Efficient calculation of exact probability distributions of integer features on RNA secondary structures.

abstract：BACKGROUND:Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem D...

journal_title：BMC genomics

authors： Schubert M,Ginolhac A,Lindgreen S,Thompson JF,Al-Rasheid KA,Willerslev E,Krogh A,Orlando L

更新日期：2012-05-10 00:00:00

abstract：BACKGROUND:Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA typing at high resolution is challenging even with whole-genome sequencing data. RESULTS:We have d...

journal_title：BMC genomics

authors： Nariai N,Kojima K,Saito S,Mimori T,Sato Y,Kawai Y,Yamaguchi-Kabata Y,Yasuda J,Nagasaki M

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Recent studies have suggested that combinations of multiple epigenetic modifications are essential for controlling gene expression. Despite numerous computational approaches have been developed to decipher the combinatorial epigenetic patterns or "epigenetic code", none of them has explicitly addressed the r...

journal_title：BMC genomics

authors： Liu Q,Bonneville R,Li T,Jin VX

更新日期：2017-05-12 00:00:00

abstract：BACKGROUND:G protein-coupled receptors (GPCRs) are major players in cell communication, regulate a whole range of physiological functions during development and throughout adult life, are affected in numerous pathological situations, and constitute so far the largest class of drugable targets for human diseases. The co...

journal_title：BMC genomics

authors： Maurel B,Le Digarcher A,Dantec C,Journot L

更新日期：2011-05-16 00:00:00

abstract：BACKGROUND:Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have b...

journal_title：BMC genomics

authors： Tran Vdu T,Chassignet P,Sheikh S,Steyaert JM

更新日期：2012-04-12 00:00:00

abstract：BACKGROUND:Malaria is the most important parasitic disease in the world with approximately two million people dying every year, mostly due to Plasmodium falciparum infection. During its complex life cycle in the Anopheles vector and human host, the parasite requires the coordinated and modulated expression of diverse s...

journal_title：BMC genomics

authors： Bischoff E,Vaquero C

更新日期：2010-01-15 00:00:00

abstract：BACKGROUND:Cadmium (Cd) is a serious heavy metal (HM) soil pollutant. To alleviate or even eliminate HM pollution in soil, environmental-friendly methods are applied. One is that special plants are cultivated to absorb the HM in the contaminated soil. As an excellent economical plant with ornamental value and sound ada...

journal_title：BMC genomics

authors： Wang MQ,Bai ZY,Xiao YF,Li Y,Liu QL,Zhang L,Pan YZ,Jiang BB,Zhang F

更新日期：2019-11-20 00:00:00

abstract：BACKGROUND:Starches are the main storage polysaccharides in plants and are distributed widely throughout plants including seeds, roots, tubers, leaves, stems and so on. Currently, microscopic observation is one of the most important ways to investigate and analyze the structure of starches. The position, shape, and siz...

journal_title：BMC genomics

authors： Guo S,Tang J,Deng Y,Xia Q

更新日期：2010-11-02 00:00:00

abstract：BACKGROUND:On a single strand of genomic DNA the number of As is usually about equal to the number of Ts (and similarly for Gs and Cs), but deviations have been noted for transcribed regions and origins of replication. RESULTS:The mouse genome is shown to have a segmented structure defined by strand bias. Transcriptio...

journal_title：BMC genomics

authors： Evans KJ

更新日期：2008-01-14 00:00:00

abstract：BACKGROUND:Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in patients with cystic fibrosis. The bacterium survives within macrophages by interfering with endocytic trafficking and delaying the maturation of the B. cenocepacia-containing phagosome. We hypothesize that B. cenoce...

journal_title：BMC genomics

authors： Tolman JS,Valvano MA

更新日期：2012-02-09 00:00:00

abstract：BACKGROUND:Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which ...

journal_title：BMC genomics

authors： Brown CW,Sridhara V,Boutz DR,Person MD,Marcotte EM,Barrick JE,Wilke CO

更新日期：2017-04-17 00:00:00

abstract：BACKGROUND:Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strateg...

journal_title：BMC genomics

authors： Anthon C,Tafer H,Havgaard JH,Thomsen B,Hedegaard J,Seemann SE,Pundhir S,Kehr S,Bartschat S,Nielsen M,Nielsen RO,Fredholm M,Stadler PF,Gorodkin J

更新日期：2014-06-10 00:00:00

abstract：BACKGROUND:The neonatal bovine mammary fat pad (MFP) surrounding the mammary parenchyma (PAR) is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. We used bioinformatics to characterize transcriptomics differences between PAR and MFP from app...

journal_title：BMC genomics

authors： Piantoni P,Bionaz M,Graugnard DE,Daniels KM,Everts RE,Rodriguez-Zas SL,Lewin HA,Hurley HL,Akers M,Loor JJ

更新日期：2010-05-26 00:00:00

abstract：BACKGROUND:High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integrat...

journal_title：BMC genomics

authors： Hermida L,Poussin C,Stadler MB,Gubian S,Sewer A,Gaidatzis D,Hotz HR,Martin F,Belcastro V,Cano S,Peitsch MC,Hoeng J

更新日期：2013-07-29 00:00:00

abstract：BACKGROUND:Human myelopoiesis is an exciting biological model for cellular differentiation since it represents a plastic process where multipotent stem cells gradually limit their differentiation potential, generating different precursor cells which finally evolve into distinct terminally differentiated cells. This stu...

journal_title：BMC genomics

authors： Ferrari F,Bortoluzzi S,Coppe A,Basso D,Bicciato S,Zini R,Gemelli C,Danieli GA,Ferrari S

更新日期：2007-08-03 00:00:00

abstract：BACKGROUND:Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental...

journal_title：BMC genomics

authors： Dueck A,Evers M,Henz SR,Unger K,Eichner N,Merkl R,Berezikov E,Engelmann JC,Weigel D,Wenzl S,Meister G

更新日期：2016-11-02 00:00:00

abstract：BACKGROUND:The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. RESULTS:In this study, the...

journal_title：BMC genomics

authors： Zhou L,Liu Z,Dong Y,Sun X,Wu B,Yu T,Zheng Y,Yang A,Zhao Q,Zhao D

更新日期：2019-08-23 00:00:00

abstract：BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...

journal_title：BMC genomics

authors： Lie KK,Tørresen OK,Solbakken MH,Rønnestad I,Tooming-Klunderud A,Nederbragt AJ,Jentoft S,Sæle Ø

更新日期：2018-03-06 00:00:00

abstract：BACKGROUND:Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy langu...

journal_title：BMC genomics

authors： Kusuma P,Cox MP,Pierron D,Razafindrazaka H,Brucato N,Tonasso L,Suryadi HL,Letellier T,Sudoyo H,Ricaut FX

更新日期：2015-03-17 00:00:00

abstract：BACKGROUND:For their transmission, African trypanosomes rely on their blood feeding insect vector, the tsetse fly (Glossina sp.). The ingested Trypanosoma brucei parasites have to overcome a series of barriers in the tsetse fly alimentary tract to finally develop into the infective metacyclic forms in the salivary glan...

journal_title：BMC genomics

authors： Matetovici I,Caljon G,Van Den Abbeele J

更新日期：2016-11-25 00:00:00

abstract：BACKGROUND:Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed ...

journal_title：BMC genomics

authors： Santana MF,Silva JC,Batista AD,Ribeiro LE,da Silva GF,de Araújo EF,de Queiroz MV

更新日期：2012-12-22 00:00:00

abstract：BACKGROUND:Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we ...

journal_title：BMC genomics

authors： Lopdell TJ,Tiplady K,Struchalin M,Johnson TJJ,Keehan M,Sherlock R,Couldrey C,Davis SR,Snell RG,Spelman RJ,Littlejohn MD

更新日期：2017-12-15 00:00:00

abstract：BACKGROUND:Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shift...

journal_title：BMC genomics

authors： Lu Y,Boswell M,Boswell W,Salinas RY,Savage M,Reyes J,Walter S,Marks R,Gonzalez T,Medrano G,Warren WC,Schartl M,Walter RB

更新日期：2020-11-11 00:00:00

abstract：BACKGROUND:Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O'Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the soybean cyst nematode (SCN) was an ancient, endemic, pest of soybean whereas F. virguliforme caus...

journal_title：BMC genomics

authors： Srour A,Afzal AJ,Blahut-Beatty L,Hemmati N,Simmonds DH,Li W,Liu M,Town CD,Sharma H,Arelli P,Lightfoot DA

更新日期：2012-08-02 00:00:00

abstract：BACKGROUND:Salmonella Typhimurium is frequently isolated from foodborne infection cases in Hong Kong, but the lack of genome sequences has hindered in-depth epidemiological and phylogenetic studies. In this study, we sought to reconstruct the phylogenetic relationship and investigate the distribution and mutation patte...

journal_title：BMC genomics

authors： Cheng CK,Cheung MK,Nong W,Law PT,Qin J,Ling JM,Kam KM,Cheung WM,Kwan HS

更新日期：2015-09-14 00:00:00

abstract：BACKGROUND:In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective val...

journal_title：BMC genomics

authors： van Hijum SA,de Jong A,Baerends RJ,Karsens HA,Kramer NE,Larsen R,den Hengst CD,Albers CJ,Kok J,Kuipers OP

更新日期：2005-05-20 00:00:00

abstract：BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...

journal_title：BMC genomics

authors： Cao F,Chen F,Sun H,Zhang G,Chen ZH,Wu F

更新日期：2014-07-19 00:00:00

abstract：BACKGROUND:Quantitative trait locus (QTL) studies show that variation in salinity tolerance in Arctic charr and rainbow trout has a genetic basis, even though both these species have low to moderate salinity tolerance capacities. QTL were observed to localize to homologous linkage group segments within putative chromos...

journal_title：BMC genomics

authors： Norman JD,Robinson M,Glebe B,Ferguson MM,Danzmann RG

更新日期：2012-08-24 00:00:00

abstract：BACKGROUND:Despite substantial progress in mosquito genomic and genetic research, few cis-regulatory elements (CREs), DNA sequences that control gene expression, have been identified in mosquitoes or other non-model insects. Formaldehyde-assisted isolation of regulatory elements paired with DNA sequencing, FAIRE-seq, i...

journal_title：BMC genomics

authors： Behura SK,Sarro J,Li P,Mysore K,Severson DW,Emrich SJ,Duman-Scheel M

更新日期：2016-05-10 00:00:00

abstract：BACKGROUND:The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal mode...

journal_title：BMC genomics

authors： Datson NA,Morsink MC,Atanasova S,Armstrong VW,Zischler H,Schlumbohm C,Dutilh BE,Huynen MA,Waegele B,Ruepp A,de Kloet ER,Fuchs E

更新日期：2007-06-25 00:00:00