Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data.

abstract：BACKGROUND:Identification of genes with ascending or descending monotonic expression patterns over time or stages of stem cells is an important issue in time-series microarray data analysis. We propose a method named Monotonic Feature Selector (MFSelector) based on a concept of total discriminating error (DEtotal) to i...

journal_title：BMC genomics

authors： Wang HW,Sun HJ,Chang TY,Lo HH,Cheng WC,Tseng GC,Lin CT,Chang SJ,Pal N,Chung IF

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the de...

journal_title：BMC genomics

authors： Amgarten D,Martins LF,Lombardi KC,Antunes LP,de Souza APS,Nicastro GG,Kitajima EW,Quaggio RB,Upton C,Setubal JC,da Silva AM

更新日期：2017-05-04 00:00:00

abstract：BACKGROUND:Single Nucleotide Polymorphisms (SNPs) can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction.In order to evaluate the potential of these technologies in pea, we selected a ...

journal_title：BMC genomics

authors： Deulvot C,Charrel H,Marty A,Jacquin F,Donnadieu C,Lejeune-Hénaut I,Burstin J,Aubert G

更新日期：2010-08-11 00:00:00

abstract：BACKGROUND:Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was...

journal_title：BMC genomics

authors： Miao Y,Liu D,Li G,Li P,Xu Y,Shen Q,Zhang R

更新日期：2015-06-16 00:00:00

abstract：BACKGROUND:Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic patho...

journal_title：BMC genomics

authors： Gross R,Guzman CA,Sebaihia M,dos Santos VA,Pieper DH,Koebnik R,Lechner M,Bartels D,Buhrmester J,Choudhuri JV,Ebensen T,Gaigalat L,Herrmann S,Khachane AN,Larisch C,Link S,Linke B,Meyer F,Mormann S,Nakunst D,Rückert

更新日期：2008-09-30 00:00:00

abstract：BACKGROUND:After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers amo...

journal_title：BMC genomics

authors： Wang Z,Wang J,Pan Y,Lei T,Ge W,Wang L,Zhang L,Li Y,Zhao K,Liu T,Song X,Zhang J,Yu J,Hu J,Wang X

更新日期：2019-03-07 00:00:00

abstract：BACKGROUND:Lack of power and reproducibility are caveats of genetic association studies of common complex diseases. Indeed, the heterogeneity of disease etiology demands that causal models consider the simultaneous involvement of multiple genes. Rothman's sufficient-cause model, which is well known in epidemiology, pro...

journal_title：BMC genomics

authors： Lynn KS,Lu CH,Yang HY,Hsu WL,Pan WH

更新日期：2013-07-23 00:00:00

abstract：BACKGROUND:There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather ...

journal_title：BMC genomics

authors： Kouduka M,Matuoka A,Nishigaki K

更新日期：2006-06-02 00:00:00

abstract：BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...

journal_title：BMC genomics

authors： Li W,Carroll JS,Brown M,Liu xS

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangem...

journal_title：BMC genomics

authors： Yue F,Zhang M,Tang J

更新日期：2008-09-16 00:00:00

abstract：BACKGROUND:Genomic inversion is one type of structural variations (SVs) and is known to play an important biological role. An established problem in sequence data analysis is calling inversions from high-throughput sequence data. It is more difficult to detect inversions because they are surrounded by duplication or ot...

journal_title：BMC genomics

authors： Wu Z,Wu Y,Gao J

更新日期：2020-03-05 00:00:00

abstract：BACKGROUND:Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expre...

journal_title：BMC genomics

authors： Gheorghe M,Snoeck M,Emmerich M,Bäck T,Goeman JJ,Raz V

更新日期：2014-02-14 00:00:00

abstract：BACKGROUND:Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of sm...

journal_title：BMC genomics

authors： Fernández P,Paniego N,Lew S,Hopp HE,Heinz RA

更新日期：2003-09-30 00:00:00

abstract：BACKGROUND:Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regio...

journal_title：BMC genomics

authors： Ramos E,Levinson BT,Chasnoff S,Hughes A,Young AL,Thornton K,Li A,Vallania FL,Province M,Druley TE

更新日期：2012-12-06 00:00:00

abstract：BACKGROUND:Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilization by genetically distinct lines of P. falciparum. These differences, if identified, may provide...

journal_title：BMC genomics

authors： Apolis L,Olivas J,Srinivasan P,Kushwaha AK,Desai SA

更新日期：2019-01-16 00:00:00

abstract：BACKGROUND:DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS:To investigate the occurrence of DNA methylation changes in LTP, we undertook ...

journal_title：BMC genomics

authors： Maag JL,Kaczorowski DC,Panja D,Peters TJ,Bramham CR,Wibrand K,Dinger ME

更新日期：2017-03-23 00:00:00

abstract：BACKGROUND:Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, cl...

journal_title：BMC genomics

authors： Orsini L,Jansen M,Souche EL,Geldof S,De Meester L

更新日期：2011-06-13 00:00:00

abstract：BACKGROUND:Gene expression analysis by reverse transcription quantitative PCR (qPCR) is the most widely used method for analyzing the expression of a moderate number of genes and also for the validation of microarray results. Several issues are crucial for a successful qPCR study, particularly the selection of internal...

journal_title：BMC genomics

authors： Robledo D,Hernández-Urcera J,Cal RM,Pardo BG,Sánchez L,Martínez P,Viñas A

更新日期：2014-08-04 00:00:00

abstract：BACKGROUND:Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequenc...

journal_title：BMC genomics

authors： Kochan KJ,Amaral ME,Agarwala R,Schäffer AA,Riggs PK

更新日期：2008-11-17 00:00:00

abstract：BACKGROUND:Alpha tubulin is a fundamental component of the cytoskeleton which is responsible for cell shape and is involved in cell division, ciliary and flagellar motility and intracellular transport. Alpha tubulin gene expression varies according to the morphological changes suffered by Leishmania in its life cycle. ...

journal_title：BMC genomics

authors： Ramírez CA,Requena JM,Puerta CJ

更新日期：2013-07-06 00:00:00

abstract：BACKGROUND:Starvation not only affects the nutritional and health status of the animals, but also the microbial composition in the host's intestine. Next-generation sequencing provides a unique opportunity to explore gut microbial communities and their interactions with hosts. However, studies on gut microbiomes have b...

journal_title：BMC genomics

authors： Xia JH,Lin G,Fu GH,Wan ZY,Lee M,Wang L,Liu XJ,Yue GH

更新日期：2014-04-05 00:00:00

abstract：BACKGROUND:The Brassicaceae family is an exemplary model for studying plant polyploidy. The Brassicaceae knowledge-base includes the well-annotated Arabidopsis thaliana reference sequence; well-established evidence for three rounds of whole genome duplication (WGD); and the conservation of genomic structure, with 24 co...

journal_title：BMC genomics

authors： Kim J,Lee J,Choi JP,Park I,Yang K,Kim MK,Lee YH,Nou IS,Kim DS,Min SR,Park SU,Kim H

更新日期：2014-07-18 00:00:00

abstract：BACKGROUND:The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we inve...

journal_title：BMC genomics

authors： Arhondakis S,Frousios K,Iliopoulos CS,Pissis SP,Tischler G,Kossida S

更新日期：2011-10-17 00:00:00

abstract：BACKGROUND:Sand fly saliva plays an important role in blood feeding and Leishmania transmission as it was shown to increase parasite virulence. On the other hand, immunity to salivary components impedes the establishment of infection. Therefore, it is most desirable to gain a deeper insight into the composition of sali...

journal_title：BMC genomics

authors： Hostomská J,Volfová V,Mu J,Garfield M,Rohousová I,Volf P,Valenzuela JG,Jochim RC

更新日期：2009-06-25 00:00:00

abstract：BACKGROUND:Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Ver...

journal_title：BMC genomics

authors： Wang X,Cheng C,Zhang K,Tian Z,Xu J,Yang S,Lou Q,Li J,Chen JF

更新日期：2018-08-03 00:00:00

abstract：BACKGROUND:Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages. RESULTS:Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic se...

journal_title：BMC genomics

authors： Liu GE,Matukumalli LK,Sonstegard TS,Shade LL,Van Tassell CP

更新日期：2006-06-07 00:00:00

abstract：BACKGROUND:Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from differe...

journal_title：BMC genomics

authors： De Pittà C,Bertolucci C,Mazzotta GM,Bernante F,Rizzo G,De Nardi B,Pallavicini A,Lanfranchi G,Costa R

更新日期：2008-01-28 00:00:00

abstract：BACKGROUND:Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene tr...

journal_title：BMC genomics

authors： Gao S,Li L,Han X,Liu T,Jin P,Cai L,Xu M,Zhang T,Zhang F,Chen J,Yang J,Zhong K

更新日期：2021-01-11 00:00:00

abstract：BACKGROUND:Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth a...

journal_title：BMC genomics

authors： Li CF,Zhu Y,Yu Y,Zhao QY,Wang SJ,Wang XC,Yao MZ,Luo D,Li X,Chen L,Yang YJ

更新日期：2015-07-29 00:00:00

abstract：BACKGROUND:Fusarium verticillioides causes ear rot in maize (Zea mays L.) and accumulation of mycotoxins, that affect human and animal health. Currently, chemical and agronomic measures to control Fusarium ear rot are not very effective and selection of more resistant genotypes is a desirable strategy to reduce contami...

journal_title：BMC genomics

authors： Lanubile A,Ferrarini A,Maschietto V,Delledonne M,Marocco A,Bellin D

更新日期：2014-08-25 00:00:00