Articles

Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes?

Martin & Koonin recently proposed that the eukaryote nucleus evolved as a quality control mechanism to prevent ribosome readthrough into introns. In their scenario, the bacterial ancestor of mitochondria was r...

Authors: Anthony M Poole

Did the last common ancestor have a biological membrane?

All theories about the origin and evolution of membrane bound cells necessarily have to cope with the nature of the last common ancestor of cellular life. One of the most important aspect of this ancestor, whe...

Authors: Gáspár Jékely

Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus

The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed...

Authors: Yuri I Wolf, Cecile Viboud, Edward C Holmes, Eugene V Koonin and David J Lipman

Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression

The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repos...

Authors: Shuyu Li, Yiqun Helen Li, Tao Wei, Eric Wen Su, Kevin Duffin and Birong Liao

The immune-body cytokine network defines a social architecture of cell interactions

Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells), one limited to parenchymal cells of organs and tissues (body c...

Authors: Ziv Frankenstein, Uri Alon and Irun R Cohen

Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation

The glyoxylate cycle is thought to be present in bacteria, protists, plants, fungi, and nematodes, but not in other Metazoa. However, activity of the glyoxylate cycle enzymes, malate synthase (MS) and isocitra...

Authors: Fyodor A Kondrashov, Eugene V Koonin, Igor G Morgunov, Tatiana V Finogenova and Marie N Kondrashova

Mathematical modeling of tumor therapy with oncolytic viruses: effects of parametric heterogeneity on cell dynamics

One of the mechanisms that ensure cancer robustness is tumor heterogeneity, and its effects on tumor cells dynamics have to be taken into account when studying cancer progression. There is no unifying theoreti...

Authors: Georgy P Karev, Artem S Novozhilov and Eugene V Koonin

The ancient Virus World and evolution of cells

Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven explorati...

Authors: Eugene V Koonin, Tatiana G Senkevich and Valerian V Dolja

Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most euk...

Authors: Pavel V Baranov, Bente Vestergaard, Thomas Hamelryck, Raymond F Gesteland, Jens Nyborg and John F Atkins

Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution

DNA microarrays are a powerful technology that can provide a wealth of gene expression data for disease studies, drug development, and a wide scope of other investigations. Because of the large volume and inhe...

Authors: Jaroslav P Novak, Seon-Young Kim, Jun Xu, Olga Modlich, David J Volsky, David Honys, Joan L Slonczewski, Douglas A Bell, Fred R Blattner, Eduardo Blumwald, Marjan Boerma, Manuel Cosio, Zoran Gatalica, Marian Hajduch, Juan Hidalgo, Roderick R McInnes…

Refuting phylogenetic relationships

Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account. ...

Authors: James Bucknam, Yan Boucher and Eric Bapteste

The signaling helix: a common functional theme in diverse signaling proteins

The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood.

Authors: Vivek Anantharaman, S Balaji and L Aravind

Codon insertion and deletion functions as a somatic diversification mechanism in human antibody repertoires

It has been suggested that codon insertion and/or deletion may represent a mechanism that, along with hypermutation, contributes to the affinity maturation of antibodies. We used repertoire cloning to examine ...

Authors: Donald C Reason and Jianhui Zhou

A system for studying evolution of life-like virtual organisms

Fitness landscapes, the dependences of fitness on the genotype, are of critical importance for the evolution of living beings. Unfortunately, fitness landscapes that are relevant to the evolution of complex bi...

Authors: Alex A Neyfakh, Natalya N Baranova and Lev J Mizrokhi

The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?

Ever since the discovery of 'genes in pieces' and mRNA splicing in eukaryotes, origin and evolution of spliceosomal introns have been considered within the conceptual framework of the 'introns early' versus 'i...

Authors: Eugene V Koonin

Phylogeographic support for horizontal gene transfer involving sympatric bruchid species

We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric.

Authors: Nadir Alvarez, Betty Benrey, Martine Hossaert-McKey, Andrea Grill, Doyle McKey and Nicolas Galtier

Transposable element derived DNaseI-hypersensitive sites in the human genome

Transposable elements (TEs) are abundant genomic sequences that have been found to contribute to genome evolution in unexpected ways. Here, we characterize the evolutionary and functional characteristics of TE...

Authors: Leonardo Mariño-Ramírez and I King Jordan

Rooting the tree of life by transition analyses

Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed – the most difficult problems in phylogeny. Protein pa...

Authors: Thomas Cavalier-Smith

Variation in fiberoptic bead-based oligonucleotide microarrays: dispersion characteristics among hybridization and biological replicate samples

Gene expression microarray technology continues to evolve and its use has expanded into all areas of biology. However, the high dimensionality of the data makes analysis a difficult challenge. Evaluating measu...

Authors: Jaroslav P Novak, Merrill C Miller III and Douglas A Bell

Genome increase as a clock for the origin and evolution of life

The size of non-redundant functional genome can be an indicator of biological complexity of living organisms. Several positive feedback mechanisms including gene cooperation and duplication with subsequent spe...

Authors: Alexei A Sharov

Clinical applications of Genome Polymorphism Scans

Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygo...

Authors: James L Weber

Positive selection on the nonhomologous end-joining factor Cernunnos-XLF in the human lineage

Cernunnos-XLF is a nonhomologous end-joining factor that is mutated in patients with a rare immunodeficiency with microcephaly. Several other microcephaly-associated genes such as ASPM and microcephalin experienc...

Authors: Adam Pavlicek and Jerzy Jurka

Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples

HIV can evolve drug resistance rapidly in response to new drug treatments, often through a combination of multiple mutations [1–3]. It would be useful to develop automated analyses of HIV sequence polymorphism th...

Authors: Lamei Chen and Christopher Lee

Similarity searches in genome-wide numerical data sets

We present psi-square, a program for searching the space of gene vectors. The program starts with a gene vector, i.e., the set of measurements associated with a gene, and finds similar vectors, derives a proba...

Authors: Galina Glazko, Michael Coleman and Arcady Mushegian

Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens

Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respecti...

Authors: Dimitris Papamichail and Nicholas Delihas

A survey of motif discovery methods in an integrated framework

There has been a growing interest in computational discovery of regulatory elements, and a multitude of motif discovery methods have been proposed. Computational motif discovery has been used with some success...

Authors: Geir Kjetil Sandve and Finn Drabløs

Method of predicting Splice Sites based on signal interactions

Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of s...

Authors: Alexander Churbanov, Igor B Rogozin, Jitender S Deogun and Hesham Ali

Hereditary profiles of disorderly transcription?

Microscopic examination of living cells often reveals that cells from some cell strains appear to be in a permanent state of disarray without obvious reason. In all probability such a disorderly state affects ...

Authors: Johannes WIM Simons

Origin and evolution of the peroxisomal proteome

Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis syst...

Authors: Toni Gabaldón, Berend Snel, Frank van Zimmeren, Wieger Hemrika, Henk Tabak and Martijn A Huynen

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

All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated (cas) genes that have been previously implicated in a...

Authors: Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf and Eugene V Koonin

Mathematical modeling of tumor therapy with oncolytic viruses: Regimes with complete tumor elimination within the framework of deterministic models

Oncolytic viruses that specifically target tumor cells are promising anti-cancer therapeutic agents. The interaction between an oncolytic virus and tumor cells is amenable to mathematical modeling using adapta...

Authors: Artem S Novozhilov, Faina S Berezovskaya, Eugene V Koonin and Georgy P Karev

Phylogenetic inference from homologous sequence data: minimum topological assumption, strict mutational compatibility consensus tree as the ultimate solution

For the purposes of phylogenetic inference from molecular data sets many different methods are currently offered as alternatives for researchers in phylogenetic systematics. The vast majority of these methods ...

Authors: Srdan V Stankov

Mutational hotspots in the TP53gene and, possibly, other tumor suppressors evolve by positive selection

The mutation spectra of the TP53 gene and other tumor suppressors contain multiple hotspots, i.e., sites of non-random, frequent mutation in tumors and/or the germline. The origin of the hotspots remains unclear,...

Authors: Galina V Glazko, Vladimir N Babenko, Eugene V Koonin and Igor B Rogozin

Various hypotheses on MHC evolution suggested by the concerted evolution of CD94L and MHC class Ia molecules

In the accompanying paper by Virginie Rouillon and myself, our demonstration that homogenisation by gene conversion occurs readily among MHC class I genes was made possible because of the exceptional conservat...

Authors: Etienne Joly

The orthology of HLA-E and H2-Qa1 is hidden by their concerted evolution with other MHC class I molecules

Whether MHC molecules undergo concerted evolution or not has been the subject of a long-standing debate.

Authors: Etienne Joly and Virginie Rouillon

A community experiment with fully open and published peer review

Authors: Eugene V Koonin, Laura F Landweber and David J Lipman