Publications

 

Al Haj Baddar N, Timoshevskaya N, Smith JJ, Guo H, Voss SR (2021) Novel Expansion of Matrix Metalloproteases in the laboratory axolotl (Ambystoma mexicanum) and other Salamander Species. Frontiers in Ecology and Evolution, In Press.

 

Voss SR, Smith JJ, Timoshevskaya N, Ponomareva LV, Thorson JS, Veliz-Cuba A, Murrugarra D (2021) HDAC Inhibitor Titration of Transcription and Axolotl Tail Regeneration. Frontiers in Cell and Developmental Biology, In Press.

 

Murach K, Peck B, Policastro R, Vechetti I, Van Pelt, D, Dungan C, Denes L, Fu X, Brightwell C, Zentner G, Dupont-Versteegden E, Richards C, Wang E, Smith JJ, Fry C, McCarthy J, Peterson C (2021) Early Satellite Cell Communication Creates a Permissive Environment for Long-Term Muscle Growth. iScience, 24:102372.

 

Schloissnig S, Kawaguchi A, Nowoshilow S, Falcon F, Otsuki L, Tardivo P, Timoshevskaya N, Keinath MC, Smith JJ, Voss SR, Tanaka EM (2021) The giant axolotl genome uncovers the evolution, scaling and transcriptional control of complex gene loci. PNAS, 118:e2017176118.

 

Timoshevskaya N, Voss SR, Labianca CN, High CR, Smith JJ* (2021) Large-scale variation in SNP density within the laboratory axolotl (Ambystoma mexicanum). Developmental Dynamics, 250:822-837.

 

Smith JJ*, Timoshevskiy VA, Saraceno C (2021) Programmed DNA Elimination in Vertebrates. Annual Review of Animal Biosciences. 9:173-201.

 

Marks RA, Smith JJ; van Buren R, McLetchie, DN (2020) Expression dynamics of dehydration tolerance in the tropical plant Marchantia inflexa. The Plant Journal, 8722.

 

Smith JJ*, Timoshevskiy VA, Saraceno C (2020) Programmed DNA Elimination in Vertebrates. Annual Review of Animal Biosciences. 9: Online ahead of in print.

 

Hess JE, Smith JJ, Timoshevskaya N, Baker C, Caudill C, Graves D, Keefer M, Kinziger A, Moser M, Laurie Porter L, Greg Silver G, Whitlock S, Narum SR (2020) Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey. Molecular Ecology, 29: 3841-3856..

 

Liscano, Y, Arenas Gómez CM, Smith JJ, Voss SR, Paul Delgado JP (2020) A tree frog (Boana pugnax) dataset of skin transcriptome for the identification of biomolecules with potential antimicrobial activities. Data in Brief, 36: 106084.

 

Voss SR, Rodgers AK, Smith JJ (2020) Identification of immune and non-immune cells in regenerating axolotl limbs by single-cell sequencing. Experimental Cell Research, 394: 112149.
 

Nail AN, Smith JJ, Peterson ML, Spear BT (2020) 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: 174-184.

 

Arenas Gómez CM, Ryan M. Woodcock RM, Smith JJ, Voss SR, Paul Delgado JP (2020) A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia. Data in Brief, 29: 105256.

 

Timoshevskiy VA, Timoshevskaya N, Smith JJ* (2019) Germline specific repetitive elements in programmatically eliminated chromosomes of the sea lamprey (Petromyzon marinus). Genes, 10: 832.

 

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 (2019) A genome-wide assessment of the ancestral neural crest gene regulatory network. Nature Communications,10: 4689.

 

Marks RA, Smith JJ, Cronk Q, Grassa CJ, McLetchie DN (2019) Genome of the tropical plant Marchantia inflexa: implications for sex chromosome evolution and dehydration tolerance. Scientific Reports, 19:8722.

 

Smith JJ*, Timoshevskaya N, Timoshevskiy VA, Keinath MC, Hardy D, Voss SR (2019) A chromosome-scale assembly of the axolotl genome. Genome Research, 29: 317-324.

 

Keinath MC, Timoshevskaya N, Timoshevskiy VA, Voss SR, Smith JJ* (2018) Miniscule differences between sex chromosomes in the giant genome of a salamander. Scientific Reports, 8:17882.

 

Arenas Gómez CM, Woodcock RM, Smith JJ, Voss SR, Delgado JP (2018) Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research. BMC Genomics, 19:704.

 

Dwaraka V, Woodcock MR, Smith JJ, Voss SR (2018) Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma. Genomics, In Press.

 

Gatto KP, Smith JJ, Lourenço LB (2018) The mitochondrial genome of the endemic Brazilian paradoxical frog Pseudis tocantins (Hylidae). Mitochondrial DNA Part B: Resources, 3:1106-1107.

 

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT (2018) The Sea Lamprey Germline Genome Provides Insights Into Programmed Genome Rearrangement and Vertebrate Evolution. Nature Genetics, 50:270-277.

 

Herman PE, Papatheodorou A, Bryant SA, Waterbury CKM, Herdy JR, Arcese AA, Buxbaum JD, Smith JJ, Morgan JR, Bloom O (2018) Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys. Scientific Reports, 8:742.

 

Marks RA, Smith JJ, Cronk Q, McLetchie DN (2017) Variation in the Bacteriome of the Tropical Liverwort, Marchantia inflexa, Between the Sexes and Across Habitats. Symbiosis, 1-9.

 

Timoshevskiy VA, Lampman RT, Hess JE, Porter LE, Smith JJ* (2017) Deep Ancestry of Programmed Genome Rearrangement in Lampreys. Developmental Biology, 429:31-34.

 

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 (2017) Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum Scientific Reports, 7:6.

 

Bryant SR, Herdy JR, Amemiya CT, Smith JJ* (2016) Characterization of Somatically-Eliminated Genes During Development: Lamprey (Petromyzon marinus). Molecular Biology and Evolution, 33:2337-2344.

 

Timoshevskiy VA, Herdy JR, Smith JJ* (2016) Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus). PLOS Genetics, 12:e1006103.

 

Keinath MC, Voss SR, Tsonis PA, Smith JJ* (2016) A Linkage Map for the Newt Notophthalmus viridescens: Insights in Vertebrate Genome and Chromosome Evolution. Developmental Biology, S0012-1206:30355-30359.

 

Gawriluk TR, Simkin, J, Thompson KL, Biswas, SK, Clare-Salzler Z, Kimani JM, Kiama SG, Smith JJ, Ezenwa VO, Seifert AW (2016) Comparative analysis of ear hole closure identifies epimorphic regeneration as a discrete trait in mammals. Nature Communications, 7:11164.

 

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 FEG, Sun Y, Hertel J, Beam MJ, Di Palma F, 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 SMJ, Aken B, Yandell M, Schneider I, Yoder JA, Volff J-N, Meyer A, Amemiya CT, Venkatesh B, Holland PWH, Guiguen Y, Bobe J, Shubin NH, Alföldi J, Lindblad-Toh K, Postlethwait JH (2016) Linking human biology to fish models: Sequence of the spotted gar genome. Nature Genetics, 48:427-437.

 

Mukendi C, Dean N, Lala R, Smith JJ, Bronner ME, Nikitina NV (2016) Evolution of the Vertebrate Claudin Gene Family: Insights from the most basal vertebrate the sea lamprey. International Journal of Developmental Biology, 60:39-51.

 

Keinath MC, Timoshevskaya, NY, Timoshevskiy VA, Tsonis PA, Voss SR, Smith JJ* (2015) Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Scientific Reports, 5:16413.

 

Smith JJ, Keinath MC (2015) The Sea Lamprey Meiotic Map Improves Resolution of Ancient Vertebrate Genome Duplications. Genome Research, 25:1081-1090.

 

Decatur WA, Hall JA, Smith JJ, Li W, Sower SA. (2013) Insight from the lamprey genome: Glimpsing early vertebrate development via neuroendocrine-associated genes and shared synteny of gonadotropin-releasing hormone (GnRH). Gen Comp Endocrinol. 192:237-245.

 

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 SMJ, 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, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner M, Warren WC, Clifton SW, Wilson RK, Li W. (2013) Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics 45:415-421.

 

 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 SMJ, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff J-N, Tabin CJ, Shubin N, Schartl M, Jaffe D, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. (2013) The African coelacanth genome provides insights into tetrapod evolution. Nature 496:311-316.

 

Voss SR, Putta S, Walker JA, Smith JJ, Maki N, Tsonis PA. (2013) Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates? Human Genomics 7:9.

 

Smith JJ, Baker C, Eichler EE, Amemiya CT (2012). Genetic consequences of programmed genome rearrangement. Current Biology 22:1524–1529. (This paper was highlighted in a Dispatch in the same issue).

 

Smith JJ, Sumiyama K, Amemiya CT (2012). A living fossil in the genome of a living fossil: active Harbinger transposons in the coelacanth genome. Molecular Biology & Evolution 29:985-993.

 

Voss SR, Kump DK, Putta S, Pauly N, Reynolds A, Henry R, Basa S, Walker JA, Smith JJ. (2011) Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes.  Genome Research 21:1306-1312.

 

Page RB, Boley MA, Smith JJ, Putta S, Voss SR (2010) A Hopeful Monster Reveals Transcriptional Signatures of Adaptive Brain Development and Evolution.  BMC Evolutionary Biology 10:199.

 

Smith JJ, Saha NR, Amemiya CT. (2010) Genome Biology of the Cyclostomes and Insights into the Evolutionary Biology of Vertebrate Genomes. Integrative and Comparative Biology 50:130-137.

 

Smith JJ, Stuart A, Sauka-Spengler T, Clifton S, Amemiya CT. (2010) Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution. Chromosoma 119:381-389.

 

Saha NR, Smith JJ, Amemiya CT. (2010) Evolution of adaptive immune recognition in jawless vertebrates. Seminars in Immunology 22:25-33.

 

Fitzpatrick BM, Johnson JR, Kump DK, Smith JJ, Voss SR, Shaffer HB (2010) Rapid spread of invasive genes into a threatened native species. PNAS 107:3606-3610.

 

Smith JJ, Antonacci F, Eichler EE, Amemiya CT. (2009) Programmed loss of millions of base pairs from a vertebrate genome. PNAS 106:11212-11217. (This paper was recognized in several news articles, including ScienceNOW.org & Science 26 June 2009: Vol. 324. no. 5935, p. 1631).

 

Fitzpatrick BM, Johnson JR, Kump DK, Shaffer HB, Smith JJ, Voss SR (2009) Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders. BMC Evolutionary Biology 9:176.

 

Smith JJ, Voss SR. ­(2009) Amphibian sex determination: segregation and linkage analysis using members of the tiger salamander species complex (Ambystoma mexicanum and A. t. tigrinum). Heredity 102:542-548. (This paper was recognized in the issue highlights).

 

Smith JJ, Putta S, Zhu W, Pao GM, Verma I, Hunter T, Bryant SV, Gardiner DM, Harkins TT, Voss SR. (2009) Genic regions of a large salamander genome contain long introns and novel genes. BMC Genomics 10:19.

 

Page RB, Voss SR, Samuels AK, Smith JJ, Putta S, Beachy CK. (2008) Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma). BMC Genomics 9: 78.

 

Smith JJ, Voss SR. ­(2007) Bird and mammal sex chromosome orthologs map to the same autosomal region in a salamander (Ambystoma). Genetics 177: 607-613. (This paper was recognized in the issue highlights).

 

* Putta S, Smith JJ, Staben C, Voss SR. ­(2007) MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes. Evolutionary Bioinformatics Online 2: 15-25.

 

Smith JJ, Voss SR. (2006) Gene order data from a model amphibian (Ambystoma): new perspectives on vertebrate genome structure and evolution. BMC Genomics 7: 219.

 

Page RB, Monaghan JR, Samuels AK, Smith JJ, Beachy CK, Voss SR. (2006) Microarray analysis identifies keratin loci as sensitive biomarkers for thyroid hormone disruption in the salamander Ambystoma mexicanum. Comparative Biochemistry and Physiology, Part C. 145: 15-27.

 

Smith JJ, Kump DK, Walker JA, Parichy DM, Voss SR. (2005) A comprehensive expressed sequence tag linkage map for tiger salamander and Mexican axolotl: enabling gene mapping and comparative genomics in Ambystoma. Genetics 171: 1161-1171.

 

* Voss SR, Smith JJ. (2005) Evolution of salamander life cycles: A major-effect quantitative trait locus contributes to discrete and continuous variation for metamorphic timing. Genetics 170: 275-281. (This paper was highlighted by the Faculty of 1000 in Biology, June 2005).

 

Smith JJ, Putta S, Walker JA, Kump DK, Samuels AK, Monaghan JR, Weisrock DW, Staben C, Voss SR. (2005) Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources. BMC Genomics 6: 181.

 

Samuels AK, Weisrock DW, Smith JJ, France KJ, Walker JA, Putta S, Voss SR. (2005) Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes. Gene 349: 43-53.

 

* 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. (2004) From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics 5: 54.

 

Voss SR, Smith JJ, Gardiner DM, Parichy DM. (2001) Conserved vertebrate chromosome segments in the large salamander genome. Genetics 158: 735-746.

Jeramiah Smith

Department of Biology

University of Kentucky

Lexington, KY 40506

jjsmit3@uky.edu

Smith LAB Lab