Google Scholar (automatically updated)
https://scholar.google.com/citations?user=UGoMxWsAAAAJ
Publication List (updated periodically)
Addiction-associated genetic variants implicate brain cell type-and region-specific cis-regulatory elements in addiction neurobiology
Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Journal of Neuroscience. 2021 (in press). doi:10.1523/JNEUROSCI.2534-20.2021
Transcriptional Diversity of Medium Spiny Neurons in the Primate Striatum
He J, Kleyman M, Alikaya A, Ozturk BE, Rothenhoefer KM, Wirthlin ME, Fish K, Byrne LCT, Pfenning AR, Stauffer WR. Current Biology. 2021 (accepted). doi:10.2139/ssrn.3904348
Manakin neurogenomics reveal the mechanisms underlying the evolution of skilled motor behavior
Wirthlin M. Integrative and Comparative Biology. 2021. 61, E987-E988
Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AJ, Kleyman M, Pfenning AR. bioRxiv. 2021. doi: 10.1101/2020.12.04.410795
Machine learning sequence prioritization for cell type-specific enhancer design
Lawler AJ, Ramamurthy E, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin ME, Zhang X, Fox G, Pfenning AR. bioRxiv. 2021. doi:10.1101/2021.04.15.439984
The Regulatory Evolution of the Primate Fine-Motor System
Wirthlin ME, Kaplow IM, Lawler AJ, He J, Phan BN, Brown AR, Stauffer WR, Pfenning AR. bioRxiv. 2020. doi:10.1101/2020.10.27.356733
ZEBrA: Zebra finch expression brain atlas—A resource for comparative molecular neuroanatomy and brain evolution studies
Lovell P, Wirthlin M, Kaser T, Buckner A, Carleton J, Snider B, McHugh A, Tolpygo A, Mitra P, Mello CV. Journal of Comparative Neurology. 2020. 1-33. doi:10.1002/cne.24879
Molecular specializations of deep cortical layer analogs in songbirds
Nevue AA, Lovell PV, Wirthlin M, Mello CV. Scientific Reports. 2020. 10(1):1-14. doi:10.1038/s41598-020-75773-4
Dense sampling of bird diversity increases power of comparative genomics
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Pacheco G, Sinding MHS, Puetz L, Cavill E, Ribeiro ÂM, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Stervander M, Hansson B, Sigeman H, Ponnikas S, Frandsen PB, Van der Zwan H, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelob A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. Nature. 2020. 587:252–257. doi:10.1038/s41586-020-2873-9
HALPER facilitates the identification of regulatory element orthologs across species
Zhang X, Kaplow IM, Wirthlin M, Park TY, Pfenning AR. Bioinformatics. 2020. 36(15):4339–4340. doi:10.1093/bioinformatics/btaa493
A Modular Approach to Vocal Learning: Disentangling the Diversity of a Complex Behavioral Trait
Wirthlin M, Chang EF, Knörnschild M, Krubitzer LA, Mello CV, Miller CT, Pfenning AR, Vernes SC, Tchernichovski O, Yartsev MM. Neuron. 2019. 104(1):87-99. doi:10.1016/j.neuron.2019.09.036
Molecular architecture of the zebra finch arcopallium
Mello CV, Kaser T, Buckner A, Wirthlin M, Lovell PV. Journal of Comparative Neurology. 2019. 525(15): 2512-2556. doi:10.1002/cne.24688
Parrot Genomes and the Evolution of Heightened Longevity and Cognition
Wirthlin M, Lima NCB, Guedes RLM, Almeida LGP, Cavaleiro NP, de Morais GL, Chaves AV, Howard JT, Teixeira MM, Schneider P, Santos FR, Schatz MC, Felipe MS, Miyaki CY, Aleixo A, Schneider MPC, Jarvis ED, Vasconcelos ATR, Prosdocimi F, Mello CV. Current Biology. 2018. 28(24): 4001 - 4008.e7. doi:10.1016/j.cub.2018.10.050
The constitutive differential transcriptome of a brain circuit for vocal learning
Lovell PV, Huizinga NA, Friedrich SR, Wirthlin M, Mello CV. BMC Genomics. 2018. 19:231. doi:10.1186/s12864-018-4578-0
Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches
Lovell PV, Huizinga NA, Getachew A, Mees G, Friedrich SR, Wirthlin M, Mello CV. BMC Research Notes. 2018. 11:309. doi:10.1186/s13104-018-3402-x
Discovery of Novel Genes and Other Lineage-Specific Features Through Comparative Genomics
Mello CV, Lovell PV, Wirthlin M. In: Gerlai R, editor. Molecular-Genetic and Statistical Techniques for Behavioral and Neural Research. San Diego: Academic Press, 2018: 225–241. doi:10.1016/B978-0-12-804078-2.00010-6
A new chicken genome assembly provides insight into avian genome structure
Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH. G3. 2017. 7(1): 109–117. doi:10.1534/g3.116.035923
Evolutionary Neurogenomic Approaches Provide Insight Into the Molecular Basis of Vocal Learning [dissertation]
Wirthlin M. 2016. Oregon Health & Science University, Portland; 136 pp. Scholar Archive. 3831. https://digitalcommons.ohsu.edu/etd/3831
A putative RA-like region in the brain of the scale-backed antbird, Willisornis poecilinotus (Furnariides, Suboscines, Passeriformes, Thamnophilidae)
de Lima JLR, Soares FA, Remedios ACS, Thom G, Wirthlin M, Aleixo A, Schneider MPC, Mello CV, Schneider PN. Genetics and Molecular Biology. 2015. 38(3). doi:10.1590/S1415-475738320150010
Response to Hron et al.
Lovell PV, Wirthlin M, Carbone L, Warren WC, Mello CV. Genome Biology. 2015. 16(165). doi:10.1186/s13059-015-0725-y
Comparative genomics reveals molecular features unique to the songbird lineage
Wirthlin M, Lovell PV, Jarvis ED, Mello CV. BMC Genomics. 2014. 15:1082. doi:10.1186/1471-2164-15-1082
Conserved syntenic clusters of protein coding genes are missing in birds
Lovell PV, Wirthlin M, Wilhelm LJ, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV. Genome Biology. 2014. 15(565) doi:10.1186/s13059-014-0565-1
Convergent transcriptional specializations in the brains of humans and song-learning birds
Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED. Science. 2014. 346(6215):1256846. doi:10.1126/science.1256846
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford M, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon F, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert D, Zhou Q, Perelman P, Driskell AC, Ruby G, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker K, Jønsson KA, Johnson W, Koepfli K-P, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards S, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Science. 2014. 346(6215):1320-1331. doi:10.1126/science.1253451
Proper Care, Husbandry, and Breeding Guidelines for the Zebra Finch, Taeniopygia guttata
Olson CR, Wirthlin M, Lovell PV, Mello CV. Cold Spring Harbor Protocols. 2014. 12:1243-8. doi:10.1101/pdb.prot084780
Signal Meaning and Function in Captive Bottlenose Dolphins (Tursiops truncatus) [BA Honors thesis]
Wirthlin M. 2009. University of Chicago, Chicago; 29 pp.
https://scholar.google.com/citations?user=UGoMxWsAAAAJ
Publication List (updated periodically)
Addiction-associated genetic variants implicate brain cell type-and region-specific cis-regulatory elements in addiction neurobiology
Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Journal of Neuroscience. 2021 (in press). doi:10.1523/JNEUROSCI.2534-20.2021
Transcriptional Diversity of Medium Spiny Neurons in the Primate Striatum
He J, Kleyman M, Alikaya A, Ozturk BE, Rothenhoefer KM, Wirthlin ME, Fish K, Byrne LCT, Pfenning AR, Stauffer WR. Current Biology. 2021 (accepted). doi:10.2139/ssrn.3904348
Manakin neurogenomics reveal the mechanisms underlying the evolution of skilled motor behavior
Wirthlin M. Integrative and Comparative Biology. 2021. 61, E987-E988
Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin
Kaplow IM, Schäffer DE, Wirthlin ME, Lawler AJ, Brown AJ, Kleyman M, Pfenning AR. bioRxiv. 2021. doi: 10.1101/2020.12.04.410795
Machine learning sequence prioritization for cell type-specific enhancer design
Lawler AJ, Ramamurthy E, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin ME, Zhang X, Fox G, Pfenning AR. bioRxiv. 2021. doi:10.1101/2021.04.15.439984
The Regulatory Evolution of the Primate Fine-Motor System
Wirthlin ME, Kaplow IM, Lawler AJ, He J, Phan BN, Brown AR, Stauffer WR, Pfenning AR. bioRxiv. 2020. doi:10.1101/2020.10.27.356733
ZEBrA: Zebra finch expression brain atlas—A resource for comparative molecular neuroanatomy and brain evolution studies
Lovell P, Wirthlin M, Kaser T, Buckner A, Carleton J, Snider B, McHugh A, Tolpygo A, Mitra P, Mello CV. Journal of Comparative Neurology. 2020. 1-33. doi:10.1002/cne.24879
Molecular specializations of deep cortical layer analogs in songbirds
Nevue AA, Lovell PV, Wirthlin M, Mello CV. Scientific Reports. 2020. 10(1):1-14. doi:10.1038/s41598-020-75773-4
Dense sampling of bird diversity increases power of comparative genomics
Feng S, Stiller J, Deng Y, Armstrong J, Fang Q, Reeve AH, Xie D, Chen G, Guo C, Faircloth BC, Petersen B, Wang Z, Zhou Q, Diekhans M, Chen W, Andreu-Sánchez S, Margaryan A, Howard JT, Pacheco G, Sinding MHS, Puetz L, Cavill E, Ribeiro ÂM, Fjeldså J, Hosner PA, Brumfield RT, Christidis L, Bertelsen MF, Tietze DT, Robertson BC, Song G, Borgia G, Claramunt S, Lovette IJ, Cowen SJ, Njoroge P, Dumbacher JP, Ryder OA, Fuchs J, Bunce M, Burt DW, Cracraft J, Meng G, Hackett SJ, Ryan PG, Jønsson KA, Jamieson IG, da Fonseca RR, Braun EL, Houde P, Mirarab S, Suh A, Stervander M, Hansson B, Sigeman H, Ponnikas S, Frandsen PB, Van der Zwan H, Balakrishnan CN, Clark AG, Fitzpatrick JW, Bowman R, Chen N, Cloutier A, Sackton TB, Foote DJ, Shakya SB, Sheldon FH, Vignal A, Soares AER, Shapiro B, González-Solís J, Ferrer-Obiol J, Rozas J, Riutort M, Tigano A, Friesen V, Dalén L, Urrutia AO, Székely T, Liu Y, Campana MG, Corvelob A, Fleischer RC, Rutherford KM, Gemmell NJ, Dussex N, Mouritsen H, Thiele N, Delmore K, Liedvogel M, Franke A, Hoeppner MP, Krone O, Fudickar AM, Milá B, Ketterson ED, Fidler AE, Friis G, Parody-Merino ÁM, Battley PF, Cox MP, Lima NCB, Prosdocimi F, Parchman TL, Schlinger BA, Loiselle BA, Blake JG, Lim HC, Day LB, Fuxjager MJ, Baldwin MW, Braun MJ, Wirthlin M, Dikow RB, Ryder TB, Camenisch G, Keller LF, DaCosta JM, Hauber ME, Louder MIM, Witt CC, McGuire JA, Mudge J, Megna LC, Carling MD, Wang B, Taylor SA, Del-Rio G, Aleixo A, Vasconcelos ATR, Mello CV, Weir JT, Haussler D, Li Q, Yang H, Wang J, Lei F, Rahbek C, Gilbert MTP, Graves GR, Jarvis ED, Paten B, Zhang G. Nature. 2020. 587:252–257. doi:10.1038/s41586-020-2873-9
HALPER facilitates the identification of regulatory element orthologs across species
Zhang X, Kaplow IM, Wirthlin M, Park TY, Pfenning AR. Bioinformatics. 2020. 36(15):4339–4340. doi:10.1093/bioinformatics/btaa493
A Modular Approach to Vocal Learning: Disentangling the Diversity of a Complex Behavioral Trait
Wirthlin M, Chang EF, Knörnschild M, Krubitzer LA, Mello CV, Miller CT, Pfenning AR, Vernes SC, Tchernichovski O, Yartsev MM. Neuron. 2019. 104(1):87-99. doi:10.1016/j.neuron.2019.09.036
Molecular architecture of the zebra finch arcopallium
Mello CV, Kaser T, Buckner A, Wirthlin M, Lovell PV. Journal of Comparative Neurology. 2019. 525(15): 2512-2556. doi:10.1002/cne.24688
Parrot Genomes and the Evolution of Heightened Longevity and Cognition
Wirthlin M, Lima NCB, Guedes RLM, Almeida LGP, Cavaleiro NP, de Morais GL, Chaves AV, Howard JT, Teixeira MM, Schneider P, Santos FR, Schatz MC, Felipe MS, Miyaki CY, Aleixo A, Schneider MPC, Jarvis ED, Vasconcelos ATR, Prosdocimi F, Mello CV. Current Biology. 2018. 28(24): 4001 - 4008.e7. doi:10.1016/j.cub.2018.10.050
The constitutive differential transcriptome of a brain circuit for vocal learning
Lovell PV, Huizinga NA, Friedrich SR, Wirthlin M, Mello CV. BMC Genomics. 2018. 19:231. doi:10.1186/s12864-018-4578-0
Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches
Lovell PV, Huizinga NA, Getachew A, Mees G, Friedrich SR, Wirthlin M, Mello CV. BMC Research Notes. 2018. 11:309. doi:10.1186/s13104-018-3402-x
Discovery of Novel Genes and Other Lineage-Specific Features Through Comparative Genomics
Mello CV, Lovell PV, Wirthlin M. In: Gerlai R, editor. Molecular-Genetic and Statistical Techniques for Behavioral and Neural Research. San Diego: Academic Press, 2018: 225–241. doi:10.1016/B978-0-12-804078-2.00010-6
A new chicken genome assembly provides insight into avian genome structure
Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH. G3. 2017. 7(1): 109–117. doi:10.1534/g3.116.035923
Evolutionary Neurogenomic Approaches Provide Insight Into the Molecular Basis of Vocal Learning [dissertation]
Wirthlin M. 2016. Oregon Health & Science University, Portland; 136 pp. Scholar Archive. 3831. https://digitalcommons.ohsu.edu/etd/3831
A putative RA-like region in the brain of the scale-backed antbird, Willisornis poecilinotus (Furnariides, Suboscines, Passeriformes, Thamnophilidae)
de Lima JLR, Soares FA, Remedios ACS, Thom G, Wirthlin M, Aleixo A, Schneider MPC, Mello CV, Schneider PN. Genetics and Molecular Biology. 2015. 38(3). doi:10.1590/S1415-475738320150010
Response to Hron et al.
Lovell PV, Wirthlin M, Carbone L, Warren WC, Mello CV. Genome Biology. 2015. 16(165). doi:10.1186/s13059-015-0725-y
Comparative genomics reveals molecular features unique to the songbird lineage
Wirthlin M, Lovell PV, Jarvis ED, Mello CV. BMC Genomics. 2014. 15:1082. doi:10.1186/1471-2164-15-1082
Conserved syntenic clusters of protein coding genes are missing in birds
Lovell PV, Wirthlin M, Wilhelm LJ, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV. Genome Biology. 2014. 15(565) doi:10.1186/s13059-014-0565-1
Convergent transcriptional specializations in the brains of humans and song-learning birds
Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED. Science. 2014. 346(6215):1256846. doi:10.1126/science.1256846
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SYW, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford M, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon F, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Samaniego JA, Velazquez AMV, Alfaro-Núñez A, Campos PF, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert D, Zhou Q, Perelman P, Driskell AC, Ruby G, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker K, Jønsson KA, Johnson W, Koepfli K-P, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards S, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MTP, Zhang G. Science. 2014. 346(6215):1320-1331. doi:10.1126/science.1253451
Proper Care, Husbandry, and Breeding Guidelines for the Zebra Finch, Taeniopygia guttata
Olson CR, Wirthlin M, Lovell PV, Mello CV. Cold Spring Harbor Protocols. 2014. 12:1243-8. doi:10.1101/pdb.prot084780
Signal Meaning and Function in Captive Bottlenose Dolphins (Tursiops truncatus) [BA Honors thesis]
Wirthlin M. 2009. University of Chicago, Chicago; 29 pp.
