Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
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Matthew W. Hahn | Simo V. Zhang | S. Koren | A. Phillippy | D. Lawson | S. Aganezov | C. Chauve | S. Bérard | É. Tannier | S. Emrich | M. Sharakhova | Livio Ruzzante | M. Reijnders | R. Waterhouse | N. Besansky | I. Sharakhov | M. Unger | P. George | Jiyoung Lee | M. Alekseyev | M. Kamali | G. Maslen | Ashley Peery | P. Howell | Y. Anselmetti | Romain Feron | M. Hahn | Cédric Chauve | Éric Tannier | Sèverine Bérard
[1] Robert M. Waterhouse,et al. Of Genes and Genomes: Mosquito Evolution and Diversity. , 2019, Trends in parasitology.
[2] M. Sharakhova,et al. Physical Genome Mapping Using Fluorescence In Situ Hybridization with Mosquito Chromosomes. , 2018, Methods in molecular biology.
[3] Felipe A. Simão,et al. Using BUSCO to Assess Insect Genomic Resources. , 2018, Methods in molecular biology.
[4] Surya Saha,et al. Long Range Sequencing and Validation of Insect Genome Assemblies. , 2018, Methods in molecular biology.
[5] Richard Durbin,et al. A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing , 2018, bioRxiv.
[6] S. Koren,et al. A chromosome-scale assembly of the major African malaria vector Anopheles funestus , 2018, bioRxiv.
[7] Sergey Koren,et al. Improved reference genome of Aedes aegypti informs arbovirus vector control , 2018, Nature.
[8] Jun Yu,et al. RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes , 2018, Genom. Proteom. Bioinform..
[9] M. Sharakhova,et al. The Development of Cytogenetic Maps for Malaria Mosquitoes , 2018, Insects.
[10] Dmitry Antipov,et al. Versatile genome assembly evaluation with QUAST-LG , 2018, Bioinform..
[11] Christophe Klopp,et al. D-GENIES: dot plot large genomes in an interactive, efficient and simple way , 2018, PeerJ.
[12] Willem Takken,et al. The Effect of Hybridization on Dosage Compensation in Member Species of the Anopheles gambiae Species Complex , 2018, bioRxiv.
[13] Cédric Chauve,et al. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes , 2018, BMC Genomics.
[14] A. N. Naumenko,et al. Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome , 2018, BMC Genomics.
[15] R. Scott Hawley,et al. GENOME REPORT: High-quality genome assemblies of 15 Drosophila species generated using Nanopore sequencing , 2018, bioRxiv.
[16] Sergey Koren,et al. Integrating Hi-C links with assembly graphs for chromosome-scale assembly , 2018, bioRxiv.
[17] Martin Hunt,et al. Inferring synteny between genome assemblies: a systematic evaluation , 2017, BMC Bioinformatics.
[18] Ivan Liachko,et al. Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly , 2017, The Journal of heredity.
[19] B. White,et al. Chromosome arm‐specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector, Anopheles funestus , 2017, Molecular ecology.
[20] Robert M. Waterhouse,et al. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics , 2017, bioRxiv.
[21] Robert M. Waterhouse,et al. Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes , 2016, bioRxiv.
[22] Jing Wang,et al. Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae , 2017, Malaria Journal.
[23] Bernardo J. Clavijo,et al. Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. , 2017, Genome research.
[24] Joana Damas,et al. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set , 2017, Genome research.
[25] Cedric Chauve,et al. DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies , 2017, Genome biology and evolution.
[26] John K. McCooke,et al. A chromosome conformation capture ordered sequence of the barley genome , 2017, Nature.
[27] S. Sim,et al. A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae , 2017, G3: Genes, Genomes, Genetics.
[28] Neva C. Durand,et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds , 2016, Science.
[29] Evgeny M. Zdobnov,et al. OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs , 2016, Nucleic Acids Res..
[30] Michael F. Covington,et al. Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population , 2016, G3: Genes, Genomes, Genetics.
[31] Son K. Pham,et al. Chromosome assembly of large and complex genomes using multiple references , 2016, bioRxiv.
[32] Xiaofang Jiang,et al. The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles , 2016, G3: Genes, Genomes, Genetics.
[33] J. Doe,et al. Fast‐Track Introgression of “QTL‐hotspot” for Root Traits and Other Drought Tolerance Traits in JG 11, an Elite and Leading Variety of Chickpea , 2016, The plant genome.
[34] L. Florea,et al. Rascaf: Improving Genome Assembly with RNA Sequencing Data , 2016, The plant genome.
[35] Max A. Alekseyev,et al. CAMSA: a tool for comparative analysis and merging of scaffold assemblies , 2016, bioRxiv.
[36] Yang Wang,et al. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. , 2016, Insect biochemistry and molecular biology.
[37] Eleazar Eskin,et al. The Genetic Basis of Host Preference and Resting Behavior in the Major African Malaria Vector, Anopheles arabiensis , 2016, PLoS genetics.
[38] Gaik Tamazian,et al. Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences , 2016, GigaScience.
[39] Max A. Alekseyev,et al. Multi-genome Scaffold Co-assembly Based on the Analysis of Gene Orders and Genomic Repeats , 2016, ISBRA.
[40] Shuai Jiang,et al. Reconstruction of ancestral genomes in presence of gene gain and loss , 2016, bioRxiv.
[41] J. Mallet,et al. Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution , 2015, G3: Genes, Genomes, Genetics.
[42] Brendan L. O’Connell,et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage , 2015, Genome research.
[43] Matthew W. Hahn,et al. AGOUTI: improving genome assembly and annotation using transcriptome data , 2015, bioRxiv.
[44] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[45] E. Baricheva,et al. A standard photomap of ovarian nurse cell chromosomes in the European malaria vector Anopheles atroparvus , 2015, Medical and veterinary entomology.
[46] Max A. Alekseyev,et al. Scaffold assembly based on genome rearrangement analysis , 2015, Comput. Biol. Chem..
[47] Annie Chateau,et al. Ancestral gene synteny reconstruction improves extant species scaffolding , 2015, bioRxiv.
[48] Janna L. Fierst,et al. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools , 2015, Front. Genet..
[49] Xiaofang Jiang,et al. Complete Dosage Compensation in Anopheles stephensi and the Evolution of Sex-Biased Genes in Mosquitoes , 2015, Genome biology and evolution.
[50] H. A. Smith,et al. Genome-wide QTL mapping of saltwater tolerance in sibling species of Anopheles (malaria vector) mosquitoes , 2015, Heredity.
[51] D. Bachtrog,et al. Numerous Transitions of Sex Chromosomes in Diptera , 2015, PLoS biology.
[52] Michael C. Schatz,et al. Metassembler: merging and optimizing de novo genome assemblies , 2015, bioRxiv.
[53] Steven L Salzberg,et al. HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.
[54] Xiaofang Jiang,et al. Extensive introgression in a malaria vector species complex revealed by phylogenomics , 2015, Science.
[55] Sandra Gesing,et al. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases , 2014, Nucleic Acids Res..
[56] James E. Allen,et al. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes , 2014, Science.
[57] Tun-Wen Pai,et al. Identification of conserved and polymorphic STRs for personal genomes , 2014, BMC Genomics.
[58] I. Sharakhov. Protocols for Cytogenetic Mapping of Arthropod Genomes , 2014 .
[59] Xiaofang Jiang,et al. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi , 2014, Genome Biology.
[60] Stephen J. Benkovic,et al. Corrigendum: RecG and UvsW catalyse robust DNA rewinding critical for stalled DNA replication fork rescue , 2014, Nature Communications.
[61] Liisa Holm,et al. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera , 2014, Nature Communications.
[62] Lars Arvestad,et al. BESST - Efficient scaffolding of large fragmented assemblies , 2014, BMC Bioinformatics.
[63] Peter Rodgers,et al. eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses , 2014, PloS one.
[64] Michael J Sailor,et al. Mesoporous silicon sponge as an anti-pulverization structure for high-performance lithium-ion battery anodes , 2014, Nature Communications.
[65] S. Salzberg,et al. Sequencing and Assembly of the 22-Gb Loblolly Pine Genome , 2014, Genetics.
[66] Matthew W. Hahn,et al. Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations , 2014, G3: Genes, Genomes, Genetics.
[67] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[68] Yahya Al-Hazmi,et al. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) , 2014, ICPP 2014.
[69] Kathleen Marchal,et al. A network-based approach to identify substrate classes of bacterial glycosyltransferases , 2014, BMC Genomics.
[70] Dan Graur,et al. Finding the missing honey bee genes: lessons learned from a genome upgrade , 2014, BMC Genomics.
[71] Lei Ma,et al. Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites , 2014, BMC Genomics.
[72] Andrew C. Adey,et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions , 2013, Nature Biotechnology.
[73] Noam Kaplan,et al. High-throughput genome scaffolding from in-vivo DNA interaction frequency , 2013, Nature Biotechnology.
[74] Michal Levy-Sakin,et al. Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. , 2013, Current opinion in biotechnology.
[75] Scott J. Emrich,et al. The Evolution of the Anopheles 16 Genomes Project , 2013, G3: Genes, Genomes, Genetics.
[76] Francisco Prosdocimi,et al. The Genome of Anopheles darlingi, the main neotropical malaria vector , 2013, Nucleic acids research.
[77] Douglas G. Scofield,et al. The Norway spruce genome sequence and conifer genome evolution , 2013, Nature.
[78] Loretta Auvil,et al. Reference-assisted chromosome assembly , 2013, Proceedings of the National Academy of Sciences.
[79] Sven Rahmann,et al. Snakemake--a scalable bioinformatics workflow engine. , 2012, Bioinformatics.
[80] Gergely J. Szöllosi,et al. Evolution of gene neighborhoods within reconciled phylogenies , 2012, Bioinform..
[81] Jian Ye,et al. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction , 2012, BMC Bioinformatics.
[82] Etsuko N. Moriyama,et al. Evolution of a Large, Conserved, and Syntenic Gene Family in Insects , 2012, G3: Genes | Genomes | Genetics.
[83] Matthew W Hahn,et al. Sex chromosomes evolved from independent ancestral linkage groups in winged insects. , 2012, Molecular biology and evolution.
[84] Evgeny M Zdobnov,et al. A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits , 2011, BMC Evolutionary Biology.
[85] Walter Pirovano,et al. BIOINFORMATICS APPLICATIONS , 2022 .
[86] Ali Mortazavi,et al. Scaffolding a Caenorhabditis nematode genome with RNA-seq. , 2010, Genome research.
[87] Ai Xia,et al. A physical map for an Asian malaria mosquito, Anopheles stephensi. , 2010, The American journal of tropical medicine and hygiene.
[88] F. C. Kafatos,et al. Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences , 2010, Science.
[89] Nikos Darzentas,et al. Circoletto: visualizing sequence similarity with Circos , 2010, Bioinform..
[90] Jeffrey A. Bailey,et al. Genome Landscape and Evolutionary Plasticity of Chromosomes in Malaria Mosquitoes , 2010, PloS one.
[91] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[92] Steven J. M. Jones,et al. Circos: an information aesthetic for comparative genomics. , 2009, Genome research.
[93] K. Lindblad-Toh,et al. Assisted assembly: how to improve a de novo genome assembly by using related species , 2009, Genome Biology.
[94] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[95] P. Pevzner,et al. Breakpoint graphs and ancestral genome reconstructions. , 2009, Genome research.
[96] Robert M. Waterhouse,et al. The Aedes aegypti genome: a comparative perspective , 2008, Insect molecular biology.
[97] Denis Duboule,et al. The rise and fall of Hox gene clusters , 2007, Development.
[98] Robert S. Harris,et al. Improved pairwise alignment of genomic dna , 2007 .
[99] Ewan Birney,et al. Update of the Anopheles gambiae PEST genome assembly , 2007, Genome Biology.
[100] Ai Xia,et al. A Standard Cytogenetic Photomap for the Mosquito Anopheles stephensi (Diptera: Culicidae): Application for Physical Mapping , 2006 .
[101] M. Sharakhova,et al. A standard cytogenetic photomap for the mosquito Anopheles stephensi (Diptera: Culicidae): application for physical mapping. , 2006, Journal of medical entomology.
[102] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[103] N. Besansky,et al. A microsatellite map of the African human malaria vector Anopheles funestus. , 2004, The Journal of heredity.
[104] Jeanne Romero-Severson,et al. Inversions and Gene Order Shuffling in Anopheles gambiae and A. funestus , 2002, Science.
[105] Jian Wang,et al. The Genome Sequence of the Malaria Mosquito Anopheles gambiae , 2002, Science.
[106] A. della Torre,et al. A Polytene Chromosome Analysis of the Anopheles gambiae Species Complex , 2002, Science.
[107] J. Wiegant,et al. A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochromelabelled RNA. , 1980, Experimental cell research.