abstract：BACKGROUND:Drug-induced liver injury (DILI) is a major safety concern characterized by a complex and diverse pathogenesis. In order to identify DILI early in drug development, a better understanding of the injury and models with better predictivity are urgently needed. One approach in this regard are in silico models w...

journal_title：Biology direct

authors： Liu A,Walter M,Wright P,Bartosik A,Dolciami D,Elbasir A,Yang H,Bender A

更新日期：2021-01-18 00:00:00

abstract：:The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation.This opinion article argues that the concepts of developmental co...

journal_title：Biology direct

authors： Salazar-Ciudad I

更新日期：2021-01-09 00:00:00

abstract：BACKGROUND:The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets p...

journal_title：Biology direct

authors： Chen JC,Tyler AD

更新日期：2020-12-10 00:00:00

abstract：:Chron's Disease is a chronic inflammatory intestinal disease, first described at the beginning of the last century. The disease is characterized by the alternation of periods of flares and remissions influenced by a complex pathogenesis in which inflammation plays a key role. Crohn's disease evolution is mediated by a...

journal_title：Biology direct

authors： Petagna L,Antonelli A,Ganini C,Bellato V,Campanelli M,Divizia A,Efrati C,Franceschilli M,Guida AM,Ingallinella S,Montagnese F,Sensi B,Siragusa L,Sica GS

更新日期：2020-11-07 00:00:00

abstract：BACKGROUND:The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for im...

journal_title：Biology direct

authors： Lisitsyna OM,Kurnaeva MA,Arifulin EA,Shubina MY,Musinova YR,Mironov AA,Sheval EV

更新日期：2020-04-28 00:00:00

abstract：:Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the s...

journal_title：Biology direct

authors： Bateman A

更新日期：2020-04-28 00:00:00

abstract：BACKGROUND:Drug-induced liver injury (DILI) is a major concern in drug development, as hepatotoxicity may not be apparent at early stages but can lead to life threatening consequences. The ability to predict DILI from in vitro data would be a crucial advantage. In 2018, the Critical Assessment Massive Data Analysis gro...

journal_title：Biology direct

authors： Chierici M,Francescatto M,Bussola N,Jurman G,Furlanello C

更新日期：2020-02-13 00:00:00

abstract：:ᅟ: Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We present a hypothesis that such transmissible tumors existed in the past and that some modern animal taxa are ...

journal_title：Biology direct

authors： Panchin AY,Aleoshin VV,Panchin YV

更新日期：2019-01-23 00:00:00

abstract：BACKGROUND:Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metageno...

journal_title：Biology direct

authors： Gerner SM,Rattei T,Graf AB

更新日期：2018-10-12 00:00:00

abstract：BACKGROUND:The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenerge...

journal_title：Biology direct

authors： Gerlitz M,Knopp M,Kapust N,Xavier JC,Martin WF

更新日期：2018-10-03 00:00:00

abstract：BACKGROUND:This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin o...

journal_title：Biology direct

authors： Tessera M

更新日期：2018-09-21 00:00:00

abstract：BACKGROUND:Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is ...

journal_title：Biology direct

authors： Kumar G,Mudgal R,Srinivasan N,Sandhya S

更新日期：2018-05-09 00:00:00

abstract：BACKGROUND:Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes...

journal_title：Biology direct

authors： Chan KL,Tatarinova TV,Rosli R,Amiruddin N,Azizi N,Halim MAA,Sanusi NSNM,Jayanthi N,Ponomarenko P,Triska M,Solovyev V,Firdaus-Raih M,Sambanthamurthi R,Murphy D,Low EL

更新日期：2017-09-08 00:00:00

abstract：BACKGROUND:A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in ...

journal_title：Biology direct

authors： Sorokina I,Mushegian A

更新日期：2017-05-31 00:00:00

abstract：BACKGROUND:While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise ...

journal_title：Biology direct

authors： Yap CK,Eisenhaber B,Eisenhaber F,Wong WC

更新日期：2016-11-29 00:00:00

abstract：BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...

journal_title：Biology direct

authors： Kozlowski LP

更新日期：2016-10-21 00:00:00

abstract：UNLABELLED: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 heterogeneous tumors respond to radiotherapy, and take a particularly close look at how the optimal radiot...

journal_title：Biology direct

authors： Badri H,Leder K

更新日期：2016-08-23 00:00:00

abstract：BACKGROUND: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 between one versus several trees. This test was successfully applied to a well-supported homologous sequen...

journal_title：Biology direct

authors： de Oliveira Martins L,Posada D

更新日期：2016-04-07 00:00:00

abstract：BACKGROUND: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 in a protein for a limited number of ligands. RESULTS:In order to address this problem, we developed...

journal_title：Biology direct

authors： Singh H,Srivastava HK,Raghava GP

更新日期：2016-03-25 00:00:00

abstract：: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 Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote cau...

journal_title：Biology direct

authors： Vianello A,Passamonti S

更新日期：2016-02-09 00:00:00

abstract：BACKGROUND:In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natur...

journal_title：Biology direct

authors： Singh S,Singh H,Tuknait A,Chaudhary K,Singh B,Kumaran S,Raghava GP

更新日期：2015-12-21 00:00:00

abstract：:In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a polynucleotide gene and a polypeptide processive polymerase) with simultaneous replication and translation and i...

journal_title：Biology direct

authors： Altstein AD

更新日期：2015-11-26 00:00:00

abstract：BACKGROUND:The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (...

journal_title：Biology direct

authors： Beiles A,Raz S,Ben-Abu Y,Nevo E

更新日期：2015-10-14 00:00:00

abstract：BACKGROUND:The N-end rule pathway is a part of the ubiquitin-dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-z...

journal_title：Biology direct

authors： Kaur G,Subramanian S

更新日期：2015-07-17 00:00:00

abstract：:Plant viruses of the recently recognized family Amalgaviridae have monopartite double-stranded (ds) RNA genomes and encode two proteins: an RNA-dependent RNA polymerase (RdRp) and a putative capsid protein (CP). Whereas the RdRp of amalgaviruses has been found to be most closely related to the RdRps of dsRNA viruses o...

journal_title：Biology direct

authors： Krupovic M,Dolja VV,Koonin EV

更新日期：2015-03-29 00:00:00

abstract：BACKGROUND:Telocytes (TCs) is an interstitial cell with extremely long and thin telopodes (Tps) with thin segments (podomers) and dilations (podoms) to interact with neighboring cells. TCs have been found in different organs, while there is still a lack of TCs-specific biomarkers to distinguish TCs from the other cells...

journal_title：Biology direct

authors： Wang J,Ye L,Jin M,Wang X

更新日期：2015-03-11 00:00:00

abstract：:All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first ...

journal_title：Biology direct

authors： Lombard J

更新日期：2014-12-19 00:00:00

abstract：BACKGROUND:Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population d...

journal_title：Biology direct

authors： White ER,Nagy JD,Gruber SH

更新日期：2014-11-18 00:00:00

abstract：BACKGROUND:A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions ass...

journal_title：Biology direct

authors： Poliakov E,Koonin EV,Rogozin IB

更新日期：2014-07-10 00:00:00

abstract：BACKGROUND:The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The ...

journal_title：Biology direct

authors： Berezovskaya FS,Wolf YI,Koonin EV,Karev GP

更新日期：2014-07-02 00:00:00

abstract：BACKGROUND:H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homolo...

journal_title：Biology direct

authors： Zhou H,Gao S,Nguyen NN,Fan M,Jin J,Liu B,Zhao L,Xiong G,Tan M,Li S,Wong L

更新日期：2014-04-08 00:00:00

abstract：:LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are capable of synthesizing DNA on their own RNA templates by harnessing reverse transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their RT are found to globally influence gene expression profiles, differentiati...

journal_title：Biology direct

authors： Belan E

更新日期：2013-09-13 00:00:00

abstract：BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...

journal_title：Biology direct

authors： Safro M,Klipcan L

更新日期：2013-07-08 00:00:00

abstract：BACKGROUND:A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS:The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a ...

journal_title：Biology direct

authors： Podar M,Makarova KS,Graham DE,Wolf YI,Koonin EV,Reysenbach AL

更新日期：2013-04-22 00:00:00

abstract：:tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified th...

journal_title：Biology direct

authors： Loss-Morais G,Waterhouse PM,Margis R

更新日期：2013-02-12 00:00:00

abstract：BACKGROUND:Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive families or families of repeats. Recently, we proposed that families of TEs originate in small populati...

journal_title：Biology direct

authors： Jurka J,Bao W,Kojima KK,Kohany O,Yurka MG

更新日期：2012-10-25 00:00:00

abstract：BACKGROUND:Recent studies suggest that gene expression profiles are a promising alternative for clinical cancer classification. One major problem in applying DNA microarrays for classification is the dimension of obtained data sets. In this paper we propose a multiclass gene selection method based on Partial Least Squa...

journal_title：Biology direct

authors： Student S,Fujarewicz K

更新日期：2012-10-02 00:00:00

abstract：BACKGROUND:The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...

journal_title：Biology direct

authors： de Crécy-Lagard V,Forouhar F,Brochier-Armanet C,Tong L,Hunt JF

更新日期：2012-09-26 00:00:00

abstract：BACKGROUND:The overwhelming majority of animal species exhibit bilateral symmetry. However, the precise evolutionary importance of bilateral symmetry is unknown, although elements of the understanding of the phenomenon have been present within the scientific community for decades. PRESENTATION OF THE HYPOTHESIS:Here w...

journal_title：Biology direct

authors： Holló G,Novák M

更新日期：2012-07-12 00:00:00

abstract：BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific...

journal_title：Biology direct

authors： Boratyn GM,Schäffer AA,Agarwala R,Altschul SF,Lipman DJ,Madden TL

更新日期：2012-04-17 00:00:00