656 results match your criteria Biology direct[Journal]


Long non-coding RNA LINC00426 contributes to doxorubicin resistance by sponging miR-4319 in osteosarcoma.

Biol Direct 2020 Jul 3;15(1):11. Epub 2020 Jul 3.

Department of Orthopaedic Trauma, Trauma Center of Fujian, The First Affiliated Hospital of Fujian Medical University, No.20, Chazhong Road, Taijiang District, Fuzhou, 350005, Fujian, China.

Background: LINC00426 is a newly identified long non-coding RNA (lncRNA) with unacknowledged biological roles. Here we set out to characterize the expression status of LINC00426 in osteosarcoma and understand its mechanistic involvement in incidence of doxorubicin (Dox) resistance.

Methods: The relative expression of LINC00426 and miR-4319 was determined by real-time PCR. Read More

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http://dx.doi.org/10.1186/s13062-020-00265-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333256PMC

Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling.

Biol Direct 2020 Jun 15;15(1):10. Epub 2020 Jun 15.

China National Center for Bioinformation, Beijing, 100101, China.

Background: Glioma is one of the most common malignant brain tumors and exhibits low resection rate and high recurrence risk. Although a large number of glioma studies powered by high-throughput sequencing technologies have led to massive multi-omics datasets, there lacks of comprehensive integration of glioma datasets for uncovering candidate biomarker genes.

Results: In this study, we collected a large-scale assemble of multi-omics multi-cohort datasets from worldwide public resources, involving a total of 16,939 samples across 19 independent studies. Read More

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http://dx.doi.org/10.1186/s13062-020-00264-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294636PMC

Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells.

Authors:
Andrew Bateman

Biol Direct 2020 Apr 28;15(1). Epub 2020 Apr 28.

Division of Experimental Medicine, Department of Medicine, McGill University, Glen Site Pavilion E, 1001 Boulevard Decarie, Montreal, Quebec, H4A 3J1, Canada.

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. Read More

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http://dx.doi.org/10.1186/s13062-020-00260-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187495PMC

Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins.

Biol Direct 2020 Apr 28;15(1). Epub 2020 Apr 28.

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.

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 import into the forming nucleus remains an open question.

Results: Here, we demonstrate that functional NLSs may be integrated in the nucleotide-binding domains of both eukaryotic and prokaryotic proteins and may coevolve with these domains. Read More

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http://dx.doi.org/10.1186/s13062-020-00263-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189692PMC

The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer?

Authors:
Mario Mencía

Biol Direct 2020 Apr 21;15(1). Epub 2020 Apr 21.

Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid - Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain.

The archaea-bacteria lipid divide is one of the big evolutionary enigmas concerning these two domains of life. In short, bacterial membranes are made of fatty-acid esters whereas archaeal ones contain isoprenoid ethers, though at present we do not have a good understanding on why they evolved differently. The lateral proton transfer mode of energy transduction in membranes posits that protons utilize the solvation layer of the membrane interface as the main route between proton pumps and ATPases, avoiding dissipation of energy to the bulk phase. Read More

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http://dx.doi.org/10.1186/s13062-020-00262-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171761PMC

Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status.

Biol Direct 2020 03 4;15(1). Epub 2020 Mar 4.

Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.

Background: Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed.

Methods: We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Read More

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http://dx.doi.org/10.1186/s13062-020-0258-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057466PMC
March 2020
4.658 Impact Factor

More support for Earth's massive microbiome.

Biol Direct 2020 03 4;15(1). Epub 2020 Mar 4.

Rush University Medical Center, Chicago, Illinois, 60612, USA.

Until recently, our planet was thought to be home to ~ 10 species, largely belonging to plants and animals. Despite being the most abundant organisms on Earth, the contribution of microbial life to global biodiversity has been greatly underestimated and, in some cases, completely overlooked. Using a compilation of data known as the Global Prokaryotic Census (GPC), it was recently claimed that there are ~ 10 extant bacterial and archaeal taxa [1], an estimate that is orders of magnitude lower than predictions for global microbial biodiversity based on the lognormal model of biodiversity and diversity-abundance scaling laws [2]. Read More

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http://dx.doi.org/10.1186/s13062-020-00261-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7055056PMC

Predictability of drug-induced liver injury by machine learning.

Biol Direct 2020 02 13;15(1). Epub 2020 Feb 13.

Fondazione Bruno Kessler, Via Sommarive 18, Trento, 38123, Italy.

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 group proposed the CMap Drug Safety challenge focusing on DILI prediction. Read More

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http://dx.doi.org/10.1186/s13062-020-0259-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7020573PMC
February 2020

Model-based exploration of the impact of glucose metabolism on the estrous cycle dynamics in dairy cows.

Biol Direct 2020 01 15;15(1). Epub 2020 Jan 15.

Computational Biology Unit, University of Bergen, Department of Informatics, Thormøhlensgate 55, Bergen, 5008, Norway.

Background: Nutrition plays a crucial role in regulating reproductive hormones and follicular development in cattle. This is visible particularly during the time of negative energy balance at the onset of milk production after calving. Here, elongated periods of anovulation have been observed, resulting from alterations in luteinizing hormone concentrations, likely caused by lower glucose and insulin concentrations in the blood. Read More

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http://dx.doi.org/10.1186/s13062-019-0256-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6964039PMC
January 2020

Diverse approaches to predicting drug-induced liver injury using gene-expression profiles.

Biol Direct 2020 01 15;15(1). Epub 2020 Jan 15.

Department of Biology, Brigham Young University, Provo, UT, USA.

Background: Drug-induced liver injury (DILI) is a serious concern during drug development and the treatment of human disease. The ability to accurately predict DILI risk could yield significant improvements in drug attrition rates during drug development, in drug withdrawal rates, and in treatment outcomes. In this paper, we outline our approach to predicting DILI risk using gene-expression data from Build 02 of the Connectivity Map (CMap) as part of the 2018 Critical Assessment of Massive Data Analysis CMap Drug Safety Challenge. Read More

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http://dx.doi.org/10.1186/s13062-019-0257-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961287PMC
January 2020

Correction to: The role of synthetic biology in climate change mitigation.

Authors:
Charles DeLisi

Biol Direct 2019 Nov 29;14(1):24. Epub 2019 Nov 29.

Department of Biomedical Engineering, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA.

After publication of this article [1], the author brought to our attention that there are some errors in the article. Read More

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http://dx.doi.org/10.1186/s13062-019-0254-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883657PMC
November 2019

Differentially expressed tRFs in CD5 positive relapsed & refractory diffuse large B cell lymphoma and the bioinformatic analysis for their potential clinical use.

Biol Direct 2019 11 27;14(1):23. Epub 2019 Nov 27.

Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong University, No.324, Jingwu Road, Jinan, Shandong, 250021, People's Republic of China.

Background: Patients diagnosed as diffuse large B cell lymphoma (DLBCL) with CD5 positive normally have a worse outcome and poorly respond to the regulatory treatment strategy.

Results: We recently reported differently expressed tRFs and their potential target-genes of tRFs in patients with CD5+ R/R DLBCL. Differently expressed tRFs were detected by Illumina NextSeq instrument and the results were verified by quantitative real-time reverse transcription-PCR. Read More

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http://dx.doi.org/10.1186/s13062-019-0255-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882323PMC
November 2019

A novel framework for horizontal and vertical data integration in cancer studies with application to survival time prediction models.

Biol Direct 2019 11 21;14(1):22. Epub 2019 Nov 21.

Faculty of Mathematics and Informatics, Sofia University, "St. Kliment Ohridski", 5 James Bourchier Blvd., Sofia, 1164, Bulgaria.

Background: Recently high-throughput technologies have been massively used alongside clinical tests to study various types of cancer. Data generated in such large-scale studies are heterogeneous, of different types and formats. With lack of effective integration strategies novel models are necessary for efficient and operative data integration, where both clinical and molecular information can be effectively joined for storage, access and ease of use. Read More

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http://dx.doi.org/10.1186/s13062-019-0249-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6868770PMC
November 2019

mPies: a novel metaproteomics tool for the creation of relevant protein databases and automatized protein annotation.

Biol Direct 2019 11 14;14(1):21. Epub 2019 Nov 14.

Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.

Metaproteomics allows to decipher the structure and functionality of microbial communities. Despite its rapid development, crucial steps such as the creation of standardized protein search databases and reliable protein annotation remain challenging. To overcome those critical steps, we developed a new program named mPies (metaProteomics in environmental sciences). Read More

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http://dx.doi.org/10.1186/s13062-019-0253-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854712PMC
November 2019

Environmental metagenome classification for constructing a microbiome fingerprint.

Biol Direct 2019 11 13;14(1):20. Epub 2019 Nov 13.

Institute of Informatics, Silesian University of Technology, Gliwice, Poland.

Background: Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Read More

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http://dx.doi.org/10.1186/s13062-019-0251-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854650PMC
November 2019

Fingerprinting cities: differentiating subway microbiome functionality.

Biol Direct 2019 10 30;14(1):19. Epub 2019 Oct 30.

Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08873, USA.

Background: Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project participants collected samples from subway surfaces in different cities and performed metagenomic sequencing. Read More

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http://dx.doi.org/10.1186/s13062-019-0252-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822482PMC
October 2019
1 Read

Retrotransposon gag-like 1 (RTL1) and the molecular evolution of self-targeting imprinted microRNAs.

Biol Direct 2019 10 22;14(1):18. Epub 2019 Oct 22.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.

Background: Transcription of the antisense strand of RTL1 produces a sense mRNA that is targeted for degradation by antisense microRNAs transcribed from the sense strand. Translation of the mRNA produces a retrotransposon-derived protein that is implicated in placental development. The sense and antisense transcripts are oppositely imprinted: sense mRNAs are expressed from the paternally-derived chromosome, antisense microRNAs from the maternally-derived chromosome. Read More

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http://dx.doi.org/10.1186/s13062-019-0250-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6805670PMC
October 2019

Gene connectivity and enzyme evolution in the human metabolic network.

Biol Direct 2019 09 3;14(1):17. Epub 2019 Sep 3.

Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain.

Background: Determining the factors involved in the likelihood of a gene being under adaptive selection is still a challenging goal in Evolutionary Biology. Here, we perform an evolutionary analysis of the human metabolic genes to explore the associations between network structure and the presence and strength of natural selection in the genes whose products are involved in metabolism. Purifying and positive selection are estimated at interspecific (among mammals) and intraspecific (among human populations) levels, and the connections between enzymatic reactions are differentiated between incoming (in-degree) and outgoing (out-degree) links. Read More

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http://dx.doi.org/10.1186/s13062-019-0248-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724310PMC
September 2019
1 Read

Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients.

Biol Direct 2019 08 23;14(1):16. Epub 2019 Aug 23.

Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, USA.

Background: Neuroblastoma is one of the most common types of pediatric cancer. In current neuroblastoma prognosis, patients can be stratified into high- and low-risk groups. Generally, more than 90% of the patients in the low-risk group will survive, while less than 50% for those with the high-risk disease will survive. Read More

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http://dx.doi.org/10.1186/s13062-019-0244-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706887PMC
August 2019
1 Read

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples.

Biol Direct 2019 08 20;14(1):15. Epub 2019 Aug 20.

Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013, Sevilla, Spain.

Background: The availability of hundreds of city microbiome profiles allows the development of increasingly accurate predictors of the origin of a sample based on its microbiota composition. Typical microbiome studies involve the analysis of bacterial abundance profiles.

Results: Here we use a transformation of the conventional bacterial strain or gene abundance profiles to functional profiles that account for bacterial metabolism and other cell functionalities. Read More

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http://dx.doi.org/10.1186/s13062-019-0246-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701120PMC

The role of synthetic biology in climate change mitigation.

Authors:
Charles DeLisi

Biol Direct 2019 08 20;14(1):14. Epub 2019 Aug 20.

Department of Biomedical Engineering, Boston University, 24 Cummington Mall, Boston, MA, 02215, USA.

There is growing agreement that the aim of United Nations Framework Convention on Climate Change, which is to avoid dangerous anthropogenic interference with the climate system, is not likely to be met without inclusion of methods to physically remove atmospheric carbon. A number of approaches have been suggested, but the community appears to be silent on the potential of one of the most revolutionary technologies of the current century, systems and synthetic biology (SSB). The potential of SSB to modulate the fast carbon cycle, and thereby mitigate climate change is in itself enormous, but if the history of genomics is any measure, it is also reasonable to expect sizeable economic returns on any investment. Read More

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http://dx.doi.org/10.1186/s13062-019-0247-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6700980PMC

Application of machine learning techniques for creating urban microbial fingerprints.

Biol Direct 2019 08 16;14(1):13. Epub 2019 Aug 16.

APC Microbiome Ireland, University College Cork, Cork, Ireland.

Background: Research has found that human associated microbial communities play a role in homeostasis and the disruption of these communities may be important in an array of medical conditions. However outside of the human body many of these communities remain poorly studied. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is characterizing the microbiomes of urban environments with the aim to improve design of mass transit systems. Read More

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http://dx.doi.org/10.1186/s13062-019-0245-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697990PMC

Massive metagenomic data analysis using abundance-based machine learning.

Biol Direct 2019 08 1;14(1):12. Epub 2019 Aug 1.

Program in Bioinformatics and Computational Biology, Saint Louis University, Saint Louis, MO, 63103, USA.

Background: Metagenomics is the application of modern genomic techniques to investigate the members of a microbial community directly in their natural environments and is widely used in many studies to survey the communities of microbial organisms that live in diverse ecosystems. In order to understand the metagenomic profile of one of the densest interaction spaces for millions of people, the public transit system, the MetaSUB international Consortium has collected and sequenced metagenomes from subways of different cities across the world. In collaboration with CAMDA, MetaSUB has made the metagenomic samples from these cities available for an open challenge of data analysis including, but not limited in scope to, the identification of unknown samples. Read More

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http://dx.doi.org/10.1186/s13062-019-0242-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6676585PMC

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data.

Biol Direct 2019 07 24;14(1):11. Epub 2019 Jul 24.

Department of Biostatistics, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.

Background: Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures of microbes. Illumina MiSeq sequencing data was provided from 12 cities in 7 different countries as part of the 2018 CAMDA "MetaSUB Forensic Challenge", including also samples from three mystery sets. We used appropriate machine learning techniques on this massive dataset to effectively identify the geographical provenance of "mystery" samples. Read More

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http://dx.doi.org/10.1186/s13062-019-0243-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657067PMC

Elusive data underlying debate at the prokaryote-eukaryote divide.

Biol Direct 2018 10 3;13(1):21. Epub 2018 Oct 3.

Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.

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 bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. Read More

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http://dx.doi.org/10.1186/s13062-018-0221-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6888934PMC
October 2018
1 Read

Associating expression and genomic data using co-occurrence measures.

Biol Direct 2019 05 9;14(1):10. Epub 2019 May 9.

Department of Plant Biotechnology and Bioinformatics, Ghent University - Imec, Technologiepark-Zwijnaarde 126, 9052, Ghent, Belgium.

Recent technological evolutions have led to an exponential increase in data in all the omics fields. It is expected that integration of these different data sources, will drastically enhance our knowledge of the biological mechanisms behind genomic diseases such as cancer. However, the integration of different omics data still remains a challenge. Read More

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http://dx.doi.org/10.1186/s13062-019-0240-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507230PMC
May 2019
2 Reads

MDA19, a novel CB2 agonist, inhibits hepatocellular carcinoma partly through inactivation of AKT signaling pathway.

Biol Direct 2019 05 3;14(1). Epub 2019 May 3.

Department of Osteology, Longyan First Hospital Affiliated to Fujian Medical University, 105 Jiuyi North Road, Longyan, 364000, Fujian, People's Republic of China.

Background: CB (cannabinoid receptor 2) agonists have been shown to exert anti-tumor activities in different tumor types. However, there is no study exploring the role of MDA19 (a novel CB agonist) in tumors. In this study we aimed to investigate the effects of MDA19 treatment on HCC cell lines, Hep3B and HepG2 and determine the relevant mechanisms. Read More

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http://dx.doi.org/10.1186/s13062-019-0241-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500002PMC
May 2019
3 Reads

Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies.

Biol Direct 2019 04 29;14(1). Epub 2019 Apr 29.

Department of Computer Engineering, Ajou University, Suwon, 16499, South Korea.

Background: Integrating the rich information from multi-omics data has been a popular approach to survival prediction and bio-marker identification for several cancer studies. To facilitate the integrative analysis of multiple genomic profiles, several studies have suggested utilizing pathway information rather than using individual genomic profiles.

Methods: We have recently proposed an integrative directed random walk-based method utilizing pathway information (iDRW) for more robust and effective genomic feature extraction. Read More

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http://dx.doi.org/10.1186/s13062-019-0239-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6489180PMC
April 2019
2 Reads

Revealing the dominant long noncoding RNAs responding to the infection with Colletotrichum gloeosporioides in Hevea brasiliensis.

Biol Direct 2019 04 15;14(1). Epub 2019 Apr 15.

Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.

Background: Rubber tree (Hevea brasiliensis) acts as an important tropic economic crop and rubber tree anthracnose, mainly caused by Colletotrichum gloeosporioides, is one of the most common fungal disease, which leads to serious loss of rubber production. Therefore, the investigation on disease resistance is of great worldwide significance. In the past decades, substantial progress has been made on coding gene families related with plant disease resistance. Read More

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http://dx.doi.org/10.1186/s13062-019-0235-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466799PMC
April 2019
1 Read
4.658 Impact Factor

A high-performance approach for predicting donor splice sites based on short window size and imbalanced large samples.

Biol Direct 2019 04 11;14(1). Epub 2019 Apr 11.

Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha, 410128, Hunan, China.

Background: Splice sites prediction has been a long-standing problem in bioinformatics. Although many computational approaches developed for splice site prediction have achieved satisfactory accuracy, further improvement in predictive accuracy is significant, for it is contributing to predict gene structure more accurately. Determining a proper window size before prediction is necessary. Read More

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http://dx.doi.org/10.1186/s13062-019-0236-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460831PMC
April 2019
4 Reads

Genome and pan-genome analysis to classify emerging bacteria.

Biol Direct 2019 02 26;14(1). Epub 2019 Feb 26.

Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.

Background: In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. Read More

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http://dx.doi.org/10.1186/s13062-019-0234-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390601PMC
February 2019
7 Reads

Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients' survival time.

Biol Direct 2019 02 13;14(1). Epub 2019 Feb 13.

Department of Medicine, Indiana University School of Medicine, Indianapolis, USA.

Background: More than 90% of neuroblastoma patients are cured in the low-risk group while only less than 50% for those with high-risk disease can be cured. Since the high-risk patients still have poor outcomes, we need more accurate stratification to establish an individualized precise treatment plan for the patients to improve the long-term survival rate.

Results: We focus on extracting features and providing a workflow to improve survival prediction for neuroblastoma patients. Read More

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http://dx.doi.org/10.1186/s13062-018-0229-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375203PMC
February 2019
23 Reads

From tumors to species: a SCANDAL hypothesis.

Biol Direct 2019 01 23;14(1). Epub 2019 Jan 23.

Institute for Information Transmission Problems, Bolshoy Karetniy Pereulok 19/1, Moscow, Russian Federation, 127051.

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 descendants of these tumors. Read More

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http://dx.doi.org/10.1186/s13062-019-0233-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343361PMC
January 2019
8 Reads

Exon skipping-rich transcriptomes of animals reflect the significance of exon-shuffling in metazoan proteome evolution.

Authors:
Laszlo Patthy

Biol Direct 2019 01 16;14(1). Epub 2019 Jan 16.

Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary.

ᅟ: Animals are known to have higher rates of exon skipping than other eukaryotes. In a recent study, Grau-Bové et al. (Genome Biology 19:135, 2018) have used RNA-seq data across 65 eukaryotic species to investigate when and how this high prevalence of exon skipping evolved. Read More

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http://dx.doi.org/10.1186/s13062-019-0231-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335736PMC
January 2019
2 Reads

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions.

Biol Direct 2019 01 15;14(1). Epub 2019 Jan 15.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.

Background: Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of residues at the interface of protein-protein complexes in conferring stability and specificity to the complex. Interface residues in a protein are well known for their interactions with sidechain and main chain atoms with the interacting protein. Read More

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http://dx.doi.org/10.1186/s13062-019-0232-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334431PMC
January 2019
3 Reads

Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.

Biol Direct 2018 11 29;13(1):26. Epub 2018 Nov 29.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.

A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mitochondrion endowed eukaryotic cells with energetic superiority over prokaryotes. The former point has been addressed previously, with no resultant changes in the conclusions, and the latter point remains inconsistent with multiple lines of empirical data. Read More

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http://dx.doi.org/10.1186/s13062-018-0228-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822690PMC
November 2018
2 Reads

Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications.

Biol Direct 2018 10 17;13(1):23. Epub 2018 Oct 17.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.

Background: It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Read More

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http://dx.doi.org/10.1186/s13062-018-0226-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545626PMC
October 2018
4 Reads
4.658 Impact Factor

Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.

Biol Direct 2018 10 12;13(1):22. Epub 2018 Oct 12.

Department Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria.

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 metagenome samples. Read More

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http://dx.doi.org/10.1186/s13062-018-0225-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889603PMC
October 2018
4 Reads

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.

Biol Direct 2018 10 26;13(1):24. Epub 2018 Oct 26.

Department of Biological Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel.

Background: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.

Results: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent ("detox"). Read More

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http://dx.doi.org/10.1186/s13062-018-0224-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889200PMC
October 2018
2 Reads

Molecular mechanisms of the juvenile form of Batten disease: important role of MAPK signaling pathways (ERK1/ERK2, JNK and p38) in pathogenesis of the malady.

Biol Direct 2018 09 25;13(1):19. Epub 2018 Sep 25.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, GSP-7, 117997, Moscow, Russia.

Background: Mutations in the CLN3 gene lead to so far an incurable juvenile-onset neuronal ceroid lipofuscinosis (JNCL) or Batten disease that starts at the age of 4-6 years with a progressive retinopathy leading to blindness. Motor disturbances, epilepsy and dementia manifest during several following years. Most JNCL patients carry the same 1. Read More

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http://dx.doi.org/10.1186/s13062-018-0212-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889328PMC
September 2018
7 Reads

Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies.

Biol Direct 2018 11 23;13(1):25. Epub 2018 Nov 23.

Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA.

Background: Reproducing cell processes using an in silico system is an essential tool for understanding the underlying mechanisms and emergent properties of this extraordinary complex biological machine. However, computational models are seldom applied in the field of intracellular trafficking. In a cell, numerous molecular interactions occur on the surface or in the interior of membrane-bound compartments that continually change position and undergo dynamic processes of fusion and fission. Read More

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http://dx.doi.org/10.1186/s13062-018-0227-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883406PMC
November 2018
4 Reads

Predicting clinical outcomes in neuroblastoma with genomic data integration.

Biol Direct 2018 09 27;13(1):20. Epub 2018 Sep 27.

Department of Computer Engineering, Antalya Bilim University, Antalya, Turkey.

Background: Neuroblastoma is a heterogeneous disease with diverse clinical outcomes. Current risk group models require improvement as patients within the same risk group can still show variable prognosis. Recently collected genome-wide datasets provide opportunities to infer neuroblastoma subtypes in a more unified way. Read More

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http://dx.doi.org/10.1186/s13062-018-0223-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889397PMC
September 2018
3 Reads

Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve.

Biol Direct 2018 12 14;13(1):27. Epub 2018 Dec 14.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

Background: Genetic parasites are ubiquitous satellites of cellular life forms most of which host a variety of mobile genetic elements including transposons, plasmids and viruses. Theoretical considerations and computer simulations suggest that emergence of genetic parasites is intrinsic to evolving replicator systems.

Results: Using methods of bifurcation analysis, we investigated the stability of simple models of replicator-parasite coevolution in a well-mixed environment. Read More

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http://dx.doi.org/10.1186/s13062-018-0230-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6822691PMC
December 2018
4 Reads

Is pre-Darwinian evolution plausible?

Authors:
Marc Tessera

Biol Direct 2018 09 21;13(1):18. Epub 2018 Sep 21.

, Meudon, France.

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 of the first systems capable of Darwinian evolution. The researchers' responses to eight crucial questions are reviewed. Read More

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http://dx.doi.org/10.1186/s13062-018-0216-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151046PMC
September 2018
3 Reads

Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival.

Biol Direct 2018 09 20;13(1):17. Epub 2018 Sep 20.

Institute of Informatics, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland.

Background: Modern experimental techniques deliver data sets containing profiles of tens of thousands of potential molecular and genetic markers that can be used to improve medical diagnostics. Previous studies performed with three different experimental methods for the same set of neuroblastoma patients create opportunity to examine whether augmenting gene expression profiles with information on copy number variation can lead to improved predictions of patients survival. We propose methodology based on comprehensive cross-validation protocol, that includes feature selection within cross-validation loop and classification using machine learning. Read More

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http://dx.doi.org/10.1186/s13062-018-0222-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148774PMC
September 2018
3 Reads

MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms.

Biol Direct 2018 08 22;13(1):15. Epub 2018 Aug 22.

Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Background: Many methods have been developed for metagenomic sequence classification, and most of them depend heavily on genome sequences of the known organisms. A large portion of sequencing sequences may be classified as unknown, which greatly impairs our understanding of the whole sample.

Result: Here we present MetaBinG2, a fast method for metagenomic sequence classification, especially for samples with a large number of unknown organisms. Read More

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http://dx.doi.org/10.1186/s13062-018-0220-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104016PMC
August 2018
6 Reads

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome.

Biol Direct 2018 08 22;13(1):16. Epub 2018 Aug 22.

Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013, Sevilla, Spain.

Background: Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40-50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used to demonstrate that the network regulating stress signaling by the c-Jun N-terminal kinase pathway played a crucial role in survival of patients with neuroblastoma irrespective of their MYCN amplification status. This demonstrates the enormous potential of computational models of biological modules for the discovery of underlying molecular mechanisms of diseases. Read More

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http://dx.doi.org/10.1186/s13062-018-0219-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106876PMC
August 2018
7 Reads

Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients.

Biol Direct 2018 07 16;13(1):14. Epub 2018 Jul 16.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, Nobels vag 12A, Karolinska Institutet, 171 77, Stockholm, PO, Sweden.

Background: Neuroblastoma is the most common pediatric malignancy with heterogeneous clinical behaviors, ranging from spontaneous regression to aggressive progression. Many studies have identified aberrations related to the pathogenesis and prognosis, broadly classifying neuroblastoma patients into high- and low-risk groups, but predicting tumor progression and clinical management of high-risk patients remains a big challenge.

Results: We integrate gene-level expression, array-based comparative genomic hybridization and functional gene-interaction network of 145 neuroblastoma patients to detect potential driver genes. Read More

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http://dx.doi.org/10.1186/s13062-018-0218-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048860PMC
July 2018
7 Reads
1 Citation
4.660 Impact Factor

Modeling protein folding in vivo.

Biol Direct 2018 07 6;13(1):13. Epub 2018 Jul 6.

, McLean, USA.

A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Read More

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http://dx.doi.org/10.1186/s13062-018-0217-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035440PMC
July 2018
9 Reads

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach.

Biol Direct 2018 06 7;13(1):12. Epub 2018 Jun 7.

Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445, Luxembourg.

Background: One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients.

Results: We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Read More

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http://dx.doi.org/10.1186/s13062-018-0214-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992838PMC
June 2018
9 Reads