·The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India.

Abd El Ghany M, Chander J, Mutreja A, Rashid M, Hill‐Cawthorne GA, Ali S, Naeem R, Thomson NR, Dougan G and Pain A

PLoS neglected tropical diseases 2014;8;7;e2981

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·Towards a molecular systems model of coronary artery disease.

Abraham G, Bhalala OG, de Bakker PI, Ripatti S and Inouye M

Current cardiology reports 2014;16;6;488

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·Editorial overview: cancer genomics: kill it. Kill it dead.

Adams D and McDermott U

Current opinion in genetics & development 2014;24;v‐vi

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·Histopathology reveals correlative and unique phenotypes in a high‐throughput mouse phenotyping screen.

Adissu HA, Estabel J, Sunter D, Tuck E, Hooks Y, Carragher DM, Clarke K, Karp NA, Project SM, Newbigging S, Jones N, Morikawa L, White JK and McKerlie C

Disease models & mechanisms 2014;7;5;515‐24

PUBMED: 24652767 ; PMC: 4007403 ; DOI: 10.1242/dmm.015263

·H3Africa: a tipping point for a revolution in bioinformatics, genomics and health research in Africa.

Adoga MP, Fatumo SA and Agwale SM

Source code for biology and medicine 2014;9;10

PUBMED: 24829612 ; PMC: 4019950 ; DOI: 10.1186/1751‐0473‐9‐10

·Allelic expression mapping across cellular lineages to establish impact of non‐coding SNPs.

Adoue V, Schiavi A, Light N, Almlöf JC, Lundmark P, Ge B, Kwan T, Caron M, Rönnblom L, Wang C, Chen SH, Goodall AH, Cambien F, Deloukas P, Ouwehand WH, Syvänen AC and Pastinen T

Molecular systems biology 2014;10;10;754

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·Human african trypanosomiasis research gets a boost: unraveling the tsetse genome.

Aksoy S, Attardo G, Berriman M, Christoffels A, Lehane M, Masiga D and Toure Y

PLoS neglected tropical diseases 2014;8;4;e2624

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·Rare variants in NR2F2 cause congenital heart defects in humans.

Al Turki S, Manickaraj AK, Mercer CL, Gerety SS, Hitz MP et al.,

American journal of human genetics 2014;94;4;574‐85

PUBMED: 24702954 ; PMC: 3980509 ; DOI: 10.1016/j.ajhg.2014.03.007

·Mutational signatures: the patterns of somatic mutations hidden in cancer genomes.

Alexandrov LB and Stratton MR

Current opinion in genetics & development 2014;24;52‐60

PUBMED: 24657537 ; PMC: 3990474 ; DOI: 10.1016/j.gde.2013.11.014

·Reading between the lines; understanding drug response in the post genomic era.

Alifrangis CC and McDermott U

Molecular o­ncology 2014

PUBMED: 24957465 ; DOI: 10.1016/j.molonc.2014.05.014

·One patient, two lesions, two o­ncogenic drivers of gastric cancer.

Alsinet C, Ranzani M and Adams DJ

Genome biology 2014;15;8;444

PUBMED: 25222187 ; PMC: 4281955 ; DOI: 10.1186/s13059‐014‐0444‐9

·Plasmodium falciparum founder populations in Western Cambodia have reduced artemisinin sensitivity in vitro.

Amaratunga C, Witkowski B, Dek D, Try V, Khim N, Miotto O, Ménard D and Fairhurst RM

Antimicrobial agents and chemotherapy 2014

PUBMED: 24867977 ; DOI: 10.1128/AAC.03055‐14

·Whole Genome Sequencing of a Methicillin‐Resistant Staphylococcus aureus Pseudo‐Outbreak in a Professional Football Team.

Anderson DJ, Harris SR, Godofsky E, Toriscelli T, Rude TH, Elder K, Sexton DJ, Pellman EJ, Mayer T, Fowler VG and Peacock SJ

Open forum infectious diseases 2014;1;3;ofu096

PUBMED: 25734164 ; PMC: 4324220 ; DOI: 10.1093/ofid/ofu096

·A syndromic form of Pierre Robin sequence is caused by 5q23 deletions encompassing FBN2 and PHAX.

Ansari M, Rainger JK, Murray JE, Hanson I, Firth HV, Mehendale F, Amiel J, Gordon CT, Percesepe A, Mazzanti L, Fryer A, Ferrari P, Devriendt K, Temple IK and FitzPatrick DR

European journal of medical genetics 2014;57;10;587‐95

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·A molecular marker of artemisinin‐resistant Plasmodium falciparum malaria.

Ariey F, Witkowski B, Amaratunga C, Beghain J, Langlois AC et al.,

Nature 2014;505;7481;50‐5

PUBMED: 24352242 ; DOI: 10.1038/nature12876

·Lipoprotein(a) levels, genotype, and incident aortic valve stenosis: a prospective Mendelian randomization study and replication in a case‐control cohort.

Arsenault BJ, Boekholdt SM, Dubé MP, Rhéaume E, Wareham NJ, Khaw KT, Sandhu MS and Tardif JC

Circulation. Cardiovascular genetics 2014;7;3;304‐10

PUBMED: 24704946 ; DOI: 10.1161/CIRCGENETICS.113.000400

·Spread of artemisinin resistance in Plasmodium falciparum malaria.

Ashley EA, Dhorda M, Fairhurst RM, Amaratunga C, Lim P, Suon S et al.,

The New England journal of medicine 2014;371;5;411‐23

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·Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.

Ashton PM, Baker KS, Gentle A, Wooldridge DJ, Thomson NR, Dallman TJ and Jenkins C

Gut pathogens 2014;6;1;7

PUBMED: 24684748 ; PMC: 3972513 ; DOI: 10.1186/1757‐4749‐6‐7

·estMOI: estimating multiplicity of infection using parasite deep sequencing data.

Assefa SA, Preston MD, Campino S, Ocholla H, Sutherland CJ and Clark TG

Bioinformatics (Oxford, England) 2014

PUBMED: 24443379 ; DOI: 10.1093/bioinformatics/btu005

·Epistasis between the haptoglobin common variant and α+thalassemia influences risk of severe malaria in Kenyan children.

Atkinson SH, Uyoga SM, Nyatichi E, Macharia AW, Nyutu G, Ndila C, Kwiatkowski DP, Rockett KA and Williams TN

Blood 2014;123;13;2008‐16

PUBMED: 24478401 ; PMC: 3968387 ; DOI: 10.1182/blood‐2013‐10‐533489

·Transcriptionally active chromatin recruits homologous recombination at DNA double‐strand breaks.

Aymard F, Bugler B, Schmidt CK, Guillou E, Caron P, Briois S, Iacovoni JS, Daburon V, Miller KM, Jackson SP and Legube G

Nature structural & molecular biology 2014;21;4;366‐74

PUBMED: 24658350 ; DOI: 10.1038/nsmb.2796

·Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes.

Ayub Q, Moutsianas L, Chen Y, Panoutsopoulou K, Colonna V, Pagani L, Prokopenko I, Ritchie GR, Tyler‐Smith C, McCarthy MI, Zeggini E and Xue Y

American journal of human genetics 2014;94;2;176‐85

PUBMED: 24412096 ; PMC: 3928649 ; DOI: 10.1016/j.ajhg.2013.12.010

·Novel mutations in penicillin‐binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant o­n susceptibility testing, but lack the mec gene.

Ba X, Harrison EM, Edwards GF, Holden MT, Larsen AR, Petersen A, Skov RL, Peacock SJ, Parkhill J, Paterson GK and Holmes MA

The Journal of antimicrobial chemotherapy 2014;69;3;594‐7

PUBMED: 24216768 ; PMC: 3922151 ; DOI: 10.1093/jac/dkt418

·TB or not TB? Genomic portraits provide answers.

Baker KS and Ellington MJ

Nature reviews. Microbiology 2014

PUBMED: 24801935 ; DOI: 10.1038/nrmicro3273

·Poxviruses in Bats … so What?

Baker KS and Murcia PR

Viruses 2014;6;4;1564‐77

PUBMED: 24704730 ; DOI: 10.3390/v6041564

·Gene conversion violates the stepwise mutation model for microsatellites in y‐chromosomal palindromic repeats.

Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho‐Silva D, Kraaijenbrink T, de Knijff P, Tyler‐Smith C and Jobling MA

Human mutation 2014;35;5;609‐17

PUBMED: 24610746 ; PMC: 4233959 ; DOI: 10.1002/humu.22542

·Toward male individualization with rapidly mutating y‐chromosomal short tandem repeats.

Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ et al.,

Human mutation 2014;35;8;1021‐32

PUBMED: 24917567 ; PMC: 4145662 ; DOI: 10.1002/humu.22599

·Multi‐species, multi‐transcription factor binding highlights conserved control of tissue‐specific biological pathways.

Ballester B, Medina‐Rivera A, Schmidt D, Gonzàlez‐Porta M, Carlucci M et al.,

eLife 2014;3

PUBMED: 25279814 ; DOI: 10.7554/eLife.02626

·Mutations in KPTN cause macrocephaly, neurodevelopmental delay, and seizures.

Baple EL, Maroofian R, Chioza BA, Izadi M, Cross HE, Al‐Turki S, Barwick K, Skrzypiec A, Pawlak R, Wagner K, Coblentz R, Zainy T, Patton MA, Mansour S, Rich P, Qualmann B, Hurles ME, Kessels MM and Crosby AH

American journal of human genetics 2014;94;1;87‐94

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·Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model.

Bard‐Chapeau EA, Nguyen AT, Rust AG, Sayadi A, Lee P, Chua BQ et al.,

Nature genetics 2014;46;1;24‐32

PUBMED: 24316982 ; PMC: 4131144 ; DOI: 10.1038/ng.2847

·A genome wide association study of mathematical ability reveals an association at chromosome 3q29, a locus associated with autism and learning difficulties: a preliminary study.

Baron‐Cohen S, Murphy L, Chakrabarti B, Craig I, Mallya U, Lakatošová S, Rehnstrom K, Peltonen L, Wheelwright S, Allison C, Fisher SE and Warrier V

PloS o­ne 2014;9;5;e96374

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·Global population structure and evolution of Bordetella pertussis and their relationship with vaccination.

Bart MJ, Harris SR, Advani A, Arakawa Y, Bottero D, Bouchez V et al.,

mBio 2014;5;2;e01074

PUBMED: 24757216 ; PMC: 3994516 ; DOI: 10.1128/mBio.01074‐14

·Capturing needles in haystacks: a comparison of B‐cell receptor sequencing methods.

Bashford‐Rogers RJ, Palser AL, Idris SF, Carter L, Epstein M, Callard RE, Douek DC, Vassiliou GS, Follows GA, Hubank M and Kellam P

BMC immunology 2014;15;29

PUBMED: 25189176 ; PMC: 4243823 ; DOI: 10.1186/s12865‐014‐0029‐0

·Considerations when investigating lncRNA function in vivo.

Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson‐Smith AC, Gingeras TR, Haerty W, Higgs DR, Miska EA and Ponting CP

eLife 2014;3;e03058

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·A Common Control Group ‐ Optimising the Experiment Design to Maximise Sensitivity.

Bate S and Karp NA

PloS o­ne 2014;9;12;e114872

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·No Evidence for Genome‐Wide Interactions o­n Plasma Fibrinogen by Smoking, Alcohol Consumption and Body Mass Index: Results from Meta‐Analyses of 80,607 Subjects.

Baumert J, Huang J, McKnight B, Sabater‐Lleal M, Steri M, Chu AY, Trompet S, Lopez LM, Fornage M, Teumer A, Tang W, Rudnicka AR, Mälarstig A et al.,

PloS o­ne 2014;9;12;e111156

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·Efficacy of a Plasmodium vivax malaria vaccine using ChAd63 and modified vaccinia Ankara expressing thrombospondin‐related anonymous protein as assessed with transgenic Plasmodium berghei parasites.

Bauza K, Malinauskas T, Pfander C, Anar B, Jones EY, Billker O, Hill AV and Reyes‐Sandoval A

Infection and immunity 2014;82;3;1277‐86

PUBMED: 24379295 ; PMC: 3957994 ; DOI: 10.1128/IAI.01187‐13

·Human post‐mortem synapse proteome integrity screening for proteomic studies of postsynaptic complexes.

Bayés À, Collins MO, Galtrey CM, Simonnet C, Roy M, Croning MD, Gou G, van de Lagemaat LN, Milward D, Whittle IR, Smith C, Choudhary JS and Grant SG

Molecular brain 2014;7;88

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·Genome sequencing of normal cells reveals developmental lineages and mutational processes.

Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J et al.,

Nature 2014;513;7518;422‐5

PUBMED: 25043003 ; PMC: 4227286 ; DOI: 10.1038/nature13448

·A Pathogenic Mosaic TP53 Mutation in Two Germ Layers Detected by Next Generation Sequencing.

Behjati S, Maschietto M, Williams RD, Side L, Hubank M, West R, Pearson K, Sebire N, Tarpey P, Futreal A, Brooks T, Stratton MR and Anderson J

PloS o­ne 2014;9;5;e96531

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·Recurrent PTPRB and PLCG1 mutations in angiosarcoma.

Behjati S, Tarpey PS, Sheldon H, Martincorena I, Van Loo P, Gundem G, Wedge DC, Ramakrishna M, Cooke SL, Pillay N, Vollan HK, Papaemmanuil E, Koss H et al.,

Nature genetics 2014;46;4;376‐9

PUBMED: 24633157 ; PMC: 4032873 ; DOI: 10.1038/ng.2921

·Keeping 53BP1 out of focus in mitosis.

Belotserkovskaya R and Jackson SP

Cell research 2014

PUBMED: 24810302 ; DOI: 10.1038/cr.2014.62

·Split reality for novel tick virus.

Bennett HM

Nature reviews. Microbiology 2014

PUBMED: 24909108 ; DOI: 10.1038/nrmicro3297

·The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion.

Bennett HM, Mok HP, Gkrania‐Klotsas E, Tsai IJ, Stanley EJ, Antoun NM, Coghlan A, Harsha B, Traini A, Ribeiro DM, Steinbiss S, Lucas SB, Allinson KS et al.,

Genome biology 2014;15;11;510

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·A high‐definition view of functional genetic variation from natural yeast genomes.

Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R and Liti G

Molecular biology and evolution 2014;31;4;872‐88

PUBMED: 24425782 ; PMC: 3969562 ; DOI: 10.1093/molbev/msu037

·Izumo meets Juno: preventing polyspermy in fertilization.

Bianchi E and Wright GJ

Cell cycle (Georgetown, Tex.) 2014;13;13;2019‐20

PUBMED: 24906131 ; PMC: 4111690 ; DOI: 10.4161/cc.29461

·Juno is the egg Izumo receptor and is essential for mammalian fertilization.

Bianchi E, Doe B, Goulding D and Wright GJ

Nature 2014;508;7497;483‐7

PUBMED: 24739963 ; PMC: 3998876 ; DOI: 10.1038/nature13203

·A loss of function screen of identified genome‐wide association study Loci reveals new genes controlling hematopoiesis.

Bielczyk‐Maczyńska E, Serbanovic‐Canic J, Ferreira L, Soranzo N, Stemple DL, Ouwehand WH and Cvejic A

PLoS genetics 2014;10;7;e1004450

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·A quantitative 14‐3‐3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response.

Blasius M, Wagner SA, Choudhary C, Bartek J and Jackson SP

Genes & development 2014

PUBMED: 25189701 ; DOI: 10.1101/gad.246272.114

·Recombination: genomic mix ‘n’ match.

Boinett CJ and Cain AK

Nature reviews. Microbiology 2014

PUBMED: 25383603 ; DOI: 10.1038/nrmicro3388

·Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.

Bolli N, Avet‐Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik‐Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM et al.,

Nature communications 2014;5;2997

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·The Scramble Conversion Tool.

Bonfield JK

Bioinformatics (Oxford, England) 2014

PUBMED: 24930138 ; DOI: 10.1093/bioinformatics/btu390

·A genome‐wide association study of anorexia nervosa.

Boraska V, Franklin CS, Floyd JA, Thornton LM, Huckins LM, Southam L, Rayner NW, Tachmazidou I, Klump KL, Treasure J, Lewis CM et al.,

Molecular psychiatry 2014;19;10;1085‐94

PUBMED: 24514567 ; PMC: 4325090 ; DOI: 10.1038/mp.2013.187

·Pre‐Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis.

Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK et al.,

Nature 2014;514;7523;494‐7

PUBMED: 25141181 ; DOI: 10.1038/nature13591

·Multiplex PCR Assay for Unequivocal Differentiation of Actinobacillus pleuropneumoniae Serovars 1 to 3, 5 to 8, 10, and 12.

Bossé JT, Li Y, Angen O, Weinert LA, Chaudhuri RR, Holden MT, Williamson SM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR and BRaDP1T consortium

Journal of clinical microbiology 2014;52;7;2380‐5

PUBMED: 24759717 ; DOI: 10.1128/JCM.00685‐14

·Human immunodeficiency virus Tat associates with a specific set of cellular RNAs.

Bouwman RD, Palser A, Parry CM, Coulter E, Rasaiyaah J, Kellam P and Jenner RG

Retrovirology 2014;11;53

PUBMED: 24990269 ; PMC: 4086691 ; DOI: 10.1186/1742‐4690‐11‐53

·Expression of a single‐chain human leukocyte antigen‐DRA/DRB3*01:01 molecule and differential binding of a monoclonal antibody in the presence of specifically bound human platelet antigen‐1a peptide.

Bouwmans EE, Smethurst PA, Garner SF, Ouwehand WH and Morley SL

Transfusion 2014;54;6;1478‐85

PUBMED: 24308361 ; DOI: 10.1111/trf.12502

·Whole‐exome sequencing in an extended family with myocardial infarction unmasks familial hypercholesterolemia.

Brænne I, Reiz B, Medack A, Kleinecke M, Fischer M, Tuna S, Hengstenberg C, Deloukas P, Erdmann J, Schunkert H and Cardiogenics consortium

BMC cardiovascular disorders 2014;14;1;108

PUBMED: 25154303 ; DOI: 10.1186/1471‐2261‐14‐108

·DECIPHER: database for the interpretation of phenotype‐linked plausibly pathogenic sequence and copy‐number variation.

Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP and Swaminathan GJ

Nucleic acids research 2014;42;Database issue;D993‐D1000

PUBMED: 24150940 ; PMC: 3965078 ; DOI: 10.1093/nar/gkt937

·A gene‐by‐gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.

Bratcher HB, Corton C, Jolley KA, Parkhill J and Maiden MC

BMC genomics 2014;15;1138

PUBMED: 25523208 ; PMC: 4377854 ; DOI: 10.1186/1471‐2164‐15‐1138

·The genomic substrate for adaptive radiation in African cichlid fish.

Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner‐Maier J, Johnson J, Alcazar R, Noh HJ et al.,

Nature 2014

PUBMED: 25186727 ; DOI: 10.1038/nature13726

·Phosphoinositide metabolism links cGMP‐dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites.

Brochet M, Collins MO, Smith TK, Thompson E, Sebastian S, Volkmann K, Schwach F, Chappell L, Gomes AR, Berriman M, Rayner JC, Baker DA, Choudhary J and Billker O

PLoS biology 2014;12;3;e1001806

PUBMED: 24594931 ; PMC: 3942320 ; DOI: 10.1371/journal.pbio.1001806

·Genetic interactions affecting human gene expression identified by variance association mapping.

Brown AA, Buil A, Viñuela A, Lappalainen T, Zheng HF, Richards JB, Small KS, Spector TD, Dermitzakis ET and Durbin R

eLife 2014

PUBMED: 24771767 ; DOI: 10.7554/eLife.01381

·Cis and trans effects of human genomic variants o­n gene expression.

Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G and Dermitzakis ET

PLoS genetics 2014;10;7;e1004461

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·A multi‐country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012.

Byrne L, Fisher I, Peters T, Mather A, Thomson N, Rosner B et al.,

Euro surveillance : bulletin Européen sur les maladies transmissibles = European communicable disease bulletin 2014;19;31;6‐13

PUBMED: 25138971

·Genome‐wide analysis of cold adaptation in indigenous Siberian populations.

Cardona A, Pagani L, Antao T, Lawson DJ, Eichstaedt CA, Yngvadottir B, Shwe MT, Wee J, Romero IG, Raj S, Metspalu M, Villems R, Willerslev E et al.,

PloS o­ne 2014;9;5;e98076

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·Single nucleotide polymorphisms with cis‐regulatory effects o­n long non‐coding transcripts in human primary monocytes.

Carlsson Almlöf J, Lundmark P, Lundmark A, Ge B, Pastinen T, Cardiogenics Consortium, Goodall AH, Cambien F, Deloukas P, Ouwehand WH and Syvänen AC

PloS o­ne 2014;9;7;e102612

PUBMED: 25025429 ; DOI: 10.1371/journal.pone.0102612

·Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Barrio AM, Pielberg G, Rafati N, Sayyab S, Turner‐Maier J, Younis S, Afonso S, Aken B et al.,

Science (New York, N.Y.) 2014;345;6200;1074‐9

PUBMED: 25170157 ; DOI: 10.1126/science.1253714

·Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound.

Carss KJ, Hillman SC, Parthiban V, McMullan DJ, Maher ER, Kilby MD and Hurles ME

Human molecular genetics 2014;23;12;3269‐77

PUBMED: 24476948 ; PMC: 4030780 ; DOI: 10.1093/hmg/ddu038

·Evolution and transmission of drug‐resistant tuberculosis in a Russian population.

Casali N, Nikolayevskyy V, Balabanova Y, Harris SR, Ignatyeva O, Kontsevaya I, Corander J, Bryant J, Parkhill J, Nejentsev S, Horstmann RD, Brown T and Drobniewski F

Nature genetics 2014

PUBMED: 24464101 ; DOI: 10.1038/ng.2878

·Whole‐genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals.

Cavanagh JP, Hjerde E, Holden MT, Kahlke T, Klingenberg C, Flægstad T, Parkhill J, Bentley SD and Sollid JU

The Journal of antimicrobial chemotherapy 2014

PUBMED: 25038069 ; DOI: 10.1093/jac/dku271

·Found in translation.

Chappell L

Nature reviews. Microbiology 2014;12;4;238

PUBMED: 24608332 ; DOI: 10.1038/nrmicro3243

·Spinster homolog 2 (spns2) deficiency causes early o­nset progressive hearing loss.

Chen J, Ingham N, Kelly J, Jadeja S, Goulding D, Pass J, Mahajan VB, Tsang SH, Nijnik A, Jackson IJ, White JK, Forge A, Jagger D and Steel KP

PLoS genetics 2014;10;10;e1004688

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·A reduction in Ptprq associated with specific features of the deafness phenotype of the miR‐96 mutant mouse diminuendo.

Chen J, Johnson SL, Lewis MA, Hilton JM, Huma A, Marcotti W and Steel KP

The European journal of neuroscience 2014

PUBMED: 24446963 ; DOI: 10.1111/ejn.12484

·Transcriptional diversity during lineage commitment of human blood progenitors.

Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk‐Maczynska E, Coe S, Farrow S, Poudel P et al.,

Science (New York, N.Y.) 2014;345;6204;1251033

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·Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm.

Chetaille P, Preuss C, Burkhard S, Côté JM, Houde C, Castilloux J, Piché J, Gosset N, Leclerc S, Wünnemann F, Thibeault M, Gagnon C, Galli A, Tuck E et al.,

Nature genetics 2014;46;11;1245‐9

PUBMED: 25282101 ; DOI: 10.1038/ng.3113

·Generation and characterization of influenza A viruses with altered polymerase fidelity.

Cheung PP, Watson SJ, Choy KT, Fun Sia S, Wong DD, Poon LL, Kellam P, Guan Y, Malik Peiris JS and Yen HL

Nature communications 2014;5;4794

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·Polygenic in vivo validation of cancer mutations using transposons.

Chew SK, Lu D, Campos LS, Scott KL, Saci A, Wang J, Collinson A, Raine K, Hinton J, Teague JW, Jones D, Menzies A, Butler AP, Gamble J, O’Meara S, McLaren S, Chin L, Liu P and Futreal PA

Genome biology 2014;15;9;455

PUBMED: 25260652 ; PMC: 4210617 ; DOI: 10.1186/s13059‐014‐0455‐6

·Dense genomic sampling identifies highways of pneumococcal recombination.

Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, Pessia A, Aanensen DM, Mather AE, Page AJ, Salter SJ, Harris D et al.,

Nature genetics 2014;46;3;305‐9

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·Comprehensive identification of single nucleotide polymorphisms associated with beta‐lactam resistance within pneumococcal mosaic genes.

Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD and Parkhill J

PLoS genetics 2014;10;8;e1004547

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·Calreticulin gene exon 9 frameshift mutations in patients with thrombocytosis.

Chi J, Nicolaou KA, Nicolaidou V, Koumas L, Mitsidou A, Pierides C, Manoloukos M, Barbouti K, Melanthiou F, Prokopiou C, Vassiliou GS and Costeas P

Leukemia 2014;28;5;1152‐4

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·International glossina genome initiative 2004‐2014: a driver for post‐genomic era research o­n the African continent.

Christoffels A, Masiga D, Berriman M, Lehane M, Touré Y and Aksoy S

PLoS neglected tropical diseases 2014;8;8;e3024

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·Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

Claessens A, Hamilton WL, Kekre M, Otto TD, Faizullabhoy A, Rayner JC and Kwiatkowski D

PLoS genetics 2014;10;12;e1004812

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·From cheek swabs to consensus sequences: an A to Z protocol for high‐throughput DNA sequencing of complete human mitochondrial genomes.

Clarke AC, Prost S, Stanton JA, White WT, Kaplan ME, Matisoo‐Smith EA and Genographic Consortium

BMC genomics 2014;15;68

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·Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.

Clarkson CS, Weetman D, Essandoh J, Yawson AE, Maslen G, Manske M, Field SG, Webster M, Antão T, MacInnis B, Kwiatkowski D and Donnelly MJ

Nature communications 2014;5;4248

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·A Selective Sweep o­n a Deleterious Mutation in CPT1A in Arctic Populations.

Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G, Pagani L, Lawson DJ, Antão T, Vicente M, Mitt M, DeGiorgio M, Faltyskova Z, Xue Y, Ayub Q et al.,

American journal of human genetics 2014;95;5;584‐589

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·PolyTB: A genomic variation map for Mycobacterium tuberculosis.

Coll F, Preston M, Guerra‐Assunção JA, Hill‐Cawthorn G et al.,

Tuberculosis (Edinburgh, Scotland) 2014

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·Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation.

Collins MO, Wright JC, Jones M, Rayner JC and Choudhary JS

Journal of proteomics 2014;103;1‐14

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·Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole‐genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M et al.,

Genome biology 2014;15;6;R88

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·Processed pseudogenes acquired somatically during cancer development.

Cooke SL, Shlien A, Marshall J, Pipinikas CP, Martincorena I, Tubio JM, Li Y, Menzies A, Mudie L, Ramakrishna M, Yates L, Davies H, Bolli N, Bignell GR et al.,

Nature communications 2014;5;3644

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·Genomic identification of a novel co‐trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi.

Cornick JE, Harris SR, Parry CM, Moore MJ, Jassi C, Kamng’ona A, Kulohoma B, Heyderman RS, Bentley SD and Everett DB

The Journal of antimicrobial chemotherapy 2014;69;2;368‐74

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·BioJS: an open source standard for biological visualisation ‐ its status in 2014.

Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F et al.,

F1000Research 2014;3;55

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·Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm.

Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P and van der Hoek L

PloS o­ne 2014;9;4;e93269

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·Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.

Cotten M, Petrova V, Phan MV, Rabaa MA, Watson SJ, Ong SH, Kellam P and Baker S

Journal of virology 2014;88;19;11056‐69

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·Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus.

Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH, Al Rabeeah AA, Alhakeem RF, Assiri A, Al‐Tawfiq JA, Albarrak A, Barry M, Shibl A et al.,

mBio 2014;5;1

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·The genome and life‐stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJ, Eves‐van den Akker S, Holroyd N, Hunt M, Mantelin S et al.,

Genome biology 2014;15;3;R43

PUBMED: 24580726 ; PMC: 4054857 ; DOI: 10.1186/gb‐2014‐15‐3‐r43

·Genome‐wide association study of sexual maturation in males and females highlights a role for body mass and menarche loci in male puberty.

Cousminer DL, Stergiakouli E, Berry DJ, Ang W, Groen‐Blokhuis MM, Körner A, Siitonen N, Ntalla I, Marinelli M, Perry JR, Kettunen J, Jansen R et al.,

Human molecular genetics 2014;23;16;4452‐64

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·Quantitation of malaria parasite‐erythrocyte cell‐cell interactions using optical tweezers.

Crick AJ, Theron M, Tiffert T, Lew VL, Cicuta P and Rayner JC

Biophysical journal 2014;107;4;846‐53

PUBMED: 25140419 ; PMC: 4142257 ; DOI: 10.1016/j.bpj.2014.07.010

·Evidence for soft selective sweeps in the evolution of pneumococcal multidrug‐resistance and vaccine escape.

Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C, Yang F, Sá‐Leão R, Beall B, Klugman KP, Parkhill J, Turner P and Bentley SD

Genome biology and evolution 2014

PUBMED: 24916661 ; DOI: 10.1093/gbe/evu120

·Diversification of bacterial genome content through distinct mechanisms over different timescales.

Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD and Hanage WP

Nature communications 2014;5;5471

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·Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug‐resistant pneumococcal clone.

Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá‐Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG and Bentley SD

BMC biology 2014;12;49

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·Time between sputum sample collection and storage significantly influences bacterial sequence composition from Cystic Fibrosis respiratory infections.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hafiz T, Hoffman LR, Carroll MP, Parkhill J, Bruce KD and van der Gast CJ

Journal of clinical microbiology 2014

PUBMED: 24920767 ; DOI: 10.1128/JCM.00764‐14

·Implications of multiple freeze‐thawing o­n respiratory samples for culture‐independent analyses.

Cuthbertson L, Rogers GB, Walker AW, Oliver A, Hoffman LR, Carroll MP, Parkhill J, Bruce KD and van der Gast CJ

Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2014

PUBMED: 25459563 ; DOI: 10.1016/j.jcf.2014.10.004

·From genome‐wide association study hits to new insights into experimental hematology.

Cvejic A

Experimental hematology 2014;42;8;630‐636

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·Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

Da Cunha V, Davies MR, Douarre PE, Rosinski‐Chupin I, Margarit I, Spinali S, Perkins T, Lechat P, Dmytruk N, Sauvage E, Ma L, Romi B et al.,

Nature communications 2014;5;4544

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·Structure and computational analysis of a novel protein with metallopeptidase‐like and circularly permuted winged‐helix‐turn‐helix domains reveals a possible role in modified polysaccharide biosynthesis.

Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A and Aravind L

BMC bioinformatics 2014;15;75

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·The correlation between reading and mathematics ability at age twelve has a substantial genetic component.

Davis OS, Band G, Pirinen M, Haworth CM, Meaburn EL, Kovas Y, Harlaar N, Docherty SJ, Hanscombe KB, Trzaskowski M, Curtis CJ, Strange A et al.,

Nature communications 2014;5;4204

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·Recurrent mutations, including NPM1c, activate a BRD4‐dependent core transcriptional program in acute myeloid leukemia.

Dawson MA, Gudgin EJ, Horton SJ, Giotopoulos G, Meduri E, Robson S, Cannizzaro E, Osaki H, Wiese M, Putwain S, Fong CY, Grove C, Craig J, Dittmann A et al.,

Leukemia 2014;28;2;311‐20

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·Spatial and temporal diversity in genomic instability processes defines lung cancer evolution.

de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, Jamal‐Hanjani M, Shafi S, Murugaesu N, Rowan AJ, Grönroos E, Muhammad MA et al.,

Science (New York, N.Y.) 2014;346;6206;251‐6

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·Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.

De Chiara M, Hood D, Muzzi A, Pickard DJ, Perkins T, Pizza M, Dougan G, Rappuoli R, Moxon ER, Soriani M and Donati C

Proceedings of the National Academy of Sciences of the United States of America 2014;111;14;5439‐44

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·Chromatin landscapes of retroviral and transposon integration profiles.

de Jong J, Akhtar W, Badhai J, Rust AG, Rad R, Hilkens J, Berns A, van Lohuizen M, Wessels LF and de Ridder J

PLoS genetics 2014;10;4;e1004250

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·Synaptic, transcriptional and chromatin genes disrupted in autism.

De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J et al.,

Nature 2014;515;7526;209‐15

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·Knowing who to trust: exploring the role of ‘ethical metadata’ in mediating risk of harm in collaborative genomics research in Africa.

de Vries J, Williams TN, Bojang K, Kwiatkowski DP, Fitzpatrick R and Parker M

BMC medical ethics 2014;15;1;62

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·Genome‐wide association meta‐analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.

Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q, Kamatani Y, Bennet AM, Tamm R, Trompet S, Guðbjartsson DF, Flachsbart F et al.,

Human molecular genetics 2014;23;16;4420‐32

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·Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.

Delaneau O, Marchini J, 1000 Genomes Project Consortium and 1000 Genomes Project Consortium

Nature communications 2014;5;3934

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·Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C and Cohen MS

Journal of acquired immune deficiency syndromes (1999) 2014;67;2;181‐95

PUBMED: 24977473 ; PMC: 4304655 ; DOI: 10.1097/QAI.0000000000000271

·Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub‐Clade within the Broadly Distributed Human Haplogroup C1.

Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JE, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W and Genographic Consortium

PloS o­ne 2014;9;2;e87612

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·Genome‐wide trans‐ancestry meta‐analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

DIAbetes Genetics Replication And Meta‐analysis (DIAGRAM) Consortium

Nature genetics 2014

PUBMED: 24509480 ; DOI: 10.1038/ng.2897

·DNA methylation and body‐mass index: a genome‐wide analysis.

Dick KJ, Nelson CP, Tsaprouni L, Sandling JK, Aïssi D, Wahl S, Meduri E, Morange PE, Gagnon F, Grallert H, Waldenberger M, Peters A, Erdmann J, Hengstenberg C, Cambien F, Goodall AH, Ouwehand WH, Schunkert H, Thompson JR, Spector TD, Gieger C, Trégouët DA, Deloukas P and Samani NJ

Lancet (London, England) 2014;383;9933;1990‐8

PUBMED: 24630777 ; DOI: 10.1016/S0140‐6736(13)62674‐4

·Open‐source electronic data capture system offered increased accuracy and cost‐effectiveness compared with paper methods in Africa.

Dillon DG, Pirie F, Pomilla C, Sandhu MS, Motala AA, Young EH and African Partnership for Chronic Disease Research (APCDR)

Journal of clinical epidemiology 2014

PUBMED: 25135245 ; DOI: 10.1016/j.jclinepi.2014.06.012

·Impact of type 2 diabetes susceptibility variants o­n quantitative glycemic traits reveals mechanistic heterogeneity.

Dimas AS, Lagou V, Barker A, Knowles JW, Mägi R, Hivert MF, Benazzo A, Rybin D, Jackson AU, Stringham HM, Song C, Fischer‐Rosinsky A et al.,

Diabetes 2014;63;6;2158‐71

PUBMED: 24296717 ; PMC: 4030103 ; DOI: 10.2337/db13‐0949

·Estimating telomere length from whole genome sequence data.

Ding Z, Mangino M, Aviv A, UK10K Consortium, Spector T and Durbin R

Nucleic acids research 2014

PUBMED: 24609383 ; DOI: 10.1093/nar/gku181

·Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X‐Chromosome Association.

Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A, Louzada S, Yang F, Dunham I, Crawford GE, Lieb JD, Durbin R, Iyer VR and Birney E

PLoS genetics 2014;10;11;e1004798

PUBMED: 25411781 ; PMC: 4238955 ; DOI: 10.1371/journal.pgen.1004798

·Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse.

DiTommaso T, Jones LK, Cottle DL, WTSI Mouse Genetics Program, Gerdin AK, Vancollie VE, Watt FM, Ramirez‐Solis R, Bradley A, Steel KP, Sundberg JP, White JK and Smyth IM

PLoS genetics 2014;10;10;e1004705

PUBMED: 25340873 ; PMC: 4207618 ; DOI: 10.1371/journal.pgen.1004705

·Epidermal Wnt/β‐catenin signaling regulates adipocyte differentiation via secretion of adipogenic factors.

Donati G, Proserpio V, Lichtenberger BM, Natsuga K, Sinclair R, Fujiwara H and Watt FM

Proceedings of the National Academy of Sciences of the United States of America 2014;111;15;E1501‐9

PUBMED: 24706781 ; PMC: 3992657 ; DOI: 10.1073/pnas.1312880111

·Novel determinants of antibiotic resistance: identification of mutated loci in highly methicillin‐resistant subpopulations of methicillin‐resistant Staphylococcus aureus.

Dordel J, Kim C, Chung M, Pardos de la Gándara M, Holden MT, Parkhill J, de Lencastre H, Bentley SD and Tomasz A

mBio 2014;5;2;e01000

PUBMED: 24713324 ; PMC: 3993859 ; DOI: 10.1128/mBio.01000‐13

·Salmonella enterica Serovar Typhi and the Pathogenesis of Typhoid Fever.

Dougan G and Baker S

Annual review of microbiology 2014;68;317‐36

PUBMED: 25208300 ; DOI: 10.1146/annurev‐micro‐091313‐103739

·Neutralization of Plasmodium falciparum Merozoites by Antibodies against PfRH5.

Douglas AD, Williams AR, Knuepfer E, Illingworth JJ, Furze JM, Crosnier C, Choudhary P, Bustamante LY, Zakutansky SE, Awuah DK, Alanine DG, Theron M, Worth A, Shimkets R, Rayner JC, Holder AA, Wright GJ and Draper SJ

Journal of immunology (Baltimore, Md. : 1950) 2014;192;1;245‐58

PUBMED: 24293631 ; PMC: 3872115 ; DOI: 10.4049/jimmunol.1302045

·A strategy to identify dominant point mutant modifiers of a quantitative trait.

Dove WF, Shedlovsky A, Clipson L, Amos‐Landgraf JM, Halberg RB, Krentz KJ, Boehm FJ, Newton MA, Adams DJ and Keane TM

G3 (Bethesda, Md.) 2014;4;6;1113‐21

PUBMED: 24747760 ; PMC: 4065254 ; DOI: 10.1534/g3.114.010595

·Mosaic aneuploidy in Leishmania: the perspective of whole genome sequencing.

Dujardin JC, Mannaert A, Durrant C and Cotton JA

Trends in parasitology 2014;30;12;554‐555

PUBMED: 25458156 ; DOI: 10.1016/j.pt.2014.09.004

·Efficient haplotype matching and storage using the Positional Burrows‐Wheeler Transform (PBWT).

Durbin R

Bioinformatics (Oxford, England) 2014

PUBMED: 24413527 ; DOI: 10.1093/bioinformatics/btu014

·The peculiar epidemiology of dracunculiasis in Chad.

Eberhard ML, Ruiz‐Tiben E, Hopkins DR, Farrell C, Toe F, Weiss A, Withers PC, Jenks MH, Thiele EA, Cotton JA, Hance Z, Holroyd N, Cama VA, Tahir MA and Mounda T

The American journal of tropical medicine and hygiene 2014;90;1;61‐70

PUBMED: 24277785 ; PMC: 3886430 ; DOI: 10.4269/ajtmh.13‐0554

·CYP6 P450 Enzymes and ACE‐1 Duplication Produce Extreme and Multiple Insecticide Resistance in the Malaria Mosquito Anopheles gambiae.

Edi CV, Djogbénou L, Jenkins AM, Regna K, Muskavitch MA, Poupardin R, Jones CM, Essandoh J, Kétoh GK, Paine MJ, Koudou BG, Donnelly MJ, Ranson H and Weetman D

PLoS genetics 2014;10;3;e1004236

PUBMED: 24651294 ; PMC: 3961184 ; DOI: 10.1371/journal.pgen.1004236

·Accumulation of human‐adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom.

Elderfield RA, Watson SJ, Godlee A, Adamson WE, Thompson CI, Dunning J, Fernandez‐Alonso M, Blumenkrantz D, Hussell T, MOSAIC Investigators, Zambon M, Openshaw P, Kellam P and Barclay WS

Journal of virology 2014;88;22;13269‐83

PUBMED: 25210166 ; PMC: 4249111 ; DOI: 10.1128/JVI.01636‐14

·Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Maria Calò C, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P, Pagani L, Tyler‐Smith C et al.,

Nature communications 2014;5;3513

PUBMED: 24781250 ; PMC: 4007635 ; DOI: 10.1038/ncomms4513

·Multiple evidence strands suggest that there may be as few as 19,000 human protein‐coding genes.

Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A and Tress ML

Human molecular genetics 2014;23;22;5866‐78

PUBMED: 24939910 ; PMC: 4204768 ; DOI: 10.1093/hmg/ddu309