Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution.

Rutledge GG, Böhme U, Sanders M, Reid AJ, Cotton JA, Maiga-Ascofare O, Djimdé AA, Apinjoh TO, Amenga-Etego L, Manske M, Barnwell JW, Renaud F, Ollomo B, Prugnolle F, Anstey NM, Auburn S, Price RN, McCarthy JS, Kwiatkowski DP, [...] Otto TD

Nature, 542(7639):101-104, 25 Jan 2017

Cited by: 111 articles | PMID: 28117441 | PMCID: PMC5326575

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites.

Reid AJ, Talman AM, Bennett HM, Gomes AR, Sanders MJ, Illingworth CJR, Billker O, Berriman M, Lawniczak MK

Elife, 7:e33105, 27 Mar 2018

Cited by: 105 articles | PMID: 29580379 | PMCID: PMC5871331

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman M

Nat Genet, 46(7):693-700, 15 Jun 2014

Cited by: 94 articles | PMID: 24929830 | PMCID: PMC5012510

Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres.

Otto TD, Böhme U, Sanders M, Reid A, Bruske EI, Duffy CW, Bull PC, Pearson RD, Abdi A, Dimonte S, Stewart LB, Campino S, Kekre M, Hamilton WL, Claessens A, Volkman SK, Ndiaye D, Amambua-Ngwa A, Diakite M, [...] Berriman M

Wellcome Open Res, 3:52, 03 May 2018

Cited by: 70 articles | PMID: 29862326 | PMCID: PMC5964635

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D, Echaide IE, Farber M, Gahlot S, Gamble J, Gupta D, Gupta Y, Jackson L, Malandrin L, Malas TB, Moussa E, Nair M, Reid AJ, Sanders M, Sharma J, [...] Pain A

Nucleic Acids Res, 42(11):7113-7131, 05 May 2014

Cited by: 69 articles | PMID: 24799432 | PMCID: PMC4066756

Population, genetic, and antigenic diversity of the apicomplexan Eimeria tenella and their relevance to vaccine development.

Blake DP, Clark EL, Macdonald SE, Thenmozhi V, Kundu K, Garg R, Jatau ID, Ayoade S, Kawahara F, Moftah A, Reid AJ, Adebambo AO, Álvarez Zapata R, Srinivasa Rao AS, Thangaraj K, Banerjee PS, Dhinakar-Raj G, Raman M, Tomley FM

Proc Natl Acad Sci U S A, 112(38):E5343-50, 09 Sep 2015

Cited by: 50 articles | PMID: 26354122 | PMCID: PMC4586875

Free full text in Europe PMC

A single-cell atlas of Plasmodium falciparum transmission through the mosquito.

Real E, Howick VM, Dahalan FA, Witmer K, Cudini J, Andradi-Brown C, Blight J, Davidson MS, Dogga SK, Reid AJ, Baum J, Lawniczak MKN

Nat Commun, 12(1):3196, 27 May 2021

Cited by: 44 articles | PMID: 34045457 | PMCID: PMC8159942

Gene3D: comprehensive structural and functional annotation of genomes.

Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C

Nucleic Acids Res, 36(database issue):D414-8, 21 Nov 2007

Cited by: 41 articles | PMID: 18032434 | PMCID: PMC2238970

Antibody-independent mechanisms regulate the establishment of chronic Plasmodium infection.

Brugat T, Reid AJ, Lin J, Cunningham D, Tumwine I, Kushinga G, McLaughlin S, Spence P, Böhme U, Sanders M, Conteh S, Bushell E, Metcalf T, Billker O, Duffy PE, Newbold C, Berriman M, Langhorne J

Nat Microbiol, 2:16276, 06 Feb 2017

Cited by: 38 articles | PMID: 28165471 | PMCID: PMC5373435

Free full text in Europe PMC

Genomic characterisation of the effector complement of the potato cyst nematode Globodera pallida.

Thorpe P, Mantelin S, Cock PJ, Blok VC, Coke MC, Eves-van den Akker S, Guzeeva E, Lilley CJ, Smant G, Reid AJ, Wright KM, Urwin PE, Jones JT

BMC Genomics, 15:923, 23 Oct 2014

Cited by: 33 articles | PMID: 25342461 | PMCID: PMC4213498

The rhoptry proteome of Eimeria tenella sporozoites.

Oakes RD, Kurian D, Bromley E, Ward C, Lal K, Blake DP, Reid AJ, Pain A, Sinden RE, Wastling JM, Tomley FM

Int J Parasitol, 43(2):181-188, 20 Dec 2012

Cited by: 29 articles | PMID: 23262303

Repeated clinical malaria episodes are associated with modification of the immune system in children.

Bediako Y, Adams R, Reid AJ, Valletta JJ, Ndungu FM, Sodenkamp J, Mwacharo J, Ngoi JM, Kimani D, Kai O, Wambua J, Nyangweso G, de Villiers EP, Sanders M, Lotkowska ME, Lin JW, Manni S, Addy JWG, Recker M, [...] Langhorne J

BMC Med, 17(1):60, 13 Mar 2019

Cited by: 28 articles | PMID: 30862316 | PMCID: PMC6415347

The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.

Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C

Structure, 17(8):1051-1062, 01 Aug 2009

Cited by: 28 articles | PMID: 19679085 | PMCID: PMC2741583

Structural basis for RIFIN-mediated activation of LILRB1 in malaria.

Harrison TE, Mørch AM, Felce JH, Sakoguchi A, Reid AJ, Arase H, Dustin ML, Higgins MK

Nature, 587(7833):309-312, 10 Jul 2020

Cited by: 25 articles | PMID: 32650338 | PMCID: PMC7116854

Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa.

Reid AJ

Parasitology, 142 Suppl 1:S57-70, 26 Sep 2014

Cited by: 24 articles | PMID: 25257746 | PMCID: PMC4413850

Review

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS, Kingsley RA, Dougan G, Salmond GP

BMC Genomics, 14:822, 22 Nov 2013

Cited by: 21 articles | PMID: 24267595 | PMCID: PMC4046660

Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).

Lawton J, Brugat T, Yan YX, Reid AJ, Böhme U, Otto TD, Pain A, Jackson A, Berriman M, Cunningham D, Preiser P, Langhorne J

BMC Genomics, 13:125, 29 Mar 2012

Cited by: 21 articles | PMID: 22458863 | PMCID: PMC3384456

Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone.

Reid AJ, Yeats C, Orengo CA

Bioinformatics, 23(18):2353-2360, 20 Aug 2007

Cited by: 19 articles | PMID: 17709341

Exclusive dependence of IL-10Rα signalling on intestinal microbiota homeostasis and control of whipworm infection.

Duque-Correa MA, Karp NA, McCarthy C, Forman S, Goulding D, Sankaranarayanan G, Jenkins TP, Reid AJ, Cambridge EL, Ballesteros Reviriego C, Sanger Mouse Genetics Project, 3i consortium, Müller W, Cantacessi C, Dougan G, Grencis RK, Berriman M

PLoS Pathog, 15(1):e1007265, 14 Jan 2019

Cited by: 15 articles | PMID: 30640950 | PMCID: PMC6347331

Comparative evolutionary analysis of protein complexes in E. coli and yeast.

Reid AJ, Ranea JA, Orengo CA

BMC Genomics, 11:79, 01 Feb 2010

Cited by: 15 articles | PMID: 20122144 | PMCID: PMC2837643

Genes involved in host-parasite interactions can be revealed by their correlated expression.

Reid AJ, Berriman M

Nucleic Acids Res, 41(3):1508-1518, 28 Dec 2012

Cited by: 14 articles | PMID: 23275547 | PMCID: PMC3561955

Defining the early stages of intestinal colonisation by whipworms.

Duque-Correa MA, Goulding D, Rodgers FH, Gillis JA, Cormie C, Rawlinson KA, Bancroft AJ, Bennett HM, Lotkowska ME, Reid AJ, Speak AO, Scott P, Redshaw N, Tolley C, McCarthy C, Brandt C, Sharpe C, Ridley C, Moya JG, [...] Berriman M

Nat Commun, 13(1):1725, 01 Apr 2022

Cited by: 12 articles | PMID: 35365634 | PMCID: PMC8976045

10-year longitudinal study of malaria in children: Insights into acquisition and maintenance of naturally acquired immunity.

Addy JWG, Bediako Y, Ndungu FM, Valetta JJ, Reid AJ, Mwacharo J, Ngoi JM, Wambua J, Otieno E, Musyoki J, Said K, Berriman M, Marsh K, Bejon P, Recker M, Langhorne J

Wellcome Open Res, 6:79, 01 Jan 2021

Cited by: 11 articles | PMID: 35141425 | PMCID: PMC8822141

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys.

Aunin E, Böhme U, Sanderson T, Simons ND, Goldberg TL, Ting N, Chapman CA, Newbold CI, Berriman M, Reid AJ

PLoS Pathog, 16(8):e1008717, 03 Aug 2020

Cited by: 11 articles | PMID: 32745123 | PMCID: PMC7425995

Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern.

Lin JW, Reid AJ, Cunningham D, Böhme U, Tumwine I, Keller-Mclaughlin S, Sanders M, Berriman M, Langhorne J

Wellcome Open Res, 3:142, 06 Dec 2018

Cited by: 11 articles | PMID: 30542666 | PMCID: PMC6259598

Finding the "dark matter" in human and yeast protein network prediction and modelling.

Ranea JA, Morilla I, Lees JG, Reid AJ, Yeats C, Clegg AB, Sanchez-Jimenez F, Orengo C

PLoS Comput Biol, 6(9):e1000945, 23 Sep 2010

Cited by: 10 articles | PMID: 20885791 | PMCID: PMC2944794

The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens.

Aunin E, Böhme U, Blake D, Dove A, Smith M, Corton C, Oliver K, Betteridge E, Quail MA, McCarthy SA, Wood J, Tracey A, Torrance J, Sims Y, Howe K, Challis R, Berriman M, Reid A

Wellcome Open Res, 6:225, 09 Sep 2021

Cited by: 9 articles | PMID: 34703904 | PMCID: PMC8515493

CODA: accurate detection of functional associations between proteins in eukaryotic genomes using domain fusion.

Reid AJ, Ranea JA, Clegg AB, Orengo CA

PLoS One, 5(6):e10908, 01 Jun 2010

Cited by: 9 articles | PMID: 20532224 | PMCID: PMC2879367

Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.

Rojas AM, Santamaria A, Malik R, Jensen TS, Körner R, Morilla I, de Juan D, Krallinger M, Hansen DA, Hoffmann R, Lees J, Reid A, Yeats C, Wehner A, Elowe S, Clegg AB, Brunak S, Nigg EA, Orengo C, [...] Ranea JA

PLoS One, 7(3):e31813, 09 Mar 2012

Cited by: 8 articles | PMID: 22427808 | PMCID: PMC3302876

Individual-level variations in malaria susceptibility and acquisition of clinical protection.

Valletta JJ, Addy JWG, Reid AJ, Ndungu FM, Bediako Y, Mwacharo J, Mohammed KS, Musyoki J, Ngoi JM, Wambua J, Otieno E, Berriman M, Bejon P, Marsh K, Langhorne J, Newbold CI, Recker M

Wellcome Open Res, 6:22, 13 Sep 2021

Cited by: 6 articles | PMID: 35310901 | PMCID: PMC8914138

Daily rhythms in gene expression of the human parasite Schistosoma mansoni.

Rawlinson KA, Reid AJ, Lu Z, Driguez P, Wawer A, Coghlan A, Sankaranarayanan G, Buddenborg SK, Soria CD, McCarthy C, Holroyd N, Sanders M, Hoffmann KF, Wilcockson D, Rinaldi G, Berriman M

BMC Biol, 19(1):255, 02 Dec 2021

Cited by: 6 articles | PMID: 34852797 | PMCID: PMC8638415

Assessment of protein domain fusions in human protein interaction networks prediction: application to the human kinetochore model.

Morilla I, Lees JG, Reid AJ, Orengo C, Ranea JA

N Biotechnol, 27(6):755-765, 17 Sep 2010

Cited by: 5 articles | PMID: 20851221

Adapting to domesticity.

Reid AJ

Nat Rev Microbiol, 10(3):163, 16 Feb 2012

Cited by: 3 articles | PMID: 22337165

The evolution of protein functions and networks: a family-centric approach.

Dessailly BH, Reid AJ, Yeats C, Lees JG, Cuff A, Orengo CA

Biochem Soc Trans, 37(pt 4):745-750, 01 Aug 2009

Cited by: 2 articles | PMID: 19614587

An increase in reactive oxygen species underlies neonatal cerebellum repair

Pakula A, El Nagar S, Bayin NS, Christensen JB, Stephen DN, Reid AJ, Koche R, Joyner AL

bioRxiv, 17 Oct 2024

Cited by: 0 articles | PPR: PPR926426

Preprint

Hypoxia promotes airway differentiation in the human lung epithelium

Dong Z, Wit N, Agarwal A, Dubal D, van den Ameele J, Reid AJ, Nathan JA, Rawlins EL

bioRxiv, 09 Aug 2024

Cited by: 0 articles | PPR: PPR893472

Preprint

A manually curated annotation characterises genomic features of P. falciparum lncRNAs

Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ, Lee MCS

bioRxiv, 09 Jul 2022

Cited by: 0 articles | PPR: PPR516393

Preprint

The Plasmodium falciparum protein PfMRP1 functions as an influx ABC transporter

Silva M, Calçada C, Osório N, Baptista V, Thathy V, Teixeira M, Reid A, Ferreira P, Fidock D, Veiga M

Research Square, 13 Jan 2022

Cited by: 0 articles | PPR: PPR442490

Preprint v1

Characterising genome architectures using Genome Decomposition Analysis

Aunin E, Berriman M, Reid AJ

bioRxiv, 02 Dec 2021

Cited by: 0 articles | PPR: PPR427671

Preprint

The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens

Aunin E, Böhme U, Blake D, Dove A, Smith M, Corton C, Oliver K, Betteridge E, Quail MA, McCarthy SA, Wood J, Tracey A, Torrance J, Sims Y, Howe K, Challis R, Berriman M, Reid A

Wellcome Open Res, 09 Sep 2021

Cited by: 0 articles | PPR: PPR392660

Preprint v1

Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system

Buddenborg SK, Tracey A, Berger DJ, Lu Z, Doyle SR, Fu B, Yang F, Reid AJ, Rodgers FH, Rinaldi G, Sankaranarayanan G, Böhme U, Holroyd N, Berriman M

bioRxiv, 13 Aug 2021

Cited by: 0 articles | PPR: PPR382876

Preprint

Daily rhythms in the transcriptomes of the human parasite Schistosoma mansoni

Rawlinson KA, Reid AJ, Lu Z, Driguez P, Wawer A, Coghlan A, Sankaranarayanan G, Buddenborg SK, Soria CD, McCarthy C, Holroyd N, Sanders M, Hoffmann K, Wilcockson D, Rinaldi G, Berriman M

bioRxiv, 22 Apr 2021

Cited by: 0 articles | PPR: PPR315753

Preprint

A single-cell atlas of Plasmodium falciparum transmission through the mosquito

Real E, Howick VM, Dahalan F, Witmer K, Cudini J, Andradi-Brown C, Blight J, Davidson MS, Dogga SK, Reid AJ, Baum J, Lawniczak MKN

bioRxiv, 11 Oct 2020

Cited by: 0 articles | PPR: PPR224524

Preprint

Defining the early stages of intestinal colonisation by whipworms

Duque-Correa MA, Goulding D, Rodgers FH, Cormie C, Rawlinson K, Gillis JA, Bancroft AJ, Bennett HM, Lotkowska M, Reid AJ, Speak A, Scott P, Redshaw N, McCarthy C, Brandt C, Sharpe C, Ridley C, Moya JG, Carneiro CM, [...] Berriman M

bioRxiv, 22 Aug 2020

Cited by: 0 articles | PPR: PPR204489

Preprint

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys

Aunin E, Böhme U, Sanderson T, Simons ND, Goldberg TL, Ting N, Chapman CA, Newbold CI, Berriman M, Reid AJ

bioRxiv, 11 Dec 2019

Cited by: 0 articles | PPR: PPR105225

Preprint

The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle

Howick VM, Russell A, Andrews T, Heaton H, Reid AJ, Natarajan KN, Butungi H, Metcalf T, Verzier LH, Rayner J, Berriman M, Herren J, Billker O, Hemberg M, Talman A, Lawniczak M

bioRxiv, 22 Jan 2019

Cited by: 0 articles | PPR: PPR68080

Preprint

Bioinformatic analysis of expression data to identify effector candidates.

Reid AJ, Jones JT

Methods Mol Biol, 1127:17-27, 01 Jan 2014

Cited by: 0 articles | PMID: 24643549

Cereal killers.

Otto TD, Reid AJ

Nat Rev Microbiol, 11(11):744, 01 Nov 2013

Cited by: 0 articles | PMID: 24129509

Genome sequencing gets func-y.

Reid AJ

Nat Rev Microbiol, 9(6):401, 01 Jun 2011

Cited by: 0 articles | PMID: 21572456

It's alive!

Reid AJ

Nat Rev Microbiol, 8(7):468, 01 Jul 2010

Cited by: 0 articles | PMID: 20551972