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Biology Direct

ISSN Print: 1745-6150

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Website: http://www.biology-direct.com

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Microevolutionary, macroevolutionary, ecological and taxonomical implications of punctuational theories of adaptive evolution

Flegr Jaroslav

Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability

Holder Thomas,Basquin Claire,Ebert Judith,Randel Nadine

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

Loss-Morais Guilherme,Waterhouse Peter M,Margis Rogerio

GABBR1 has a HERV-W LTR in its regulatory region – a possible implication for schizophrenia

Hegyi Hedi

Surprisingly high number of Twintrons in vertebrates

Janice Jessin,J？kalski Marcin,Maka？owski Wojciech

Next-generation phylogenomics

Chan Cheong Xin,Ragan Mark A

Archaeal origin of tubulin

Natalya Yutin, Eugene V Koonin

Amino acid fermentation at the origin of the genetic code

Harold P de Vladar

Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen

Kiyotaka Takishita, Yoshito Chikaraishi, Michelle M Leger, Eunsoo Kim, Akinori Yabuki, Naohiko Ohkouchi, Andrew J Roger

Modeling the relationship between body weight and energy intake: A molecular diffusion-based approach

Zhejun Gong, Zhefeng Gong

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a

Harold S Bernhardt

Reaction-Diffusion-Delay Model for EPO/TNF-α Interaction in articular cartilage lesion abatement

Jason M Graham, Bruce P Ayati, Lei Ding, Prem S Ramakrishnan, James A Martin

Primordial soup or vinaigrette: did the RNA world evolve at acidic pH?

Harold S Bernhardt, Warren P Tate

Pathway-based classification of cancer subtypes

Shinuk Kim, Mark Kon, Charles DeLisi

Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes

Sergei A Filichkin, Todd C Mockler

The manoeuvrability hypothesis to explain the maintenance of bilateral symmetry in animal evolution

Gábor Holló, Mihály Novák

Increased burst size in multiply infected cells can alter basic virus dynamics

Kara W Cummings, David N Levy, Dominik Wodarz

Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions

Jinzhuang Dou, Xiqiang Zhao, Xiaoteng Fu, Wenqian Jiao, Nannan Wang, Lingling Zhang, Xiaoli Hu, Shi Wang, Zhenmin Bao

Evolution before genes

Vera Vasas, Chrisantha Fernando, Mauro Santos, Stuart Kauffman, E？rs Szathmáry

A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses

Geoffrey S Diemer, Kenneth M Stedman

Structure based hypothesis of a mitochondrial ribosome rescue mechanism

Martijn A Huynen, Isabel Duarte, Zofia M. A. Chrzanowska-Lightowlers, Sander B Nabuurs

Rate and breadth of protein evolution are only weakly correlated

Sergey A Naumenko, Alexey S Kondrashov

IgG3 deficiency extends lifespan and attenuates progression of glomerulonephritis in MRL/lpr mice

Neil S Greenspan, Myro A Lu, Jacob W Shipley, Xuedong Ding, Qing Li, Dilara Sultana, Maria Kollaros, John R Schreiber, Pingfu Fu, Chaim Putterman, Steven N Emancipator

Origin and evolution of spliceosomal introns

Igor B Rogozin, Liran Carmel, Miklos Csuros, Eugene V Koonin

On the complexity of miRNA-mediated regulation in plants: novel insights into the genomic organization of plant miRNAs

Moreno Colaiacovo, Antonella Lamontanara, Letizia Bernardo, Renzo Alberici, Cristina Crosatti, Lorenzo Giusti, Luigi Cattivelli, Primetta Faccioli

On the molecular mechanism of GC content variation among eubacterial genomes

Hao Wu, Zhang Zhang, Songnian Hu, Jun Yu

The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes

Kira S Makarova, Eugene V Koonin, Zvi Kelman

Domain enhanced lookup time accelerated BLAST

Grzegorz M Boratyn, Alejandro A Schaffer, Richa Agarwala, Stephen F Altschul, David J Lipman, Thomas L Madden

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics

Dapeng Zhang, Robson F de Souza, Vivek Anantharaman, Lakshminarayan M Iyer, L. Aravind

Ethanolamine utilization in Vibrio alginolyticus

Khatri Neelam,Khatri Indu,Subramanian Srikrishna,Raychaudhuri Saumya

Identifying the mechanisms of intron gain: progress and trends

Yenerall Paul,Zhou Leming

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

Wood Derrick E,Lin Henry,Levy-Moonshine Ami,Swaminathan Rajiswari

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

Jalali Saakshi,Jayaraj Gopal,Scaria Vinod

AID/APOBEC cytosine deaminase induces genome-wide kataegis

Lada Artem G,Dhar Alok,Boissy Robert J,Hirano Masayuki

Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios

Lyubetsky Vassily A,Rubanov Lev I,Rusin Leonid Y,Gorbunov Konstantin Yu

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

Wolf Yuri I,Makarova Kira S,Yutin Natalya,Koonin Eugene V

Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

de Crécy-Lagard Valérie,Forouhar Farhad,Brochier-Armanet Céline,Tong Liang

Bioinformatics clouds for big data manipulation

Dai Lin,Gao Xin,Guo Yan,Xiao Jingfa

Detection of a common chimeric transcript between human chromosomes 7 and 16

Fang Wenwen,Wei Yong,Kang Yibin,Landweber Laura F

The origin of life is a spatially localized stochastic transition

Wu Meng,Higgs Paul G

Does the central dogma still stand?

Koonin Eugene V

Early evolution of efficient enzymes and genome organization

Szilágyi András,Kun ádám,Szathmáry E？rs

Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

Makarova Kira S,Anantharaman Vivek,Aravind L,Koonin Eugene V

Somatic transposition in the brain has the potential to influence the biosynthesis of metabolites involved in Parkinson’s disease and schizophrenia

Abrusán Gy？rgy

Modeling RNA polymerase interaction in mitochondria of chordates

Lyubetsky Vassily A,Zverkov Oleg A,Pirogov Sergey A,Rubanov Lev I

CRISPR transcript processing: a mechanism for generating a large number of small interfering RNAs

Djordjevic Marko,Djordjevic Magdalena,Severinov Konstantin

Stop codons in bacteria are not selectively equivalent

Povolotskaya Inna S,Kondrashov Fyodor A,Ledda Alice,Vlasov Peter K

Evasion of tumours from the control of the immune system: consequences of brief encounters

Al-Tameemi Mohannad,Chaplain Mark,d’Onofrio Alberto

Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches

Delavat Fran？ois,Lett Marie-Claire,Lièvremont Didier

ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons

Iyer Lakshminarayan M,Aravind L

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