Literature DB >> 32650287

Recent advances and future perspectives in vector-omics.

Austin Compton1, Igor V Sharakhov2, Zhijian Tu3.   

Abstract

We have reviewed recent progress and the remaining challenges in vector-omics. We have highlighted several technologies and applications that facilitate novel biological insights beyond achieving a reference-quality genome assembly. Among other topics, we have discussed the applications of chromatin conformation capture, chromatin accessibility assays, optical mapping, full-length RNA sequencing, single cell RNA analysis, proteomics, and population genomics. We anticipate that we will witness a great expansion in vector-omics research not only in its application in a broad range of species, but also its ability to uncover novel genetic elements and tackle previously inaccessible regions of the genome. It is our hope that the continued innovation in device portability, cost reduction, and informatics support will in the foreseeable future bring vector-omics to every vector laboratory and field station in the world, which will have an unparalleled impact on basic research and the control of vector-borne infectious diseases.
Copyright © 2020. Published by Elsevier Inc.

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Year:  2020        PMID: 32650287      PMCID: PMC8041138          DOI: 10.1016/j.cois.2020.05.006

Source DB:  PubMed          Journal:  Curr Opin Insect Sci            Impact factor:   5.186


  66 in total

1.  Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions.

Authors:  Joshua N Burton; Andrew Adey; Rupali P Patwardhan; Ruolan Qiu; Jacob O Kitzman; Jay Shendure
Journal:  Nat Biotechnol       Date:  2013-11-03       Impact factor: 54.908

2.  Errors in long-read assemblies can critically affect protein prediction.

Authors:  Mick Watson; Amanda Warr
Journal:  Nat Biotechnol       Date:  2019-02       Impact factor: 54.908

Review 3.  CTCF: an architectural protein bridging genome topology and function.

Authors:  Chin-Tong Ong; Victor G Corces
Journal:  Nat Rev Genet       Date:  2014-03-11       Impact factor: 53.242

4.  De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.

Authors:  Olga Dudchenko; Sanjit S Batra; Arina D Omer; Sarah K Nyquist; Marie Hoeger; Neva C Durand; Muhammad S Shamim; Ido Machol; Eric S Lander; Aviva Presser Aiden; Erez Lieberman Aiden
Journal:  Science       Date:  2017-03-23       Impact factor: 47.728

5.  Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Authors:  Daniel E Neafsey; Robert M Waterhouse; Mohammad R Abai; Sergey S Aganezov; Max A Alekseyev; James E Allen; James Amon; Bruno Arcà; Peter Arensburger; Gleb Artemov; Lauren A Assour; Hamidreza Basseri; Aaron Berlin; Bruce W Birren; Stephanie A Blandin; Andrew I Brockman; Thomas R Burkot; Austin Burt; Clara S Chan; Cedric Chauve; Joanna C Chiu; Mikkel Christensen; Carlo Costantini; Victoria L M Davidson; Elena Deligianni; Tania Dottorini; Vicky Dritsou; Stacey B Gabriel; Wamdaogo M Guelbeogo; Andrew B Hall; Mira V Han; Thaung Hlaing; Daniel S T Hughes; Adam M Jenkins; Xiaofang Jiang; Irwin Jungreis; Evdoxia G Kakani; Maryam Kamali; Petri Kemppainen; Ryan C Kennedy; Ioannis K Kirmitzoglou; Lizette L Koekemoer; Njoroge Laban; Nicholas Langridge; Mara K N Lawniczak; Manolis Lirakis; Neil F Lobo; Ernesto Lowy; Robert M MacCallum; Chunhong Mao; Gareth Maslen; Charles Mbogo; Jenny McCarthy; Kristin Michel; Sara N Mitchell; Wendy Moore; Katherine A Murphy; Anastasia N Naumenko; Tony Nolan; Eva M Novoa; Samantha O'Loughlin; Chioma Oringanje; Mohammad A Oshaghi; Nazzy Pakpour; Philippos A Papathanos; Ashley N Peery; Michael Povelones; Anil Prakash; David P Price; Ashok Rajaraman; Lisa J Reimer; David C Rinker; Antonis Rokas; Tanya L Russell; N'Fale Sagnon; Maria V Sharakhova; Terrance Shea; Felipe A Simão; Frederic Simard; Michel A Slotman; Pradya Somboon; Vladimir Stegniy; Claudio J Struchiner; Gregg W C Thomas; Marta Tojo; Pantelis Topalis; José M C Tubio; Maria F Unger; John Vontas; Catherine Walton; Craig S Wilding; Judith H Willis; Yi-Chieh Wu; Guiyun Yan; Evgeny M Zdobnov; Xiaofan Zhou; Flaminia Catteruccia; George K Christophides; Frank H Collins; Robert S Cornman; Andrea Crisanti; Martin J Donnelly; Scott J Emrich; Michael C Fontaine; William Gelbart; Matthew W Hahn; Immo A Hansen; Paul I Howell; Fotis C Kafatos; Manolis Kellis; Daniel Lawson; Christos Louis; Shirley Luckhart; Marc A T Muskavitch; José M Ribeiro; Michael A Riehle; Igor V Sharakhov; Zhijian Tu; Laurence J Zwiebel; Nora J Besansky
Journal:  Science       Date:  2014-11-27       Impact factor: 47.728

6.  Spatial organization of chromosomes in the salivary gland nuclei of Drosophila melanogaster.

Authors:  M Hochstrasser; D Mathog; Y Gruenbaum; H Saumweber; J W Sedat
Journal:  J Cell Biol       Date:  1986-01       Impact factor: 10.539

7.  Massively parallel digital transcriptional profiling of single cells.

Authors:  Grace X Y Zheng; Jessica M Terry; Phillip Belgrader; Paul Ryvkin; Zachary W Bent; Ryan Wilson; Solongo B Ziraldo; Tobias D Wheeler; Geoff P McDermott; Junjie Zhu; Mark T Gregory; Joe Shuga; Luz Montesclaros; Jason G Underwood; Donald A Masquelier; Stefanie Y Nishimura; Michael Schnall-Levin; Paul W Wyatt; Christopher M Hindson; Rajiv Bharadwaj; Alexander Wong; Kevin D Ness; Lan W Beppu; H Joachim Deeg; Christopher McFarland; Keith R Loeb; William J Valente; Nolan G Ericson; Emily A Stevens; Jerald P Radich; Tarjei S Mikkelsen; Benjamin J Hindson; Jason H Bielas
Journal:  Nat Commun       Date:  2017-01-16       Impact factor: 14.919

8.  BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files.

Authors:  Alexander Payne; Nadine Holmes; Vardhman Rakyan; Matthew Loose
Journal:  Bioinformatics       Date:  2019-07-01       Impact factor: 6.937

Review 9.  Single-cell transcriptome sequencing: recent advances and remaining challenges.

Authors:  Serena Liu; Cole Trapnell
Journal:  F1000Res       Date:  2016-02-17

10.  Identification of Aedes aegypti cis-regulatory elements that promote gene expression in olfactory receptor neurons of distantly related dipteran insects.

Authors:  Keshava Mysore; Ping Li; Molly Duman-Scheel
Journal:  Parasit Vectors       Date:  2018-07-11       Impact factor: 3.876

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  3 in total

Review 1.  Selective targeting of biting females to control mosquito-borne infectious diseases.

Authors:  Bianca B Kojin; Austin Compton; Zach N Adelman; Zhijian Tu
Journal:  Trends Parasitol       Date:  2022-06-13

Review 2.  Chromatin Structure and Function in Mosquitoes.

Authors:  Óscar M Lezcano; Miriam Sánchez-Polo; José L Ruiz; Elena Gómez-Díaz
Journal:  Front Genet       Date:  2020-12-07       Impact factor: 4.599

3.  The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression.

Authors:  José L Ruiz; Lisa C Ranford-Cartwright; Elena Gómez-Díaz
Journal:  NAR Genom Bioinform       Date:  2021-01-20
  3 in total

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