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| Open AccessA genomic basis of vocal rhythm in birds
Little is known about the genetic basis of the rhythmic component of bird song, an important trait in sexual selection and species recognition. By studying a system with innate vocalizations, the Pogoniulus tinkerbirds, this study finds candidate genes that underlie differences in speed in vocal rhythm in this system.
- Matteo Sebastianelli
- , Sifiso M. Lukhele
- & Alexander N. G. Kirschel
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Article
| Open AccessHigh temperature delays and low temperature accelerates evolution of a new protein phenotype
The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.
- Jia Zheng
- , Ning Guo
- & Andreas Wagner
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Article
| Open AccessReal-time monitoring of replication errors’ fate reveals the origin and dynamics of spontaneous mutations
An interdisciplinary approach following replication errors in Escherichia coli unveils that many spontaneous mutations originate from inefficient repair, and that repair capacity is variable between single cells within a bacterial population.
- Chiara Enrico Bena
- , Jean Ollion
- & Marina Elez
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Article
| Open AccessMacroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.
- Mirjana Domazet-Lošo
- , Tin Široki
- & Tomislav Domazet-Lošo
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Article
| Open AccessGWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle
Endogenous retroviruses constitute 5–10% of mammalian genome space. This study characterize the bovine ERVK[2-1- LTR] clade showing that its activity varies between individuals as a function of the number of inherited autonomous elements, yet that most de novo insertions are non-autonomous elements lacking functional genes.
- Lijing Tang
- , Benjamin Swedlund
- & Carole Charlier
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Article
| Open AccessImplications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
The spatial organization of eukaryotic genomes is linked to their biological functions. Here, the authors study the 3D genome organization of the phytopathogenic fungus Verticillium dahliae, revealing links to evolutionary features conserved throughout the Verticillium genus.
- David E. Torres
- , H. Martin Kramer
- & Bart P. H. J. Thomma
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Article
| Open AccessEvolution and expression patterns of the neo-sex chromosomes of the crested ibis
The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.
- Lulu Xu
- , Yandong Ren
- & Gang Li
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Article
| Open AccessGenomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.
- Xiao Feng
- , Qipian Chen
- & Ziwen He
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Article
| Open AccessExperimental evidence for cancer resistance in a bat species
Bats have been suggested to be resistant to cancer due to mechanisms related to their evolved longevity, but the associated molecular drivers are still understudied. Here, the authors examine cancer resistance mechanisms across seven bat species using in vitro and in vivo models, and identify HIF1A, COPS5, and RPS3 as related genes.
- Rong Hua
- , Yuan-Shuo Ma
- & Zhen Liu
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Article
| Open AccessDiversity and evolution of the vertebrate chemoreceptor gene repertoire
Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.
- Maxime Policarpo
- , Maude W. Baldwin
- & Walter Salzburger
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Article
| Open AccessT-bet+ B cells are activated by and control endogenous retroviruses through TLR-dependent mechanisms
Endogenous retroviruses (ERV) can induce immune responses and the control of these viruses uses immune mechanisms also involved in autoimmunity. Here, the authors characterize the control of ERVs in mice and show age-associated B cell control and nucleic acid sensing TLR pathway involvement.
- Eileen Rauch
- , Timm Amendt
- & Philipp Yu
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Article
| Open AccessRepeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling
The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.
- Tom Carruthers
- , Michelangelo S. Moerland
- & Wolf L. Eiserhardt
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Article
| Open AccessThe origin and structural evolution of de novo genes in Drosophila
It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, through systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.
- Junhui Peng
- & Li Zhao
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Article
| Open AccessA histone demethylase links the loss of plasticity to nongenetic inheritance and morphological change
A challenge for understanding plasticity is connecting macroevolutionary patterns to molecular mechanisms. Using a nematode model, this study identifies a mediator of nongenetic inheritance which is linked to multigenerational shifts in plasticity and morphology.
- Nicholas A. Levis
- & Erik J. Ragsdale
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Article
| Open AccessUbiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers
Meiotic drivers of the wtf family kill progeny lacking the driver by producing a toxin and an antidote. Here, authors reveal that ubiquitination-mediated sorting of the antidote prevents it from becoming toxic and enables it to neutralize the toxin.
- Jin-Xin Zheng
- , Tong-Yang Du
- & Li-Lin Du
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Article
| Open AccessEvolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle
Hyaluronic acid is believed to plays a critical role in cancer resistance and longevity of the naked mole rat. Here, Zhao and colleagues show that accumulation of high levels of hyaluronic acid has co-evolved repeatedly in mammalian clades with adaptation to subterranean habitats.
- Yang Zhao
- , Zhizhong Zheng
- & Vera Gorbunova
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Article
| Open AccessLocal adaptation and future climate vulnerability in a wild rodent
A species’ response to anthropogenic climate change may depend on its adaptations to past climate changes. Here, the authors use whole-genome resequencing and genetic-environment association to identify genes important for local adaptation and project adaptation under future climate scenarios across bank vole populations in Britain.
- Silvia Marková
- , Hayley C. Lanier
- & Petr Kotlík
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Article
| Open AccessUnappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology studies
European ancestry individuals are not typically treated as admixed in genetic studies. Here, the authors detect higher than expected admixture in European populations, which could potentially affect the results of genetic studies if it is not accounted for.
- Mateus H. Gouveia
- , Amy R. Bentley
- & Daniel Shriner
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Article
| Open AccessEvolution of a ZW sex chromosome system in willows
Investigation of heterogametic transitions in sex chromosomes is challenging but fascinating from an evolutionary perspective. Here, Hu et al. have identified a transition from an XY to a ZW system in the genus Salix (willows) where both the Z and W chromosomes have originated from the ancestral Y.
- Nan Hu
- , Brian J. Sanderson
- & Matthew S. Olson
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Article
| Open AccessMitogenomic evolutionary rates in bilateria are influenced by parasitic lifestyle and locomotory capacity
The diversity of mitogenomic evolutionary rates among animal lineages remains poorly explained. Here, an analysis of mitogenomes of almost 11,000 bilaterian species provides evidence that parasitism and locomotory capacity are major variables explaining elevation of mitogenomic evolutionary rates.
- Ivan Jakovlić
- , Hong Zou
- & Dong Zhang
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Article
| Open AccessThe pan-genome and local adaptation of Arabidopsis thaliana
Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.
- Minghui Kang
- , Haolin Wu
- & Jianquan Liu
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Article
| Open AccessThe genomic footprint of whaling and isolation in fin whale populations
Industrial whaling drove several species to near extinction. From an analysis of 50 whole-genomes from fin whale populations, this study shows that the fin whale population in the Eastern North Pacific was reduced 99% during whaling but has maintained genomic diversity, whereas the Gulf of California population remained small and isolated, resulting in increased genetic load.
- Sergio F. Nigenda-Morales
- , Meixi Lin
- & Robert K. Wayne
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Article
| Open AccessGenome mining shows that retroviruses are pervasively invading vertebrate genomes
Ongoing retroviral invasion into vertebrates has been rarely documented. Here the authors have identified 412 endogenous retroviruses that are invading the genomes of over a hundred vertebrate species. This may be relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
- Jianhua Wang
- & Guan-Zhu Han
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Article
| Open AccessDomain loss enabled evolution of novel functions in the snake three-finger toxin gene superfamily
3-finger toxins are unique to the venoms of caenophidian snakes. This study traces the evolution of these toxins in snakes, highlighting a key shift from membrane-bound to secretory proteins. This transformation, involving the loss of a membrane-anchoring domain and changes in gene expression, paved the way for their venomous function.
- Ivan Koludarov
- , Tobias Senoner
- & Burkhard Rost
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Article
| Open AccessEvolutionary genomics of camouflage innovation in the orchid mantis
Camouflage is a widespread phenomenon in nature, and the orchid mantis is a particularly striking example. Here the authors use evolutionary genomics to uncover the genetic mechanisms behind the colour and morphology that produce innovative camouflage in the orchid mantis and dead leaf mantis.
- Guangping Huang
- , Lingyun Song
- & Fuwen Wei
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Article
| Open AccessRapid gene content turnover on the germline-restricted chromosome in songbirds
Songbirds have an extra chromosome with unknown function found only in their germline. This study assembles and compares this chromosome in two closely related nightingale species, finding large differences in genetic content and only one conserved gene with probable essential function.
- Stephen A. Schlebusch
- , Jakub Rídl
- & Radka Reifová
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Article
| Open AccessInsertion sequence transposition inactivates CRISPR-Cas immunity
CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, the authors show that insertion sequences can efficiently insert into cas genes, thus inactivating CRISPR defenses and increasing bacterial susceptibility to foreign DNA invasion.
- Yong Sheng
- , Hengyu Wang
- & Qianjin Kang
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Article
| Open AccessIntegrating full and partial genome sequences to decipher the global spread of canine rabies virus
Although pathogen whole genome sequencing is becoming more common, for many pathogens far more partial sequences are available. In this study, the authors develop a phylogenetic pipeline to efficiently combine whole and partial viral genome sequences and demonstrate its application using rabies virus sequences.
- Andrew Holtz
- , Guy Baele
- & Anna Zhukova
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Article
| Open AccessDivergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries
The egg membrane protein Bouncer is an important mediator of gamete interaction and prevents cross-fertilisation between medaka and zebrafish. This study demonstrates unique functional and structural differences in Bouncer proteins of these and other distantly related fish species which may determine which species can hybridize.
- Krista R. B. Gert
- , Karin Panser
- & Andrea Pauli
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Article
| Open AccessHolocentromeres can consist of merely a few megabase-sized satellite arrays
The centromere is required for the segregation of chromosomes. Here, the authors report the organization and dynamic of holocentric chromosomes, each containing 7 to 11 evenly spaced megabase-sized centromere-specific histone H3-positive units.
- Yi-Tzu Kuo
- , Amanda Souza Câmara
- & Andreas Houben
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Article
| Open AccessGenomics of cold adaptations in the Antarctic notothenioid fish radiation
The notothenioid radiation is a remarkable group of fish adapted to life in the icy waters of the Southern Ocean. This study investigates the evolutionary history of this group and the basis of their adaption to cold environments through genomic analysis of 24 new genome assemblies.
- Iliana Bista
- , Jonathan M. D. Wood
- & Richard Durbin
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Article
| Open AccessIndependent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor
Whole genome duplication can generate new genes and support survival through mass extinctions. Here, the authors show that paddlefish and sturgeon shared a genome duplication event 200 million years ago that was previously unrecognised due to the mixed signals from independent rediploidisation.
- Anthony K. Redmond
- , Dearbhaile Casey
- & Aoife McLysaght
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Article
| Open AccessDistinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms
Annelid worms have colonised extreme ecological niches, such as hydrothermal vents and whale falls thanks to symbiotic bacteria. This study finds that Osedax worms and the related Vestimentifera have evolved different genomic adaptations to sustain their bacterial symbioses and exploit different resources, such as decaying bone.
- Giacomo Moggioli
- , Balig Panossian
- & José M. Martín-Durán
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Article
| Open AccessHigher-order epistasis shapes natural variation in germ stem cell niche activity
Stem cell niches regulate proliferation of stem cells, but variation in this control across natural populations has not been explored. Here they combine quantitative genetics and gene editing to show that natural variation in C. elegans germ stem cell niche activity is shaped by complex gene-gene interactions.
- Sarah R. Fausett
- , Asma Sandjak
- & Christian Braendle
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Article
| Open AccessDNMT1 mutant ants develop normally but have disrupted oogenesis
The role of DNA methylation in insects is poorly understood. Here, the authors knock out the DNA methyltransferase DNMT1 in an ant and find no obvious effects on development, rather showing that this enzyme seems to play a crucial role during early oogenesis.
- Iryna Ivasyk
- , Leonora Olivos-Cisneros
- & Daniel J. C. Kronauer
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Article
| Open AccessA thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen
Zymoseptoria tritici is an important fungal pathogen of wheat which has spread globally. Here, the authors perform genomic analyses on a collection of ~1100 Z. tritici samples from 42 countries to describe its global spread and elucidate mechanisms of adaptation to different environmental conditions.
- Alice Feurtey
- , Cécile Lorrain
- & Daniel Croll
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Article
| Open AccessApplication of high-throughput single-nucleus DNA sequencing in pancreatic cancer
Implementing high-throughput single-cell DNA sequencing for the study of solid tumours has been challenging. Here, the authors present an optimised approach for snap-frozen tissue single nuclei extraction and DNA sequencing, which can be applied to study pancreatic ductal adenocarcinoma evolution and heterogeneity.
- Haochen Zhang
- , Elias-Ramzey Karnoub
- & Christine A. Iacobuzio-Donahue
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Article
| Open AccessMicro and macroevolution of sea anemone venom phenotype
Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.
- Edward G. Smith
- , Joachim M. Surm
- & Yehu Moran
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Article
| Open AccessImmunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia
Seahorses may have required adaptations to avoid immunological rejection of allogenic embryos by males. The authors show that a single substitution in tlx1 is associated with loss of the spleen in seahorses, and that across the clade, degree of male pregnancy is negatively correlated with immune gene repertoire complexity.
- Yali Liu
- , Meng Qu
- & Qiang Lin
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Article
| Open AccessCompensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1
Evolution of the SARS-CoV-2 spike protein is likely driven by many factors, including immune escape and receptor binding. Here, by measuring the binding affinity of more than 30,000 variants of the SARS-CoV-2 RBD to its receptor ACE2, Moulana et al. show that the evolution of the Omicron BA.1 variant was driven by interactions between mutations.
- Alief Moulana
- , Thomas Dupic
- & Michael M. Desai
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Article
| Open AccessRepeated genetic adaptation to altitude in two tropical butterflies
Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.
- Gabriela Montejo-Kovacevich
- , Joana I. Meier
- & Chris D. Jiggins
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Matters Arising
| Open AccessReply to: “Steller’s sea cow uncertain history illustrates importance of ecological context when interpreting demographic histories from genomes”
- Fedor S. Sharko
- , Sergey M. Rastorguev
- & Artem V. Nedoluzhko
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Article
| Open AccessGenomic evidence for homoploid hybrid speciation between ancestors of two different genera
Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.
- Zefu Wang
- , Minghui Kang
- & Jianquan Liu
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Article
| Open AccessAnopheles mosquitoes reveal new principles of 3D genome organization in insects
Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.
- Varvara Lukyanchikova
- , Miroslav Nuriddinov
- & Veniamin Fishman
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Article
| Open AccessPopulation-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
Even in well-studied species, there is still substantial natural genetic variation that has not been characterized. Here, the authors use long read sequencing to discover transposable elements in the Drosophila genome not detected by short read sequencing, and link them to gene expression.
- Gabriel E. Rech
- , Santiago Radío
- & Josefa González
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Article
| Open AccessA natural timeless polymorphism allowing circadian clock synchronization in “white nights”
The genus Drosophila originate in subSaharan Africa and spread North up to the polar circle where they experience long days in the summer or even constant light. Here, the authors show that a form of the TIMELESS protein enables flies to synchronise their behavioural activity to long summer days
- Angelique Lamaze
- , Chenghao Chen
- & Ralf Stanewsky
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Article
| Open AccessParallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
- Andrea Fulgione
- , Célia Neto
- & Angela M. Hancock
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Article
| Open AccessIntralocus conflicts associated with a supergene
‘A supergene that underlies variation in male mating phenotypes has consequences for female reproduction. Here, the authors use evolutionary models to show that the rarest variant of this supergene is maintained by disproportionally high male reproductive success.’
- Lina M. Giraldo-Deck
- , Jasmine L. Loveland
- & Clemens Küpper
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Article
| Open AccessPervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants
The small size (≤15-nt) of micorexons poses difficulties for genome annotation and identification using standard RNA sequence mapping approaches. Here, the authors develop computational pipelines to discover and predict microexons in plants and reveal diverse evolutionary trajectories via genomewide microexon modeling.
- Huihui Yu
- , Mu Li
- & Chi Zhang