Publications

The following papers were produced by members of the Jarvis Lab or in collaboration with the Jarvis Lab. They are available for downloading.

2012

• Convergent Differential Regulation of Parvalbumin in the Brains of Vocal Learners.
  Erina Hara, Miriam V. Rivas, James M. Ward, Kazuo Okanoya, Erich D. Jarvis (2012) Public Library of Science ONE. 7(1):e29457.

2011

• Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics.
  Benoit Nabholz, Axel Kunstner, Rui Wang, Erich D. Jarvis and Hans Ellegren (2011) Molecular Biology and Evolution. 28(8):2197–2210.
• Microproteomics: Quantitative Proteomic Profiling of Small Numbers of Laser-Captured Cells.
  Petra L. Roulhac, James M. Ward, J. Will Thompson, Erik J. Soderblom, Michael Silva, M. Arthur Moseley III, and Erich D. Jarvis (2011) Cold Spring Harbor Protocols.

2010

• Obtaining mtDNA genomes from next-generation transcriptome sequencing: A case study on the basal Passerida (Aves: Passeriformes) phylogeny .
  Benoit Nabholz, Erich D. Jarvis, Hans Ellegren.(2010) Molecular Phylogenetics and Evolution. 57 (2010) 466–470.
• Empowering 21st Century Biology.
  Gene E. Robinson, Jody A. Banks, Dianna K. Padilla, Warren W. Burggren, C. Sarah Cohen, Charles F. Delwiche, Vicki Funk, Hopi E. Hoekstra, Erich D. Jarvis, et.al. (2010) BioScience. vol 60, no 11: 923-930.
• Evolution of dynamic coordination.
  Balaban E, Edelman S, Grillner S, Grodzinski U, Jarvis ED, Kaas JH, Laurent G, Pipa G. (2010). In: Dynamic Coordination in the Brain: From Neurons to Mind. Malsburg C von der, Phillips WA, Singer W (eds). Strungmann Forum Reports. Lupp J (series Ed.) MIT Press, Cambridge MA. 59-82.
• The dusp1 Immediate Early Gene is Regulated by Natural Stimuli Predominantly in Sensory Input Neurons.
  Haruhito Horita, Kazuhiro Wada, Miriam V. Rivas, Erina Hara, Erich D. Jarvis (2010) The Journal of Comparative Neurology. 518:2873–2901
• The genome of a songbird.
  Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, et al (2010) Nature. 464:757-762.
  Supplementary Information Supplementary Accessory
• Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
  Axel Kunstner, Jochen B. W. Wolf, Niclas Backstrom, Osceola Whitney, Christopher N. Balakrishnan, Lainy Day, Scott V. Edwards, Daniel E. Janes, Barney A. Schlinger, Richard K. Wilson, Erich D. Jarvis, Wesley C. Warren and Hans Ellegran (2010) Molecular Ecology. 19 (Suppl. 1), 266–276.
• Dopamine receptors in a songbird brain.
  Lubica Kubikova, Kazuhiro Wada, Erich D. Jarvis (2010) Journal of Comparative Neurology. 518:741-769.
  Supporting figures Cover Photo

2009

• Behaviorally regulated mRNA and protein expression in the songbird brain
  Rivas M, Jarvis ED (2009) In: Neuroproteomics. Frontiers in Neuroscience series. Alzate O (ed). pp. 239-262.
• Evolution of the Pallium in Birds and Reptiles.
  Erich D. Jarvis (2009) In: New Encyclopedia of Neuroscience. Marc D. Binder, Nobutaka Hirokawa and Uwe Windhorst (eds). Ann Butler (sub-ed). Springer-Verlag GmbH Berlin Heidelberg. 15 pages.
• Assessing visual requirements for social ceontext-dependent activation of the songbird song system .
  Hara E, Kubikova L, Hessler NA, Jarvis ED. (2009) Proc. R. Soc. B 276:279-289.
• Bird Song Systems: Evolution .
  Erich D. Jarvis (2009) In: Encyclopedia of Neuroscience. Squire LR (eds). volume 2, pp. 217-225. Oxford: Academic Press.
• Bird Brain: Evolution .
  Erich D. Jarvis (2009) In: Encyclopedia of Neuroscience. Squire LR (eds). volume 2, pp. 209-215. Oxford: Academic Press.

2008

• Early onset of deafening-induced song deterioration and differential requirements of the pallial-basal ganglia vocal pathway.
  Horita H, Wada K, Jarvis ED. (2008) Eur. J. Neurosci. 28:2519-2532
• Songbirds and the revised avian brain nomenclature.
  Reiner A, Perkel DJ, Mello CV, Jarvis ED. (2008) In: The Neuroscience of Birdsong. Zeigler and Marler (eds). Cambridge University Press. pp. 58-62.
• Behavior-dependent expression of inducible genes in vocal learning birds..
  Mello CV, Jarvis ED (2008) In: The Neuroscience of Birdsong. Ziegler and Marler (eds). Cambridge University Press. pp. 381-397.
• Molecular Mapping of Movement-Associated Areas in the Avian Brain: A Motor Theory for Vocal Learning Origin.
  Gesa Feenders, Miriam Liedvogel, Miriam Rivas, Manuela Zapka, Haruhito Horita, Erina Hara, Kazuhiro Wada, Henrik Mouritsen, Erich D. Jarvis. (2008) Public Library of Science ONE 3(3): e1768. doi:10.1371/journal.pone.0001768
  Supplementary materials
• Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics.
  Raphael Pinaud, Cristina Osorio, Oscar Alzate, Erich D. Jarvis. (2008) European Journal of Neuroscience 27:1409-1422

2007

• Neural systems for vocal learning in birds and humans: a synopsis.
  Erich. D Jarvis. (2007) Journal of Ornithology 143:S35-44.
  (Invited paper of a plenary lecture for the 24th international ornithology congress.)
• Role of midbrain dopaminergic system in the modulation of vocal brain activation by social context.
  Erina Hara, Lubica Kubikova, Neal A Hessler, Erich D. Jarvis. (2007) European Journal of Neuroscience 25:3406-3416.
  Supplementary figure and audios
• The pallial-basal ganglia pathway modulates the behaviorally-driven gene expression of the motor pathway.
  Lubica Kubikova, Elena Turner , Erich D. Jarvis. (2007) European Journal of Neuroscience 25:2154-2160.
• Lateralized activation of Cluster N in the brains of migratory songbirds.
  Miriam Liedvogel, Gesa Feenders, Kazuhiro Wada, Nikolaus F. Troje, Erich D. Jarvis and Henrik Mouritsen (2007) European Journal of Neuroscience 25:1166-1173.

2006

• Evolution of vocal learning systems in birds and humans.
  Jarvis ED (2006) In: Evolution of Nervous Systems. Kaas J (ed). 2:213-228.
• Computational inference of neural information flow networks.
  Victoria A. Smith, Jing Yu, Tom V. Smulders, Alexander J. Hartemink, Erich D. Jarvis (2006) PLoS Comp. Biol. 2:1436-1449.
  Supplementary figures and text Powerpoint animation (Most viewed research article of this issue when published.)
• Vocalizations and associated behaviors of the sombre hummingbird (aphantochroa cirrhoclhloris) and the rufous-breasted hermit (glaucis hirsutus).(13MB)
  Adriana R.J. Ferreira, Tom V. Smulders, Koichi Sameshima, Claudio V. Mello, Erich D. Jarvis (2006) Auk 123: 1129-1148.
  Supplementary figures and sounds of of hummingbird vocalizations
• A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.
  Kazuhiro Wada, Jason T. Howard, Patrick McConnell, Osceola Whitney, Thierry Lints, Miriam V. Rivas, Haruhito Horita, Michael A. Patterson, Stephanie A. White, Constance Scharff, Sebastian Haesler, Shengli Zhao, Hironobu Sakaguchi, Masatoshi Hagiwara, Toshiyuki Shiraki, Tomoko Hirozane-Kishikawa, Pate Skene, Yoshihide Hayashizaki, Piero Carninci, and Erich D. Jarvis (2006) Proc Natl Acad Sci USA 103: 15212-15217.
  Supporting material: Supporting Appendix (pages 1-24), Supporting Figures 8-21, Supporting Tables 1-6.
• Social context-dependent singing-regulated dopamine.
  Aya Sasaki, Tatyana D. Sotnikova, Raul R. Gainetdinov, and Erich D. Jarvis (2006) Journal of Neuroscience 26: 9010?014.
• Selection for and against vocal learning in birds and mammals.
  Erich D. Jarvis (2006) Ornithology Science 5: 5-14. Special Issue on the Neuroecology of Birdsong
• Evolution of brain structures for vocal learning in birds: a synopsis.
  Erich D. Jarvis (2006) Acta Zoologica Sinica. Proc 23rd IOC Conf 52: 85-89.

2005

• Rapid behavioral and genomic response to social opportunity.
  Sabrina S. Burmiester, Erich D. Jarvis, and Russell D. Fernald (2005) PLoS Biology 3: 1996-2004.
• Night-vision brain area in migratory songbirds.
  Henrik Mouritsen, G Feenders, M Liedvogel, K Wada, ED Jarvis (2005). Proc. Natl. Acad. Sci. vol 102, no 23: 8339-8344.
  High Resolution Graphics: Figure 1 ( 6.3 MB pdf ), Figure 2 ( 1.5 MB pdf ), Figure 3 ( 2.5 MB pdf )
• Avian brains and a new understanding of vertebrate evolution.
  The Avian Brain Nomenclature Consortium: ED Jarvis, O Güntürkün, L Bruce, A Csillag, H Karten, W Kuenzel, L Medina, G Paxinos, DJ Perkel, T Shimizu, G Striedter, JM Wild, GF Ball, J Dugas-Ford, SE Durand, GE Hough, S Husband, L Kubikova, DW Lee, CV Mello, A Powers, C Siang, TV Smulders, K Wada, SA White, K Yamamoto, J Yu, A Reiner and AB Butler. Nature Rev. Neurosc. 6: 151-159 (2005)

2004

• Learned Birdsong and the Neurobiology of Human Language.
  Erich D. Jarvis. Ann. N.Y. Acad. Sci. 1016: 749-777 (2004)
• Differential Expression of Glutamate Receptors in Avian Neural Pathways for Learned Vocalization.
  Kazuhiro Wada, Hironobi Sakaguchi, Erich D. Jarvis, Masatoshi Hagiwara. J. Comp. Neurol. 476:44-64 (2004)
• Advances to Bayesian Network Inference for Generating Causal Networks from Observational Biological Data.
  Jing Yu, VA Smith, PP Wang, AJ Hartemink, ED Jarvis. Bioinformatics Vol. 20, No. 18: 3594-3603 (2004)
  Supplementary Figures. Source Code.
• Songbirds and the Revised Avian Brain Nomenclature.
  A Reiner, DJ Perkel, CV Mello, ED Jarvis. Ann. N.Y. Acad. Sci. 1016: 77-108 (2004)
• Revised Nomenclature for Avian Telencephalon and Some Related Brainstem Nuclei.(15.8 MB pdf)
  A Reiner, DJ Perkel, L Bruce, AB Butler, A Csillag, W Kuenzel, L Medina, G Paxinos, T Shimizu, GF Striedter, M Wild, GF Ball, S Durand, O Güntürkün, DW Lee, CV Mello, A Powers, SA White, G Hough, L Kubikova, TV Smulders, K Wada, J Dugas-Ford, S Husband, K Yamamoto, J Yu, C Siang, ED Jarvis (2004) J. Comp. Neurol. 473:377-414.
• The Avian Brain Nomenclature Forum: Terminology for a New Century in Comparative Neuroanatomy.
  A Reiner, DJ Perkel, et al. (2004) J. Comp. Neurol. 473: E1-E6.
• Fox P2 Expression in Avian Vocal Learners and Non-Learners
  S Haesler, K Wada, A Nshdejan, E Morriesey, T Lints, ED Jarvis, and C Scharff (2004) Journal of Neuroscience 24(13):3164-3175.
  Supplementary Figures.
• Brains and birdsong.
  ED Jarvis (2004). In Nature’s Music: The Science of BirdSong. Marler P, Slaberkorn H (eds).

2003

• Analysis of the Mouse Transcriptome for Genes Involved in the Function of the Nervous System.
  Stefano Gustincich, Serge Batalov, Kirk W. Beisel, Hidemasa Bono, Piero Carninci, Colin F. Fletcher, Sean Grimmond, Nobutaka Hirokawa, Erich D. Jarvis, Tim Jegla, Yuka Kawasawa, Julianna LeMieux, Harukata Miki, Elio Raviola, Rohan D. Teasdale, Naoko Tominaga, Ken Yagi, Andreas Zimmer, RIKEN GER Group and GSL Members, Yoshihide Hayashizaki, and Yasushi Okazaki (2003) Genome Research 13: 1395-1401.
  Supplementary Material: Table 1 (Neurotransmitter Receptors) Table 2 (Channels) Table 3 (Neural RNAs)
• Influence of Network Topology and Data Collection on Network Inference.
  VA Smith, ED Jarvis, AJ Hatermink.(2003) Pacific Symposium on Biocomputing 2003, pp. 164-175

2002

• Induction of Hippocampal Long-Term Potentiation during Waking Leads to Increased Extrahippocampal zif-268 Expression during Ensuing Rapid-Eye-Movement Sleep
  S Ribeiro, CV Mello, T Velho, TJ Gardner, ED Jarvis, and C Pavlides (2002) Journal of Neuroscience 22(24):10914-10923.
• Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
  The FANTOM Consortium, RIKEN Genome Exploration Research Group Phase I & II Team (2002) Nature 420: 563-573. Cover Photo
  Supplementary Material: http://www.nature.com/nature/journal/v420/n6915/suppinfo/nature01266.html
• Evaluating functional network inference using simulation of complex biological systems.
  VA Smith, ED Jarvis, AJ Hatermink.(2002) Bioinformatics 18 Suppl. 1: S216-S224.
• A framework for integrating the songbird brain.
  ED Jarvis, VA Smith, MV Rivas, K Wada, M McElroy, TV Smulders, P Carnici, Y Hayashisaki, F Dietrich, X Wu, P Wang, S Lin (2002) J. Comp. Physiol. A 188:961-980.

2000

• Site-specific retinoic acid production in the brain of adult songbirds.
  N Nehrbass, ED Jarvis, C Scharff, F Nottebohm & CV Mello (2000). Neuron 27:359-370.
• A relation between behavior, neurotrophin expression, and neuronal survival.
  XC Li, ED Jarvis, B Alvarez-Bordo, D Lim, & F Nottebohm (2000). Proc. Natl. Acad. Sci. 97:8584-8589.
• Behaviorally-driven gene expression reveals hummingbird brain song nuclei.
  ED Jarvis, S Ribeiro, J. Vielliard, M DaSilva, D. Ventura, CV Mello (2000). Nature 406:628-632.
• Molecular mapping of brain areas involved in parrot vocal communication.
  ED Jarvis & CV Mello (2000). J. Comp. Neurol. 419:1-31. Cover Photo.
• A membrane-associated progesterone-binding protein, 25-Dx, is regulated by progesterone in brain regions involved in female reproductive behaviors.
  CJ Krebs, ED Jarvis, J Chan, JP Lydon, S Ogawa, DW Pfaff (2000).Proc. Natl. Acad. Sci. 97:12816-12821.
• Modulation of movement by the basal ganglia.
  W Hall, M Nicolelis, ED Jarvis (2000). Neuroscience, 2^nd edition. Purves, Augustine, Fitzpatrick, Katz, McNamara, Williams (eds). Sinauer Associates, MA. pp. 391-407.
• Modulation of movement by the cerrebellum.
  W Hall, ED Jarvis (2000). Neuroscience, 2^nd edition. Purves, Augustine, Fitzpatrick, Katz, McNamara, Williams (eds). Sinauer Associates, MA. pp. 409-426.

1999

• The 70-kDa heat shock cognate protein (Hsc73) gene is enhanced by ovarian hormones in the ventromedial hypothalamus.
  Christopher J. Krebs, E.D. Jarvis, D.W. Pfaff (1999) Proc. Natl. Acad. Sci. 96:1686-1691.
• Applying differential display to brain research .
  CV Mello, ED Jarvis (1999). Techniques for Behavioral and Neural Sciences. WE Crusio & RT Gerlai (eds). Elsevier Science, Netherlands, Amsterdam. 13:200-211.

1998

• For whom the bird sings: context-dependent gene expression.
  ED Jarvis, C Scharff, M Grossman, JA Ramos & F Nottebohm (1998). Neuron 21:775-788.
  Commentary on Jarvis et al 1998 by Schmidt (1998). Neuron 21:645-642. Neuron.
• Classification and genetic characterization of pattern forming Bacilli.
  Rudner R, Martsinkevich O, Leung W, ED Jarvis (1998). Molec. Microbio. 27:387-703.
  Commentary on Rudner et al. 1998.

1997

• Selective expression of insulin-like growth factor II in the songbird brain.
  M Holzenberger, ED Jarvis, C Chong, M Grossman, F Nottebohm & C Scharff (1997). J. Neurosci. 17:6974-6987.
• Isolation of song-regulated genes in the brain of songbirds.
  CV Mello, ED Jarvis, N Denisenko, M Rivas (1997). In Methods in Molecular Biology, Differential Display Methods and Protocols vol. 85, pp205-217. P Liang, AB Pardee (eds), Humana Press, NJ.
• Brain gene regulation by territorial singing behavior in freely ranging songbirds.
  ED Jarvis, H Schawbl, S Ribeiro, CV Mello (1997). NeuroReport 8:2073-2077.
• Motor-driven gene expression.
  ED Jarvis & F Nottebohm (1997). Proc. Natl. Acad. Sci. 94:4097-4102.
• Identification of aberrantly regulated genes in diseased skin using the cDNA differential display technique.
  Rivas M, ED Jarvis, Morisaki S, Carbonado H, Gottleb AB, Krueger J. (1997). J. Invest. Derm. 108:188-194.

1995

• Decrements in auditory responses to a repeated conspecific song are long-lasting and require two periods of protein synthesis in the songbird forebrain.
  SJ Chew, CV Mello, F Nottebohm, ED Jarvis & D Vicario (1995). Proc. Natl. Acad. Sci. 92:3406-3410.
• Associative learning and stimulus novelty influence the song-induced expression of an immediate early gene in the canary forebrain.
  ED Jarvis, CV Mello, F Nottebohm (1995). Learning & Memory. 2:62-80.

1994

• Determination of restriction fragment length polymorphisms in bacteria using ribosomal RNA genes
  Rudner R, Studamire B, ED Jarvis (1994). Methods in Enzymology. 235:184-196.

1993

• Two tRNA gene clusters associated with ribosomal RNA operons rrnD and rrnE in Bacillus subtilis.
  Rudner R, Severestt A, Buchholz S, Studamire B, White AM, ED Jarvis (1993). J. Bacteriol. 175: 503-509.

1990

• Genetic structure and DNA sequences at junctions involved in the rearrangements of Bacillus subtilis strains carrying the trpE26 mutation.
  ED Jarvis, Cheng S, Rudner R (1990). Genetics 126: 785-797.
• The structure of the trpE, trpD and 5′ trpC genes of Bacillus pumilus.
  Rivas MV, ED Jarvis, Rudner R (1990). Gene 87: 71-78.

1988

• Chromosomal Organizations of rRNA operons in Bacillus subtilis.
  ED Jarvis, Widom R, LaFauci G, Setoguchi Y, Richter IR, Rudner R (1988). Genetics 120: 625-635.
• Instability of rRNA operons in Bacillus subtilis.
  Widom RL, ED Jarvis, LaFauci G, Rudner R (1988). J. Bacteriol. 170: 605-610.

1986

• Mapping of rRNA genes with integrable plasmids in Bacillus subtilis.
  LaFauci G, Widom RL, Eisner R, Jarvis ED, Rudner R (1986). J Bacteriol. 165: 204-214.