatics Symposium. December, 2014.
  • Pickett B, Ridge PG. Comparison of next-generation sequencing alignment programs using 15 whole genomes from the Cache County Study on Memory Health. American Society of Human Genetics Annual Meeting. October, 2014.
  • Wadsworth M, Ridge PG. The Variant Characterization of 211 Whole Genome Sequences: The Cache County Study on Memory Health and Aging. American Society of Human Genetics Annual Meeting. October, 2014.
  • Seeley M, Clement MJ, Giraud-Carrier CG, Snell QO, Bodily PM, Fujimoto MS, Ridge PG. A Structured Approach to Ensemble Learning for Alzheimer’s Disease Prediction. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. September, 2014.
  • Bodily PM, Clement MJ, Fujimoto MS, Snell QO, Ridge PG. Haplotype-Centered Mapping for Improved Alignments and Genetic Association Studies. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. September, 2014.
  • Wadsworth M, Ridge PG. An application of the Variant Tool Chest. Biotechnology and Bioinformatics Symposium. December, 2013.
  • Ridge PG. Mitochondrial genomic variation associated with higher mitochondrial copy number: The Cache County Study on Memory Health and Aging. Biotechnology and Bioinformatics Symposium. December, 2013.
  • Ebbert MT, Ridge PG. Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files. Biotechnology and Bioinformatics Symposium. December, 2013.
Perry Ridge Jr