Jeramiah Smith

jjsmit3's picture
  • Associate Professor
  • Bioinformatics and Computational Biology
  • Cell and Developmental Biology
  • Ecology and Evolutionary Biology
  • Genetics and Genomics
  • Biology
jjsmit3@uky.edu
200 Thomas Hunt Morgan
(859) 257-0124
PDF icon JSmith_CV_longform_03192019.pdf
Lab Website
Research Interests:
  • Genome Biology
  • Vertebrate Evolution
  • Pluripotency
  • Cancer
  • Regeneration
  • biology
Education

Postdoctoral Fellow, U. Washington Dept. Genome Sciences & Benaroya Res. Inst. at Virginia Mason (2007 - 2011)
University of Kentucky, Ph.D. in Biology, 2007
Colorado State University, M.S. in Biology, 2002
Black Hills State University, B.S. in Biology, cum laude, 1998

Research

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CURRENTLY ACCEPTING GRADUATE STUDENTS - 2019/20 20/21 (FALL/SUMMER) FOR NSF and NIH-FUNDED RESEARCH ASSISTANT TO STUDY PROGRAMMED GENOME REARRANGEMENT

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CLICK HERE FOR SMITH LAB WEBPAGE

 

 

PubMed Publications*: 
  • Rodgers, AK ;Smith, JJ ;Voss, SR "Identification of immune and non-immune cells in regenerating axolotl limbs by single-cell sequencing." Experimental cell research 394, 2 (2020): 112149. Details. Full text
  • Hess, JE ;Smith, JJ ;Timoshevskaya, N ;Baker, C.;Caudill, CC ;Graves, D ;Keefer, ML ;Kinziger, AP ;Moser, ML ;Porter, LL ;Silver, G ;Whitlock, SL ;, "Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey." Molecular ecology (2020): Details. Full text
  • Smith, JJ ;Timoshevskiy, VA ;Saraceno, C "Programmed DNA Elimination in Vertebrates." Annual review of animal biosciences (2020): Details.
  • Gómez, CM Arenas;Woodcock, MR ;Smith, JJ ;Voss, SR ;Delgado, JP "A <i>de novo</i> reference transcriptome for <i>Bolitoglossa vallecula</i>, an Andean mountain salamander in Colombia." Data in brief 29, (2020): 105256. Details. Full text
  • Nail, AN ;Smith, JJ ;Peterson, ML ;Spear, BT "Evolutionary Analysis of the Zinc Finger and Homeoboxes Family of Proteins Identifies Multiple Conserved Domains and a Common Early Chordate Ancestor." Genome biology and evolution 12, 3 (2020): 174-184. Details. Full text
  • Smith, JJ ;Timoshevskaya, N ;Timoshevskiy, VA ;Keinath, MC ;Hardy, D ;Voss, SR "A chromosome-scale assembly of the axolotl genome." Genome research 29, 2 (2019): 317-324. Details. Full text
  • Marks, RA ;Smith, JJ ;Cronk, Q ;Grassa, CJ ;McLetchie, DN "Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance." Scientific reports 9, 1 (2019): 8722. Details. Full text
  • Hockman, D ;Chong-Morrison, V ;Green, SA ;Gavriouchkina, D ;Candido-Ferreira, I ;Ling, ITC ;Williams, RM ;Amemiya, CT ;Smith, JJ ;Bronner, ME ;Sauka-Spengler, T. "A genome-wide assessment of the ancestral neural crest gene regulatory network." Nature communications 10, 1 (2019): 4689. Details. Full text
  • Timoshevskiy, VA ;Timoshevskaya, NY ;Smith, JJ "Germline-Specific Repetitive Elements in Programmatically Eliminated Chromosomes of the Sea Lamprey (<i>Petromyzon marinus</i>)." Genes 10, 10 (2019): Details. Full text
  • Herman, PE ;Papatheodorou, A ;Bryant, SA ;Waterbury, CKM ;, ;Arcese, AA ;Buxbaum, JD ;Smith, JJ ;Morgan, JR ;Bloom, O "Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys." Scientific reports 8, 1 (2018): 742. Details. Full text
  • Smith, JJ "Programmed DNA Elimination: Keeping Germline Genes in Their Place." Current biology : CB 28, 10 (2018): R601-R603. Details. Full text
  • Gómez, CM Arenas;Woodcock, RM ;Smith, JJ ;Voss, RS ;Delgado, JP "Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research." BMC genomics 19, 1 (2018): 704. Details. Full text
  • Timoshevskiy, VA ;Lampman, RT ;Hess, JE ;Porter, LL ;Smith, JJ "Deep ancestry of programmed genome rearrangement in lampreys." Developmental biology 429, 1 (2017): 31-34. Details. Full text
  • de Lomana, López García;Kaur, A ;Turkarslan, S ;Beer, KD ;Mast, FD ;Smith, JJ ;Aitchison, JD ;Baliga, NS "Adaptive Prediction Emerges Over Short Evolutionary Time Scales." Genome biology and evolution 9, 6 (2017): 1616-1623. Details. Full text
  • Dillard, DA ;Avey, JP ;Robinson, RF ;Smith, JJ ;Beals, J ;Manson, SM ;Comtois, KA "Demographic, Clinical, and Service Utilization Factors Associated with Suicide-Related Visits among Alaska Native and American Indian Adults." Suicide & life-threatening behavior 47, 1 (2017): 27-37. Details. Full text
  • Woodcock, MR ;Vaughn-Wolfe, J ;Elias, A ;Kump, DK ;Kendall, KD ;Timoshevskaya, N ;Timoshevskiy, V ;Perry, DW ;Smith, JJ ;Spiewak, JE ;Parichy, DM ;Voss, SR "Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum." Scientific reports 7, 1 (2017): 6. Details. Full text
  • Parang, B ;Kaz, AM ;Barrett, CW ;Short, SP ;Ning, W ;Keating, CE ;Mittal, MK ;Naik, RD ;Washington, MK ;Revetta, FL ;Smith, JJ ;Chen, X.;Wilson, KT ;Brand, T ;Bader, DM ;Tansey, WP ;Chen, R.;Brentnall, TA ;Grady, WM ;Williams, CS "BVES regulates c-Myc stability via PP2A and suppresses colitis-induced tumourigenesis." Gut 66, 5 (2017): 852-862. Details. Full text
  • Wang, Z.;Danziger, SA ;Heavner, BD ;Ma, S.;Smith, JJ ;Li, S.;Herricks, T ;Simeonidis, E ;Baliga, NS ;Aitchison, JD ;Price, ND "Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast." PLoS computational biology 13, 5 (2017): e1005489. Details. Full text
  • Braasch, I.;Gehrke, AR ;Smith, JJ ;Kawasaki, K ;Manousaki, T.;Pasquier, J ;Amores, A ;Desvignes, T ;Batzel, P ;Catchen, J ;Berlin, AM ;Campbell, MS ;Barrell, D ;Martin, KJ ;Mulley, JF ;Ravi, V.;Lee, AP ;Nakamura, T ;Chalopin, D.;Fan, S.;Wcisel, D ;Cañestro, C ;Sydes, J ;Beaudry, FE ;Sun, Y ;Hertel, J ;Beam, MJ ;Fasold, M ;Ishiyama, M ;Johnson, J.;Kehr, S ;Lara, M.;Letaw, JH ;Litman, GW ;Litman, RT ;Mikami, M ;Ota, T.;Saha, NR ;Williams, L.;Stadler, PF ;Wang, H.;Taylor, JS ;Fontenot, Q ;Ferrara, A ;Searle, SM ;Aken, B.;Yandell, M.;Schneider, I.;Yoder, JA ;Volff, JN ;Meyer, A.;Amemiya, CT ;Venkatesh, B.;Holland, PW ;Guiguen, Y ;Bobe, J ;Shubin, NH ;Di Palma, F.;Alföldi, J.;Lindblad-Toh, K.;Postlethwait, JH "The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons." Nature genetics 48, 4 (2016): 427-37. Details. Full text
  • Bryant, SA ;, ;Amemiya, CT ;Smith, JJ "Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus)." Molecular biology and evolution 33, 9 (2016): 2337-44. Details. Full text
  • Voss, SR ;Putta, S.;Walker, JA ;Smith, JJ ;Maki, N.;Tsonis, PA "Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates?" Human genomics 7, (2013): 9. Details. Full text
  • Amemiya, CT ;Alföldi, J.;Lee, AP ;Fan, S.;Philippe, H.;Maccallum, I.;Braasch, I.;Manousaki, T.;Schneider, I.;Rohner, N.;Organ, C.;Chalopin, D.;Smith, JJ ;Robinson, M.;Dorrington, RA ;Gerdol, M.;Aken, B.;Biscotti, MA ;Barucca, M.;Baurain, D.;Berlin, AM ;Blatch, GL ;Buonocore, F.;Burmester, T.;Campbell, MS ;Canapa, A.;Cannon, JP ;Christoffels, A.;De Moro, G.;Edkins, AL ;Fan, L.;Fausto, AM ;Feiner, N.;Forconi, M.;Gamieldien, J.;Gnerre, S.;Gnirke, A.;Goldstone, JV ;Haerty, W.;Hahn, ME ;Hesse, U.;Hoffmann, S.;Johnson, J.;Karchner, SI ;Kuraku, S.;Lara, M.;Levin, JZ ;Litman, GW ;Mauceli, E.;Miyake, T.;Mueller, MG ;Nelson, DR ;Nitsche, A.;Olmo, E.;Ota, T.;Pallavicini, A.;Panji, S.;Picone, B.;Ponting, CP ;Prohaska, SJ ;Przybylski, D.;Saha, NR ;Ravi, V.;Ribeiro, FJ ;Sauka-Spengler, T.;Scapigliati, G.;Searle, SM ;Sharpe, T.;Simakov, O.;Stadler, PF ;Stegeman, JJ ;Sumiyama, K.;Tabbaa, D.;Tafer, H.;Turner-Maier, J.;Heusden, P.;White, S.;Williams, L.;Yandell, M.;Brinkmann, H.;Volff, JN ;Tabin, CJ ;Shubin, N.;Schartl, M.;Jaffe, DB ;Postlethwait, JH ;Venkatesh, B.;Di Palma, F.;Lander, ES ;Meyer, A.;Lindblad-Toh, K. "The African coelacanth genome provides insights into tetrapod evolution." Nature 496, 7445 (2013): 311-6. Details. Full text
  • Smith, JJ ;Kuraku, S.;Holt, C.;Sauka-Spengler, T.;Jiang, N.;Campbell, MS ;Yandell, MD ;Manousaki, T.;Meyer, A.;Bloom, OE ;Morgan, JR ;Buxbaum, JD ;Sachidanandam, R.;Sims, C.;Garruss, AS ;Cook, M.;Krumlauf, R.;Wiedemann, LM ;Sower, SA ;Decatur, WA ;Hall, JA ;Amemiya, CT ;Saha, NR ;Buckley, KM ;Rast, JP ;Das, S.;Hirano, M.;McCurley, N.;Guo, P.;Rohner, N.;Tabin, CJ ;Piccinelli, P.;Elgar, G.;Ruffier, M.;Aken, BL ;Searle, SM ;Muffato, M.;Pignatelli, M.;Herrero, J.;Jones, M.;Brown, CT ;Chung-Davidson, YW ;Nanlohy, KG ;Libants, SV ;Yeh, CY ;McCauley, DW ;Langeland, JA ;Pancer, Z.;Fritzsch, B.;Jong, PJ ;Zhu, B.;Fulton, LL ;Theising, B.;Flicek, P.;Bronner, ME ;Warren, WC ;Clifton, SW ;Wilson, RK ;Li, W. "Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution." Nature genetics 45, 4 (2013): 415-21, 421e1-2. Details. Full text
  • Smith, JJ ;Sumiyama, K.;Amemiya, CT "A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome." Molecular biology and evolution 29, 3 (2012): 985-93. Details. Full text
  • Smith, JJ ;Baker, C.;Eichler, EE ;Amemiya, CT "Genetic consequences of programmed genome rearrangement." Current biology : CB 22, 16 (2012): 1524-9. Details. Full text
  • Voss, SR ;Kump, DK ;Putta, S.;Pauly, N.;Reynolds, A.;Henry, RJ ;Basa, S.;Walker, JA ;Smith, JJ "Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes." Genome research 21, 8 (2011): 1306-12. Details. Full text
  • Smith, JJ ;Saha, NR ;Amemiya, CT "Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes." Integrative and comparative biology 50, 1 (2010): 130-7. Details. Full text
  • Page, RB ;Boley, MA ;Smith, JJ ;Putta, S.;Voss, SR "Microarray analysis of a salamander hopeful monster reveals transcriptional signatures of paedomorphic brain development." BMC evolutionary biology 10, (2010): 199. Details. Full text
  • Smith, JJ ;Stuart, AB ;Sauka-Spengler, T.;Clifton, SW ;Amemiya, CT "Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution." Chromosoma 119, 4 (2010): 381-9. Details. Full text
  • Smith, JJ ;Putta, S.;Zhu, W.;Pao, GM ;Verma, IM ;Hunter, T.;Bryant, SV ;Gardiner, DM ;Harkins, TT ;Voss, SR "Genic regions of a large salamander genome contain long introns and novel genes." BMC genomics 10, (2009): 19. Details. Full text
  • Smith, JJ ;Antonacci, F.;Eichler, EE ;Amemiya, CT "Programmed loss of millions of base pairs from a vertebrate genome." Proceedings of the National Academy of Sciences of the United States of America 106, 27 (2009): 11212-7. Details. Full text
  • Smith, JJ ;Voss, SR "Amphibian sex determination: segregation and linkage analysis using members of the tiger salamander species complex (Ambystoma mexicanum and A. t. tigrinum)." Heredity 102, 6 (2009): 542-8. Details. Full text
  • Page, RB ;Voss, SR ;Samuels, AK ;Smith, JJ ;Putta, S.;Beachy, CK "Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma)." BMC genomics 9, (2008): 78. Details. Full text
  • Smith, JJ ;Voss, SR "Bird and mammal sex-chromosome orthologs map to the same autosomal region in a salamander (ambystoma)." Genetics 177, 1 (2007): 607-13. Details. Full text
  • Putta, S.;Smith, JJ ;Staben, C.;Voss, SR "MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes." Evolutionary bioinformatics online 3, (2007): 15-25. Details.
  • Page, RB ;Monaghan, JR ;Samuels, AK ;Smith, JJ ;Beachy, CK ;Voss, SR "Microarray analysis identifies keratin loci as sensitive biomarkers for thyroid hormone disruption in the salamander Ambystoma mexicanum." Comparative biochemistry and physiology. Toxicology & pharmacology : CBP 145, 1 (2007): 15-27. Details. Full text
  • Smith, JJ ;Voss, SR "Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution." BMC genomics 7, (2006): 219. Details. Full text
  • Smith, JJ ;Putta, S.;Walker, JA ;Kump, DK ;Samuels, AK ;Monaghan, JR ;Weisrock, DW ;Staben, C.;Voss, SR "Sal-Site: integrating new and existing ambystomatid salamander research and informational resources." BMC genomics 6, (2005): 181. Details. Full text
  • Samuels, AK ;Weisrock, DW ;Smith, JJ ;France, KJ ;Walker, JA ;Putta, S.;Voss, SR "Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes." Gene 349, (2005): 43-53. Details. Full text
  • Smith, JJ ;Kump, DK ;Walker, JA ;Parichy, DM ;Voss, SR "A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma." Genetics 171, 3 (2005): 1161-71. Details. Full text
  • Voss, SR ;Smith, JJ "Evolution of salamander life cycles: a major-effect quantitative trait locus contributes to discrete and continuous variation for metamorphic timing." Genetics 170, 1 (2005): 275-81. Details. Full text
  • Putta, S.;Smith, JJ ;Walker, JA ;Rondet, M.;Weisrock, DW ;Monaghan, J.;Samuels, AK ;Kump, K.;King, DC ;Maness, NJ ;Habermann, B.;Tanaka, E.;Bryant, SV ;Gardiner, DM ;Parichy, DM ;Voss, SR "From biomedicine to natural history research: EST resources for ambystomatid salamanders." BMC genomics 5, 1 (2004): 54. Details. Full text
  • Danziger, SA ;Miller, LR ;Singh, K ;Whitney, GA ;Peskind, ER ;Li, G ;Lipshutz, RJ ;Aitchison, JD ;Smith, JJ "An indicator cell assay for blood-based diagnostics." PloS one 12, 6 (0): e0178608. Details. Full text
* Publications are automatically pulled from pubmed.gov based on a user-specific query. Results may include incorrect citations. See: Tutorial on improving PubMed results.
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