Whole-genome analyses resolve early branches in the tree of life of modern birds
- E. Jarvis, S. Mirarab, Guojie Zhang
- BiologyScience
- 12 December 2014
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
The genome of a songbird
- W. Warren, D. Clayton, R. Wilson
- BiologyNature
- 1 April 2010
This work shows that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets and shows evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience.
Comparative genomics reveals insights into avian genome evolution and adaptation
- Guojie Zhang, Cai Li, Jun Wang
- BiologyScience
- 12 December 2014
This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Advances to Bayesian network inference for generating causal networks from observational biological data
- Jing Yu, V. Smith, Paul P. Wang, A. Hartemink, E. Jarvis
- Computer ScienceBioinform.
- 12 December 2004
A novel influence score for DBNs is developed that attempts to estimate both the sign (activation or repression) and relative magnitude of interactions among variables and reduces a significant portion of false positive interactions in the recovered networks.
Hybrid error correction and de novo assembly of single-molecule sequencing reads
- S. Koren, M. Schatz, A. Phillippy
- BiologyNature Biotechnology
- 31 May 2012
This work introduces a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences, leading to substantially better assemblies than current sequencing strategies.
Revised nomenclature for avian telencephalon and some related brainstem nuclei
The standard nomenclature that has been used for many telencephalic and related brainstem structures in birds is reviewed, with a rationale for each name change and evidence for any homologies implied by the new names.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
- K. Bradnam, Joseph N. Fass, I. Korf
- BiologyGigaScience
- 23 January 2013
The high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
For Whom The Bird Sings Context-Dependent Gene Expression
- E. Jarvis, C. Scharff, Matthew Grossman, Joana A Ramos, F. Nottebohm
- Biology, PsychologyNeuron
- 1 October 1998
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
- Y. Okazaki, M. Furuno, Y. Hayashizaki
- BiologyNature
- 1 December 2002
The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Decrements in auditory responses to a repeated conspecific song are long-lasting and require two periods of protein synthesis in the songbird forebrain.
- S. Chew, C. Mello, F. Nottebohm, E. Jarvis, D. Vicario
- Biology, PsychologyProceedings of the National Academy of Sciences…
- 11 April 1995
At least two waves of gene induction appear to be necessary for long-lasting habituation to a particular song in awake male zebra finches.
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