A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data. #RNAisoforms #GTEx #LongReads #Sequencing #Genomics #Bioinformatics #BMCgenomics
link.springer.com/article/10.1...

Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023. #mRNA #GenomeAnnotation #EnsemblGenes #Isoforms #BMCgenomics
link.springer.com/article/10.1...

Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress. #SingleCell #scRNAseq #PlateBasedAssay #10X #Genomics #BMCgenomics
link.springer.com/article/10.1...

Commentary: a review of technical considerations for planning an RNA-Sequencing experiment. #RNAseq #TechnicalConsidertions #ExperimentDesign #LibraryPrep #DataAnalysis #BMCgenomics 🧪🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

BestopCloud: an integrated one-stop solution for single-cell RNA sequencing data analysis. #SingleCell #scRNAseq #DataAnalysis #WebTool #OpenSource #Rshiny #BMCgenomics @NatureGenet
bmcgenomics.biomedcentral.com/articles/10....

Performance comparison of four exome capture platforms on DNBSEQ-Series high throughput sequencer. #Exome #Sequencing #Benchmarking #DNBSEQ #Genomics #BMCgenomics 🧪🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

🌟Call for Papers: Genomics of Symbiosis🌟 I am a guest editor for BMC Genomics. Looking forward to your exciting manuscripts on all types of symbiosis on earth including symbiotic fungi and their hosts! 🌿🍄 biomedcentral.com/collections/... #BMCgenomics

A closed-loop method for precise genome size estimation using HiFi reads. #GenomeSize #HiFi #LongReads #Genomics #Bioinformatics #BMCgenomics 🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data. #mtDNA #SingleCell #scRNAseq #Sequencing #Genomics #Bioinformatics #BMCgenomics
bmcgenomics.biomedcentral.com/articles/10....

High-quality, haplotype-resolved reference genomes of the Dutch warmblood horse and Friesian horse using trio binning. #HorseGenomes #TrioBinning #HaplotypeResolvedGenome #BMCgenomics
bmcgenomics.biomedcentral.com/articles/10....

MitoCOMON: whole mitochondrial DNA sequencing by primer design and long overlapping amplicon assembly. #mtDNA #MitochondrialDNA #Sequencing #PrimerDesign #AmpliconAssembly #BMCgenomics
bmcgenomics.biomedcentral.com/articles/10....

Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis. #HMW #DNAextraction #LongRead #Sequencing #StructuralVariants #BMCgenomics 🧬
bmcgenomics.biomedcentral.com/articles/10....

A scalable distributed pipeline for reference-free variants calling - BMC Genomics Background Precision medicine pipelines typically begin with variant calling to identify disease-related mutations for optimal treatment selection. Reference-free approaches assess variations in the…

A scalable distributed pipeline for reference-free variants calling. #VariantCalling #ReferenceFreeCalling #Bioinformatics #Genomics #BMCgenomics 🖥️ 🧪
bmcgenomics.biomedcentral.com/articles/10....

Image shows female stolon. Credit: Maria Teresa Aguado and Guillermo Ponz-Segrelles; Organisms Diversity & Evolution, DOI: 10.1007/s13127-021-00538-4; licensed under CC BY 4.0

Image showing male stolon (right hand side) growing at the tip of a branch of the worm's body. The tiny red dots show where its eyes are sprouting. Image: Maria Teresa Aguado and Guillermo Ponz-Segrelles; BMC Genomics, DOI: 10.1186/s12864-025-11587-w; licensed under CC BY 4.0

A head and a hundred tails: how does branching worm manage reproduction?

Independent reproductive units known as stolons form at the tip of the tails and swim free. Researchers investigated gene expression: www.uni-goettingen.de/en/3240.html...

Research #BMCGenomics: doi.org/10.1186/s128...

🌟Call for Papers: Genomics of Symbiosis in BMC Genomics🌟 Looking forward to your exciting manuscripts on all types of symbiosis on earth including symbiotic fungi and their hosts! 🌿🍄 biomedcentral.com/collections/... #BMCGenomics @biomedcentral.bsky.social 🧪🧬🖥️

BenchAMRking: a Galaxy-based platform for illustrating the major issues associated with current antimicrobial resistance (AMR) gene prediction workflows - BMC Genomics Background The Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) networks ‘Seq4AMR’ and ‘B2B2B AMR Dx’ were established to promote collaboration between microbial whole genome sequenci...

From #BMCGenomics | BenchAMRking: a @galaxyproject.bsky.social -based platform for illustrating the major issues associated with current antimicrobial resistance (#AMR) gene prediction #workflows | 🧬 🖥️ 🧪 #UseGalaxy | bmcgenomics.biomedcentral.com/articles/10....

CNV GWAS + bulk transcriptome
Duck🦆Gonad development

CNVcaller▶️>5k CNV regions, 288 on ChrW, 162 on ChrZ (ZW♀️ ZZ♂️)

CNVR492 explains 26% testis weight variance◀️LncRNA LOC106019197, CDH19

TYW5 (CNVR891)▶️ovary weight

Hehe Liu lab #BMCGenomics 2024
bmcgenomics.biomedcentral.com/articles/10....

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes - BMC Genomics Background Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustere...

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes. #BiosyntheticGeneCluster #Metagenomes #HiFi @pacbio.bsky.social #BMCgenomics 🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes - BMC Genomics Background Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustere...

HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes. #Metagenomics #LongRead #HiFi #Sequencing @pacbio.bsky.social
#BMCgenomics
bmcgenomics.biomedcentral.com/articles/10....

Multi-tissue metabolomic profiling reveals the crucial metabolites and pathways associated with scallop growth - BMC Genomics Background Bivalves represent a vital economic resource in aquaculture for their high productivity and extensive market demand. Growth is one of the most important and desired aquaculture traits for b...

Multi-tissue metabolomic profiling reveals the crucial metabolites and pathways associated with scallop growth #BMCGenomics #MassSpec bmcgenomics.biomedcentral.com/articles/10....

lncRNAs involved in the Shade Avoidance Syndrome (SAS) in... Background Plant long non-coding RNAs (lncRNAs) have impo...

Happy to share the latest research from the #RegRNALab #BMCGenomics

We identify 3 #lncRNAs likely involved in shade avoidance ☀️🌑 in Arabidopsis🌱 using RNA-seq + gene co-expression networks🕸️

https://doi.org/10.1186/s12864-024-10718-z

Due to the wind whirl of moving, I missed our recent publication being out on #BMCGenomics @BioMedCentral! We characterized RNA-DNA interactions in lizards 🦎 for the 1st time!

Props to @Yoyemaye for driving this work and to the whole team - more...

Enhanced genome assembly and a new official gene set for ... Background The red flour beetle Tribolium castaneum has e...

New Tribolium #genome assembly, Tcas5.2, and new annotation OGS3 with 16,593 #genes bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... in #BMCGenomics @BMC_series

Babesia microti from humans and ticks hold a genomic sign... Background Babesia microti is an emerging tick-borne apic...

Babesia microti from humans and ticks hold a genomic signature of strong population structure in the United States bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... #bmcgenomics

Impressive new study from Mark Stevens's lab:

Using TraDIS to study ability of Salmonella Typhimurium 4/74 to colonise Mesenteric Lymph Nodes & Ileum of cattle.

bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... #bmcgenomics

Transcriptomic buffering of cryptic genetic variation con... Background Commensal bacteria like Neisseria meningitidis...

Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... #bmcgenomics

#bmcgenomics

Primordial origin and diversification of plasmids in Lyme... Background With approximately one-third of their genomes ...

Primordial origin and persistent maintenance of Borreliella (Borrelia) plasmid types support their functional indispensability & evolutionary roles in facilitating genome diversity

bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... #bmcgenomics

Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral - BMC Genomics Background Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization. Results Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are “primed” for settlement. Rise of competence through development was accompanied by up-regulation of sensory and signal transduction genes such as ion channels, genes involved in neuropeptide signaling, and G-protein coupled receptor (GPCRs). A drug screen targeting components of GPCR signaling pathways confirmed a role in larval settlement behavior and metamorphosis. Conclusions These results gives insight into the molecular complexity underlying these transitions and reveals receptors and pathways that, if altered by changing environments, could affect dispersal capabilities of reef-building corals. In addition, this dataset provides a toolkit for asking broad questions about sensory capacity in multicellular animals and the evolution of development.

Molecular characterization of larval development from fertilization to metamorphosis in a reef-buil... bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... #bmcgenomics

Lost in plasmids: next generation sequencing and the comp... Background Borrelia (B.) burgdorferi sensu lato, includin...

Lost in plasmids: next generation sequencing and the complex genome of the tick-borne pathogen Borr... bmcgenomics.biomedcentral.com/articles/10.1186/s12864-... #bmcgenomics