Articles

Cancer heterogeneity and multilayer spatial evolutionary games

Evolutionary game theory (EGT) has been widely used to simulate tumour processes. In almost all studies on EGT models analysis is limited to two or three phenotypes. Our model contains four main phenotypes. Mo...

Authors: Andrzej Świerniak and Michał Krześlak

Unexpected links reflect the noise in networks

Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of play...

Authors: Anatoly Yambartsev, Michael A. Perlin, Yevgeniy Kovchegov, Natalia Shulzhenko, Karina L. Mine, Xiaoxi Dong and Andrey Morgun

Emergence of heterogeneity in acute leukemias

Leukemias are malignant proliferative disorders of the blood forming system. Sequencing studies demonstrate that the leukemic cell population consists of multiple clones. The genetic relationship between the d...

Authors: Thomas Stiehl, Christoph Lutz and Anna Marciniak-Czochra

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes

It has been demonstrated that a pathway-based feature selection method that incorporates biological information within pathways during the process of feature selection usually outperforms a gene-based feature ...

Authors: Suyan Tian, Howard H. Chang and Chi Wang

The essence of life

Although biology has achieved great successes in recent years, we have not got a clear idea on “what is life?” Actually, as explained here, the main reason for this situation is that there are two completely d...

Authors: Wentao Ma

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks

PDZ domains recognize short sequence stretches usually present in C-terminal of their interaction partners. Because of the involvement of PDZ domains in many important biological processes, several attempts ha...

Authors: Neetu Sain and Debasisa Mohanty

Computational inference of a genomic pluripotency signature in human and mouse stem cells

Recent analyses of next-generation sequencing datasets have shown that cell-specific regulatory elements in stem cells are marked with distinguishable patterns of transcription factor (TF) binding and epigenet...

Authors: Esra Kurum, Bérénice A. Benayoun, Ankit Malhotra, Joshy George and Duygu Ucar

Cpf1 nucleases demonstrate robust activity to induce DNA modification by exploiting homology directed repair pathways in mammalian cells

Cpf1 nucleases have recently been repurposed for site-specific genome modification. Two members of the Cpf1 family, the AsCpf1 from Acidaminococcus sp. and the LbCpf1 from Lachnospiraceae bacterium were shown to ...

Authors: Eszter Tóth, Nóra Weinhardt, Petra Bencsura, Krisztina Huszár, Péter I. Kulcsár, András Tálas, Elfrieda Fodor and Ervin Welker

Essential functions linked with structural disorder in organisms of minimal genome

Intrinsically disordered regions (IDRs) of proteins fulfill important regulatory roles in most organisms. However, the proteins of certain endosymbiont and intracellular pathogenic bacteria with extremely redu...

Authors: Rita Pancsa and Peter Tompa

Profuse evolutionary diversification and speciation on volcanic islands: transposon instability and amplification bursts explain the genetic paradox

Species-rich adaptive radiations arising from rare plant and animal colonizers are common on remote volcanic archipelagoes. However, they present a paradox. The severe genetic bottleneck of founder events and ...

Authors: Elysse M. Craddock

Tracking the evolution of cancer cell populations through the mathematical lens of phenotype-structured equations

A thorough understanding of the ecological and evolutionary mechanisms that drive the phenotypic evolution of neoplastic cells is a timely and key challenge for the cancer research community. In this respect, ...

Authors: Tommaso Lorenzi, Rebecca H. Chisholm and Jean Clairambault

The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts

Colon and intestinal crypts serve as an important model system for adult stem cell proliferation and differentiation. We develop a spatial stochastic model to study the rate of somatic evolution in a normal cr...

Authors: Leili Shahriyari, Natalia L. Komarova and Alexandra Jilkine

Should tissue structure suppress or amplify selection to minimize cancer risk?

It has been frequently argued that tissues evolved to suppress the accumulation of growth enhancing cancer inducing mutations. A prominent example is the hierarchical structure of tissues with high cell turnov...

Authors: Laura Hindersin, Benjamin Werner, David Dingli and Arne Traulsen

Optimal treatment and stochastic modeling of heterogeneous tumors

In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how hetero...

Authors: Hamidreza Badri and Kevin Leder

Primary and metastatic tumor dormancy as a result of population heterogeneity

Existence of tumor dormancy, or cancer without disease, is supported both by autopsy studies that indicate presence of microscopic tumors in men and women who die of trauma (primary dormancy), and by long peri...

Authors: Irina Kareva

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics

For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have per...

Authors: Johann-Mattis List, Jananan Sylvestre Pathmanathan, Philippe Lopez and Eric Bapteste

Compartmentalization in PVC super-phylum: evolution and impact

The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomy...

Authors: Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Jean Pierre Baudoin and Isabelle Pagnier

The multiple evolutionary origins of the eukaryotic N-glycosylation pathway

The N-glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. It shares mechanistic similarities based...

Authors: Jonathan Lombard

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

Retroposition, one of the processes of copying the genetic material, is an important RNA-mediated mechanism leading to the emergence of new genes. Because the transcription controlling segments are usually not...

Authors: Marcin Jąkalski, Kazutaka Takeshita, Mathieu Deblieck, Kanako O. Koyanagi, Izabela Makałowska, Hidemi Watanabe and Wojciech Makałowski

Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α p...

Authors: Mauro Degli Esposti, Diego Cortez, Luis Lozano, Simon Rasmussen, Henrik Bjørn Nielsen and Esperanza Martinez Romero

Stem-like features of cancer cells on their way to metastasis

More than 90 % of cancer-related deaths are due to the development of a systemic metastatic disease. Clearly, much remains to be understood about the biological principles that govern human cancer metastasis, ...

Authors: Sofia Gkountela and Nicola Aceto

The evolutionary scope and neurological disease linkage of yeast-prion-like proteins in humans

Prions are proteinaceous particles that propagate alternative protein conformations/states to further copies of the same proteins, and are transmitted from cell-to-cell, and organism-to-organism. Prions are us...

Authors: Lu An and Paul M. Harrison

Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily sta...

Authors: Alena Orlenko, Ashley I. Teufel, Peter B. Chi and David A. Liberles

Intrinsic protein disorder in histone lysine methylation

Histone lysine methyltransferases (HKMTs), catalyze mono-, di- and trimethylation of lysine residues, resulting in a regulatory pattern that controls gene expression. Their involvement in many different cellul...

Authors: Tamas Lazar, Eva Schad, Beata Szabo, Tamas Horvath, Attila Meszaros, Peter Tompa and Agnes Tantos

Erratum to: What can ecosystems learn? Expanding evolutionary ecology with learning theory

Authors: Daniel A. Power, Richard A. Watson, Eörs Szathmáry, Rob Mills, Simon T. Powers, C. Patrick Doncaster and Błazej Czapp

Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis

The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis)...

Authors: Alexander V. Markov and Ilya S. Kaznacheev

Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria

Evolutionary relationship between class III nucleotide cyclases and an uncharacterized set of bacterial proteins from Actinobacteria, Bacteroidetes and Proteobacteria has been recognized and analyzed. Detailed...

Authors: Gayatri Ramakrishnan, Abha Jain, Nagasuma Chandra and Narayanaswamy Srinivasan

Gene overlapping and size constraints in the viral world

Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified evolutionary explanation that accounts for...

Authors: Nadav Brandes and Michal Linial

Biochemical and biophysical characterization of cell-free synthesized Rift Valley fever virus nucleoprotein capsids enables in vitro screening to identify novel antivirals

Viral capsid assembly involves the oligomerization of the capsid nucleoprotein (NP), which is an essential step in viral replication and may represent a potential antiviral target. An in vitro transcription-tr...

Authors: Sean Broce, Lisa Hensley, Tomoharu Sato, Joshua Lehrer-Graiwer, Christian Essrich, Katie J. Edwards, Jacqueline Pajda, Christopher J. Davis, Rami Bhadresh, Clarence R. Hurt, Beverly Freeman, Vishwanath R. Lingappa, Colm A. Kelleher and Marcela V. Karpuj

Estimation of ribosome profiling performance and reproducibility at various levels of resolution

Ribosome profiling (or Ribo-seq) is currently the most popular methodology for studying translation; it has been employed in recent years to decipher various fundamental gene expression regulation aspects.

Authors: Alon Diament and Tamir Tuller

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development

Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights ...

Authors: Bálint Mészáros, András Zeke, Attila Reményi, István Simon and Zsuzsanna Dosztányi

Beyond Turing: mechanochemical pattern formation in biological tissues

During embryogenesis, chemical (morphogen) and mechanical patterns develop within tissues in a self-organized way. More than 60 years ago, Turing proposed his famous reaction-diffusion model for such processes...

Authors: Moritz Mercker, Felix Brinkmann, Anna Marciniak-Czochra and Thomas Richter

The cyclin D1 carboxyl regulatory domain controls the division and differentiation of hematopoietic cells

The family of D cyclins has a fundamental role in cell cycle progression, but its members (D1, D2, D3) are believed to have redundant functions. However, there is some evidence that contradicts the notion of m...

Authors: Miguel Chaves-Ferreira, Gerald Krenn, Florence Vasseur, Aleksandr Barinov, Pedro Gonçalves, Orly Azogui, Ana Cumano, Zhi Li, Sandra Pellegrini, Benedita Rocha and Diego Laderach

Ribosome reinitiation at leader peptides increases translation of bacterial proteins

Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation re...

Authors: Semen A. Korolev, Oleg A. Zverkov, Alexandr V. Seliverstov and Vassily A. Lyubetsky

Infinitely long branches and an informal test of common ancestry

The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison betwee...

Authors: Leonardo de Oliveira Martins and David Posada

Conservation and divergence of the histone code in nucleomorphs

Nucleomorphs, the remnant nuclei of photosynthetic algae that have become endosymbionts to other eukaryotes, represent a unique example of convergent reductive genome evolution in eukaryotes, having evolved in...

Authors: Georgi K. Marinov and Michael Lynch

The Columbian Exchange as a source of adaptive introgression in human populations

The term “Columbian Exchange” refers to the massive transfer of life between the Afro-Eurasian and American hemispheres that was precipitated by Columbus’ voyage to the New World. The Columbian Exchange is wid...

Authors: I. King Jordan

Nucleic acids delivery methods for genome editing in zygotes and embryos: the old, the new, and the old-new

In the recent years, sequence-specific nucleases such as ZFNs, TALENs, and CRISPR/Cas9 have revolutionzed the fields of animal genome editing and transgenesis. However, these new techniques require microinject...

Authors: Masahiro Sato, Masato Ohtsuka, Satoshi Watanabe and Channabasavaiah B. Gurumurthy

Viroids: “living fossils” of primordial RNAs?

The discovery of the viroid in 1971, which initiated the third major expansion of the biosphere towards smaller living entities—after discovery of the “subvisual” microorganisms in 1675 and that of the “submic...

Authors: Theodor O. Diener

A web server for analysis, comparison and prediction of protein ligand binding sites

One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites i...

Authors: Harinder Singh, Hemant Kumar Srivastava and Gajendra P. S. Raghava

Onset, timing, and exposure therapy of stress disorders: mechanistic insight from a mathematical model of oscillating neuroendocrine dynamics

The hypothalamic-pituitary-adrenal (HPA) axis is a neuroendocrine system that regulates numerous physiological processes. Disruptions in the activity of the HPA axis are correlated with stress-related diseases...

Authors: Lae U. Kim, Maria R. D’Orsogna and Tom Chou

Numerical simulation of vascular tumour growth under antiangiogenic treatment: addressing the paradigm of single-agent bevacizumab therapy with the use of experimental data

Antiangiogenic agents have been recently added to the oncological armamentarium with bevacizumab probably being the most popular representative in current clinical practice. The elucidation of the mode of acti...

Authors: Katerina D. Argyri, Dimitra D. Dionysiou, Fay D. Misichroni and Georgios S. Stamatakos

Preservation of methylated CpG dinucleotides in human CpG islands

CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cyto...

Authors: Alexander Y. Panchin, Vsevolod J. Makeev and Yulia A. Medvedeva

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data

Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, ...

Authors: Yeongjun Jang, Namhee Yu, Jihae Seo, Sun Kim and Sanghyuk Lee

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms

The CRISPR-Cas system of prokaryotic adaptive immunity displays features of a mechanism for directional, Lamarckian evolution. Indeed, this system modifies a specific locus in a bacterial or archaeal genome by...

Authors: Eugene V. Koonin and Yuri I. Wolf

Altools: a user friendly NGS data analyser

Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to ...

Authors: Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu

Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology

Functional biologists, like Claude Bernard, ask “How?”, meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Char...

Authors: Angelo Vianello and Sabina Passamonti

Characterizing exons and introns by regularity of nucleotide strings

Translation of nucleotides into a numeric form has been approached in many ways and has allowed researchers to investigate the properties of protein-coding sequences and noncoding sequences. Typically, more pr...

Authors: Tonya Woods, Thanawadee Preeprem, Kichun Lee, Woojin Chang and Brani Vidakovic

A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their ...

Authors: Marek Eliáš, Vladimír Klimeš, Romain Derelle, Romana Petrželková and Jan Tachezy

BLAST-based structural annotation of protein residues using Protein Data Bank

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of th...

Authors: Harinder Singh and Gajendra P. S. Raghava