The Dictyostelium genome encodes numerous RasGEFs with multiple biological roles.

abstract：BACKGROUND:The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities,...

journal_title：Genome biology

authors： Tarallo R,Giurato G,Bruno G,Ravo M,Rizzo F,Salvati A,Ricciardi L,Marchese G,Cordella A,Rocco T,Gigantino V,Pierri B,Cimmino G,Milanesi L,Ambrosino C,Nyman TA,Nassa G,Weisz A

更新日期：2017-10-06 00:00:00

abstract：:We assess five years of usage of the major genome-wide collections of mutants from Saccharomyces cerevisiae: single deletion mutants, double mutants conferring 'synthetic' lethality and the 'TRIPLES' collection of mutants obtained by random transposon insertion. Over 100 experimental conditions have been tested and mo...

journal_title：Genome biology

authors： Scherens B,Goffeau A

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:The H subunit of the purple bacterial photosynthetic reaction center (PRC-H) is important for the assembly of the photosynthetic reaction center and appears to regulate electron transfer during the reduction of the secondary quinone. It contains a distinct cytoplasmic beta-barrel domain whose fold has no clo...

journal_title：Genome biology

authors： Anantharaman V,Aravind L

更新日期：2002-10-14 00:00:00

abstract：BACKGROUND:Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacte...

journal_title：Genome biology

authors： Woodhams DC,Bletz MC,Becker CG,Bender HA,Buitrago-Rosas D,Diebboll H,Huynh R,Kearns PJ,Kueneman J,Kurosawa E,LaBumbard BC,Lyons C,McNally K,Schliep K,Shankar N,Tokash-Peters AG,Vences M,Whetstone R

更新日期：2020-02-03 00:00:00

abstract：:Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a ma...

journal_title：Genome biology

authors： Adamson SI,Zhan L,Graveley BR

更新日期：2018-06-01 00:00:00

abstract：BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...

journal_title：Genome biology

authors： Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y

更新日期：2021-01-04 00:00:00

abstract：BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

journal_title：Genome biology

authors： Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

更新日期：2020-03-17 00:00:00

abstract：BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

journal_title：Genome biology

authors： Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...

journal_title：Genome biology

authors： Tamames J,Moya A,Valencia A

更新日期：2007-01-01 00:00:00

abstract：:Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...

journal_title：Genome biology

authors： Xing S,Chen K,Zhu H,Zhang R,Zhang H,Li B,Gao C

更新日期：2020-09-03 00:00:00

abstract：:The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome. ...

journal_title：Genome biology

authors： Eakin GS,Hadjantonakis AK

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Previous methods employed for the identification of synergistic transcription factors (TFs) are based on either TF enrichment from co-regulated genes or phylogenetic footprinting. Despite the success of these methods, both have limitations. RESULTS:We propose a new strategy to identify synergistic TFs by fu...

journal_title：Genome biology

authors： Hu Z,Hu B,Collins JF

更新日期：2007-01-01 00:00:00

abstract：:A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...

journal_title：Genome biology

authors： Iwanicki MP,Brugge JS

更新日期：2009-01-01 00:00:00

abstract：:As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold ...

journal_title：Genome biology

authors： Langmead B,Schatz MC,Lin J,Pop M,Salzberg SL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and expres...

journal_title：Genome biology

authors： Reichwald K,Lauber C,Nanda I,Kirschner J,Hartmann N,Schories S,Gausmann U,Taudien S,Schilhabel MB,Szafranski K,Glöckner G,Schmid M,Cellerino A,Schartl M,Englert C,Platzer M

更新日期：2009-02-11 00:00:00

abstract：BACKGROUND:Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserve...

journal_title：Genome biology

authors： Milde S,Hemmrich G,Anton-Erxleben F,Khalturin K,Wittlieb J,Bosch TC

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...

journal_title：Genome biology

authors： Huang M,Ding S,Wang H,Zhu X

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence element...

journal_title：Genome biology

authors： Gama-Carvalho M,Barbosa-Morais NL,Brodsky AS,Silver PA,Carmo-Fonseca M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

journal_title：Genome biology

authors： Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

更新日期：2013-06-25 00:00:00

abstract：:The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

journal_title：Genome biology

authors： van der Graaff E,Laux T,Rensing SA

更新日期：2009-01-01 00:00:00

abstract：:The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics. ...

journal_title：Genome biology

authors： Soltis DE,Albert VA,Leebens-Mack J,Palmer JD,Wing RA,dePamphilis CW,Ma H,Carlson JE,Altman N,Kim S,Wall PK,Zuccolo A,Soltis PS

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Gene duplication followed by divergence is one of the main sources of metabolic versatility. The patchwork and stepwise models of metabolic evolution help us to understand these processes, but their assumptions are relatively simplistic. We used a network-based approach to determine the influence of metaboli...

journal_title：Genome biology

authors： Díaz-Mejía JJ,Pérez-Rueda E,Segovia L

更新日期：2007-01-01 00:00:00

abstract：:Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...

journal_title：Genome biology

authors： Davidson NM,Hawkins ADK,Oshlack A

更新日期：2017-08-04 00:00:00

abstract：BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

journal_title：Genome biology

authors： Henry CS,Zinner JF,Cohoon MP,Stevens RL

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Protein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally ...

journal_title：Genome biology

authors： Triant DA,Pearson WR

更新日期：2015-05-15 00:00:00

abstract：:mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available ...

journal_title：Genome biology

authors： Jiménez JL,Hegemann B,Hutchins JR,Peters JM,Durbin R

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:The human genome contains "dark" gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these gene regions that may be relevant to human disease. Here, we identify regions with few mappable reads ...

journal_title：Genome biology

authors： Ebbert MTW,Jensen TD,Jansen-West K,Sens JP,Reddy JS,Ridge PG,Kauwe JSK,Belzil V,Pregent L,Carrasquillo MM,Keene D,Larson E,Crane P,Asmann YW,Ertekin-Taner N,Younkin SG,Ross OA,Rademakers R,Petrucelli L,Fryer JD

更新日期：2019-05-20 00:00:00

abstract：:Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...

journal_title：Genome biology

authors： Yang S,Corbett SE,Koga Y,Wang Z,Johnson WE,Yajima M,Campbell JD

更新日期：2020-03-05 00:00:00

abstract：BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signat...

journal_title：Genome biology

authors： Li Z,Wang M,Lin K,Xie Y,Guo J,Ye L,Zhuang Y,Teng W,Ran X,Tong Y,Xue Y,Zhang W,Zhang Y

更新日期：2019-07-15 00:00:00

abstract：:The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...

journal_title：Genome biology

authors： Kelley ST,Gilbert JA

更新日期：2013-02-28 00:00:00