Some bibliography

2Ome 3′ UTR 3′ end 454 5′ UTR 5mC 7SK 8-oxo-G 96-wells AI Alu BCR Bioconductor Biotechnology Brenner C33a CAGE CDR3 COVID-19 CRISPR CaSki ChIP Ciona CpG Crick DGT DNA DNAi DNAse I DNase-hypersensitivity DTT Dictyostelium Drosophila EBV ENCODE ES EcoP15I EpiSC Fluidigm FoxP3 Fritillaria Fucci H2AX H3K27ac H3K27me3 H3K36me3 H3K4me1 H3K4me2 H3K4me3 H3K4me4 H3K9ac H3K9me2 H3K9me3 H3S10p H3S28p H3S31p H3T3p H42K20me2 H4K16Ac H4K20me2 H4K8Ac HDAC HIV HPV HeLa Helicos HepG2 LAST LNA LPA LTR MHC MRI OIST OSC Oikopleura Okinawa Olf-1 Oxford plot PCR PEG PETM PLA PRDM9 Parkinson’s disease QTL RACE RNA RNA-inheritance RNA-protein RNA-seq RNA polymerase RNAse R RNP granules RT-PCR RdRP SAGE SARS-CoV-2 SNP SRA STRT Sanger SiHa TATA-box TCR TFBS Taq Trizol UTR adenylylation adipocyte agarose ageing alignment allelic expression amplification analysis annotation antibody antisense application aptamer arabidopsis archaea artefact assembly auto immunity automation bHLH bacteria barcode bat beads benchmark betaine bias bidirectional bioRxiv biochemistry biotin bistable blood brain buffer cDNA calcium cancer cap capture catecholaminergic cell-cell interaction cell conversion cell culture cell cycle cell type cellulose centromere cephalopod cerebellum chicken chimeric transcript chimpanzee chromatin chromosome chromothripsis circuit circular RNA click climate clock cloning clustering comparison compartment complex-loci copy number coral cytometry cytoplasm damage database degradation demethylase dendrite detection development diagnostic differentiation dog dosage droplet drug drug delivery dsRNA eDNA eQTL editing education electrophoresis elongation embryo embryoid body emulsion endosymbiosis enhancer environment enzyme epicentre epigenetic evolution exon painting exonuclease exosome experiment design expression factory fingerprint fish fixation floor-plate flow cytometry fluorescence format fractionation frog function fusion transcript genetics genome germ line global warming graft granule growth guanylation hair hairpin haplotype heart heavy chain hemichordate heterodimer heterogeneity high-throughput histone historical human hybridisation iPS imaging immune-system immunity immunoglobulin imprinting in situ in vivo infection information inhibition inosine integration intellectual-property intron isoform isothermal journal club karyotype knock-out labelling lamin lariat laser-capture library ligase lineage lipid live liver localisation locus boundary loop lymphocyte lysis m6A mC mRNA machine learning manganese mangrove mass spectroscopy maternal mechanical force mechanism medaka meiosis metabolism methanol method methylation miRNA microarray microfluidic microplastic microscopy missing-method mitochondrion model modification modified base monkey mosquito motif mouse muller element multiplex muscle mutation mycoplasma nanoCAGE nanopore natural selection nematode network neurogenin neuron nick noise nomenclature non-coding non-polyadenylated non coding normalisation not read nuclear body nucleolus nucleosome nucleotides nucleus occupancy ocean acidification ocular-dominance olfaction oligo-capping oligonucleotides open data open science organoid outreach pH paired-end parasite parvalbumin patent peak peroxydase pharmacology pheromones phosphatase phylogeny physiology piRNA pig plankton plant plasticity policy polony poly-A polymerase polyploid polysome population population transcriptomics post translational modification power law primase prion privacy product profile program prokaryote promoter promotome protein proteome proteomics publishing purification purkinje pyrophosphatase qPCR radioisotope random priming rat recombination recycle regulation repair repeat repertoire replication repression reprogramming reticulocyte reverse transcription review ribosome ribozyme richness robot sRNA scale-free screen selection selex sequence tags sequencing sex siRNA silencing single cell single chain single gene single molecule single strand size small RNA small samples snoRNA software somatic mutation sorting speciation spike splicing ssbp statistics stem cell storage structure subgenome superfamily supergene synapse synteny synthetic systems biology tRNA tag taxonomy telomere temperature template switching termination theory therapy thermo-enhancement thymus to read trans-splicing transcript transcript count transcription transcription factor transcriptome translation translatome transolcation transport transposase transposon trehalose triple helix tunicate turnover ultraconserved ultrasound unicellular unnatural base vaccine vanadium variants virus visual cortex yeast zebrafish α chain αβ chains β chain γH2AX μORF

Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes.

PLoS Genet. 2008 Aug 1;4(8):e1000142. doi:10.1371/journal.pgen.1000142.

Simcox A, Mitra S, Truesdell S, Paul L, Chen T, Butchar JP, Justiniano S.

Dequéant ML, Fagegaltier D, Hu Y, Spirohn K, Simcox A, Hannon GJ, Perrimon N.

Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.

Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):12974-9. doi:10.1073/pnas.1517729112

“Common immortalized cells are related to adult muscle precursors (AMPs)”

Xie S, Li J, Chen W, Fong LJM, Huang C, Feng Y, Ai Q, Zhao M, Mank JE, Wu H.

Genome Res. 2025 Jun 2;35(6):1325-1336. doi:10.1101/gr.280161.124

Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad.

“Population genetic data showed high rates of sex-reversed XY-type females, and recombination between the X and Y Chromosomes in these individuals helps maintain the integrity of sequence and gene expression on the Y Chromosome.” “Despite this large size and the assumption that inversions catalyze recombination suppression between the X and Y Chromosomes, we found little evidence of XY structural variation.” “High collinearity and similarity between X and Y haplotypes implicate a pre-existing pattern of low recombination itself, likely predating the origin of Chr 1 as the sex chromosomes, rather than structural variation, in sex chromosome formation.”

Nat Genet. 2025 Jun;57(6):1524-1534. doi: 10.1038/s41588-025-02202-5

Phan MHQ, Zehnder T, Puntieri F, Magg A, Majchrzycka B, Antonović M, Wieler H, Lo BW, Baranasic D, Lenhard B, Müller F, Vingron M, Ibrahim DM.

Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.

“Interspecies point projection (IPP) [is] a synteny-based algorithm designed to map corresponding genomic locations in highly diverged genomes”. “We term [...] sequence-diverged orthologs ‘indirectly conserved’ (IC)”

Julia D Sigwart, Yunlong Li, Zeyuan Chen, Katarzyna Vončina, Jin Sun

Elife 2025 Apr 17:13:RP102542. doi:10.7554/eLife.102542

Still waters run deep in large-scale genome rearrangements of morphologically conservative Polyplacophora

“Heterozygocity ranging from almost 1% in Deshayesiella to 4.12% in Callochiton” “There are major changes [of karyotype] between congeners in different ocean basins (the Pacific A. rubrolineata) but also between two species in the NE Atlantic (A. discrepans and A. crinita) that are morphologically and ecologically almost indistinguishable.” “Living species of Lepidopleurida retain more plesiomorphic morphology and this clade has a deep fossil record extending to the lower Carboniferous; yet the exemplar of this order shows the most deviations from the reconstructed ancestral karyotype.”

Chen YC, Vendrami DLJ, Huber ML, Handel LEY, Cooney CR, Hoffman JI, Gossmann TI.

Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes.

Genome Res. 2025 Jun 2;35(6):1313-1324. doi:10.1101/gr.279428.124

“we demonstrate that many mitochondrial-coding NUMTs exhibit signs of long-term selection”

Kanai Y, Shibai A, Yokoi N, Tsuru S, Furusawa C.

Nucleic Acids Res. 2025 May 10;53(9):gkaf331. doi:10.1093/nar/gkaf331

Laboratory evolution of the bacterial genome structure through insertion sequence activation.

“we developed an E. coli strain with high IS activity and demonstrated rapid IS-mediated genome evolution under relaxed selection in the laboratory, simulating the natural evolution of symbionts and pathogens. In just ten weeks, we observed numerous IS insertions, IS-mediated duplications, and deletions, contributing to at most −4.4% to 9.2% genome size changes (Fig. 4).” “We detected a total of 457 large-scale rearrangements, including 54 inversions, 363 deletions, and 40 duplications. [...] The median size of inversions was 84 kbp (range: 2.2 kbp–1.7 Mbp). All three inversions exceeding 1 Mbp were nearly symmetric to the ori-ter axis, consistent with observations of large inversions in nature. [...] Deletions ranged from 102 bp to 163 kbp (Fig. 3C), with the largest deletion being a deletion of a duplicated region. [...] Duplications had a median size of 40 kbp (range: 4830 bp–372 kbp). Surprisingly, the majority of the duplications resulted from transpositions of composite transposons with a copy of IS at each end (25/40), rather than tandem duplications. [...] The rearrangements led to genome size changes ranging from 174 kbp reduction to 369 kbp increase or −4.4% to 9.2%. However, overall, deletions were offset by the genome size increase from duplications and IS insertions, resulting in negligible changes in the median genome sizes”

Sandoval-Navarrete, C. A., Hernández-Márquez, S., Zamudio-Resendiz, M. E. ., Núñez-Resendiz, M. L. ., Márquez-Valdelamar, L. M. ., & Sentíes, A

Acta Zoológica Lilloana, 68(2), 309–341. doi:10.30550/j.azl/1974

Nuevos registros de Appendicularia (Urochordata) y otras especies de zooplancton en el Pacífico tropical mexicano

“the first molecular confirmation of Oikopleuradioicain Mexico stands out, revealing high genetic similarity with populations in Japan, highlighting the shared distribution between the northeastern and northwestern parts of the Pacific Ocean.”

Cheng L, Zhao S, Li T, Hou S, Luo Z, Xu J, Yu W, Jiang S, Monti M, Schindler D, Zhang W, Hou C, Ma Y, Cai Y, Boeke JD, Dai J.

Nat Commun. 2024 Jan 26;15(1):770. doi:10.1038/s41467-023-44511-5

Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae.

“SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes” “LOH and aneuploidy are frequently detected in SCRaMbLEd heterozygous diploids” “the proportion of rearrangement events was 10-fold higher in haploid than in diploid cells.”

Frith MC, Ni S.

Mol Biol Evol. 2023 Dec 1;40(12):msad275. doi: 10.1093/molbev/msad275

DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development.

“Here, we report 25 regulatory DNA segments conserved across bilaterian animals, of which 7 are also conserved in cnidaria (coral and sea anemone).” “On the other hand, no conserved segments were found in fly (Drosophila melanogaster), roundworm (Caenorhabditis elegans), or leech (Helobdella robusta).”

See all articles.