# | Title | Journal | Year | Citations |
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1 | A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action | Biology Direct | 2006 | 961 |
2 | Domain enhanced lookup time accelerated BLAST | Biology Direct | 2012 | 705 |
3 | The ancient Virus World and evolution of cells | Biology Direct | 2006 | 559 |
4 | Designing of interferon-gamma inducing MHC class-II binders | Biology Direct | 2013 | 484 |
5 | CAIcal: A combined set of tools to assess codon usage adaptation | Biology Direct | 2008 | 447 |
6 | Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics | Biology Direct | 2012 | 440 |
7 | Transcript length bias in RNA-seq data confounds systems biology | Biology Direct | 2009 | 422 |
8 | Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes | Biology Direct | 2009 | 390 |
9 | Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems | Biology Direct | 2011 | 379 |
10 | Splign: algorithms for computing spliced alignments with identification of paralogs | Biology Direct | 2008 | 329 |
11 | IPC – Isoelectric Point Calculator | Biology Direct | 2016 | 308 |
12 | Origin and evolution of spliceosomal introns | Biology Direct | 2012 | 292 |
13 | The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? | Biology Direct | 2006 | 247 |
14 | Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements | Biology Direct | 2009 | 232 |
15 | Evolution before genes | Biology Direct | 2012 | 225 |
16 | Is evolution Darwinian or/and Lamarckian? | Biology Direct | 2009 | 224 |
17 | Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3′-untranslated regions | Biology Direct | 2013 | 223 |
18 | Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing | Biology Direct | 2013 | 221 |
19 | Exosomal transfer of proteins and RNAs at synapses in the nervous system | Biology Direct | 2007 | 217 |
20 | Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia | Biology Direct | 2008 | 216 |
21 | Component retention in principal component analysis with application to cDNA microarray data | Biology Direct | 2007 | 214 |
22 | The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner | Biology Direct | 2008 | 207 |
23 | The struggle for life of the genome's selfish architects | Biology Direct | 2011 | 198 |
24 | Rooting the tree of life by transition analyses | Biology Direct | 2006 | 196 |
25 | The origins of phagocytosis and eukaryogenesis | Biology Direct | 2009 | 190 |
26 | Prokaryotic evolution and the tree of life are two different things | Biology Direct | 2009 | 188 |
27 | Massive comparative genomic analysis reveals convergent evolution of specialized bacteria | Biology Direct | 2009 | 187 |
28 | The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a | Biology Direct | 2012 | 183 |
29 | Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria | Biology Direct | 2009 | 179 |
30 | Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus | Biology Direct | 2006 | 176 |
31 | On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization | Biology Direct | 2007 | 173 |
32 | Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution | Biology Direct | 2010 | 165 |
33 | A new rhesus macaque assembly and annotation for next-generation sequencing analyses | Biology Direct | 2014 | 165 |
34 | Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea | Biology Direct | 2007 | 164 |
35 | PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues | Biology Direct | 2015 | 164 |
36 | Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees | Biology Direct | 2010 | 154 |
37 | Origin and evolution of the peroxisomal proteome | Biology Direct | 2006 | 152 |
38 | Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution | Biology Direct | 2007 | 146 |
39 | Evolutionary primacy of sodium bioenergetics | Biology Direct | 2008 | 144 |
40 | Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer | Biology Direct | 2012 | 142 |
41 | A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses | Biology Direct | 2012 | 141 |
42 | MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs | Biology Direct | 2018 | 141 |
43 | A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land | Biology Direct | 2009 | 138 |
44 | A survey of motif discovery methods in an integrated framework | Biology Direct | 2006 | 135 |
45 | Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation | Biology Direct | 2006 | 135 |
46 | An extension of the coevolution theory of the origin of the genetic code | Biology Direct | 2008 | 134 |
47 | pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model | Biology Direct | 2007 | 131 |
48 | Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees | Biology Direct | 2009 | 128 |
49 | Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold | Biology Direct | 2007 | 127 |
50 | Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes | Biology Direct | 2012 | 125 |