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Items: 32

1.

Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA.

Gombolay AL, Vannberg FO, Storici F.

Nucleic Acids Res. 2019 Jan 10;47(1):e5. doi: 10.1093/nar/gky874.

2.

Mapping-free variant calling using haplotype reconstruction from k-mer frequencies.

Audano PA, Ravishankar S, Vannberg FO.

Bioinformatics. 2018 May 15;34(10):1659-1665. doi: 10.1093/bioinformatics/btx753.

3.

First Full Draft Genome Sequence of Plasmodium brasilianum.

Talundzic E, Ravishankar S, Nayak V, Patel DS, Olsen C, Sheth M, Batra D, Loparev V, Vannberg FO, Udhayakumar V, Barnwell JW.

Genome Announc. 2017 Feb 9;5(6). pii: e01566-16. doi: 10.1128/genomeA.01566-16.

4.

Molecular Epidemiology of Plasmodium falciparum kelch13 Mutations in Senegal Determined by Using Targeted Amplicon Deep Sequencing.

Talundzic E, Ndiaye YD, Deme AB, Olsen C, Patel DS, Biliya S, Daniels R, Vannberg FO, Volkman SK, Udhayakumar V, Ndiaye D.

Antimicrob Agents Chemother. 2017 Feb 23;61(3). pii: e02116-16. doi: 10.1128/AAC.02116-16. Print 2017 Mar.

5.

Chocó, Colombia: a hotspot of human biodiversity.

Medina-Rivas MA, Norris ET, Rishishwar L, Conley AB, Medrano-Trochez C, Valderrama-Aguirre A, Vannberg FO, Mariño-Ramírez L, Jordan IK.

Rev Biodivers Neotrop. 2016 Jan-Jun;6(1):45-54.

6.

Lymphatic transport of exosomes as a rapid route of information dissemination to the lymph node.

Srinivasan S, Vannberg FO, Dixon JB.

Sci Rep. 2016 Apr 18;6:24436. doi: 10.1038/srep24436.

7.

Whole-Genome Sequencing to Determine Origin of Multinational Outbreak of Sarocladium kiliense Bloodstream Infections.

Etienne KA, Roe CC, Smith RM, Vallabhaneni S, Duarte C, Escadon P, Castaneda E, Gomez BL, de Bedout C, López LF, Salas V, Hederra LM, Fernandez J, Pidal P, Hormazabel JC, Otaiza F, Vannberg FO, Gillece J, Lemmer D, Driebe EM, Englethaler DM, Litvintseva AP.

Emerg Infect Dis. 2016 Mar;22(3):476-81. doi: 10.3201/eid2203.151193.

8.

Genetic variants of MARCO are associated with susceptibility to pulmonary tuberculosis in a Gambian population.

Bowdish DM, Sakamoto K, Lack NA, Hill PC, Sirugo G, Newport MJ, Gordon S, Hill AV, Vannberg FO.

BMC Med Genet. 2013 Apr 23;14:47. doi: 10.1186/1471-2350-14-47.

9.

Identifying recent adaptations in large-scale genomic data.

Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL; 1000 Genomes Project, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2013 Feb 14;152(4):703-13. doi: 10.1016/j.cell.2013.01.035.

10.

Effect of HIV-2 infection on HIV-1 disease progression.

Vannberg FO, McDermid JM, Jaye A; MRC Gambia HIV Clinical Cohort Study; Wellcome Trust Case Control Consortium 3.

N Engl J Med. 2012 Nov 15;367(20):1962; author reply 1962-3. doi: 10.1056/NEJMc1210334. No abstract available.

PMID:
23150975
11.

PTX3 genetic variation and dizygotic twinning in the Gambia: could pleiotropy with innate immunity explain common dizygotic twinning in Africa?

Sirugo G, Edwards DR, Ryckman KK, Bisseye C, White MJ, Kebbeh B, Morris GA, Adegbola RA, Tacconelli A, Predazzi IM, Novelli G, Vannberg FO, Odunsi K, Page GP, Williams SM.

Ann Hum Genet. 2012 Nov;76(6):454-63. doi: 10.1111/j.1469-1809.2012.00723.x. Epub 2012 Jul 27.

12.

Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles.

Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC.

Nat Genet. 2012 Mar 25;44(5):502-10. doi: 10.1038/ng.2205.

13.

Common variants at 11p13 are associated with susceptibility to tuberculosis.

Thye T, Owusu-Dabo E, Vannberg FO, van Crevel R, Curtis J, Sahiratmadja E, Balabanova Y, Ehmen C, Muntau B, Ruge G, Sievertsen J, Gyapong J, Nikolayevskyy V, Hill PC, Sirugo G, Drobniewski F, van de Vosse E, Newport M, Alisjahbana B, Nejentsev S, Ottenhoff TH, Hill AV, Horstmann RD, Meyer CG.

Nat Genet. 2012 Feb 5;44(3):257-9. doi: 10.1038/ng.1080.

14.

Human genetic susceptibility to intracellular pathogens.

Vannberg FO, Chapman SJ, Hill AV.

Immunol Rev. 2011 Mar;240(1):105-16. doi: 10.1111/j.1600-065X.2010.00996.x. Review.

PMID:
21349089
15.

A common haplotype of the TNF receptor 2 gene modulates endotoxin tolerance.

Fairfax BP, Davenport EE, Makino S, Hill AV, Vannberg FO, Knight JC.

J Immunol. 2011 Mar 1;186(5):3058-65. doi: 10.4049/jimmunol.1001791. Epub 2011 Jan 31.

16.

Common NFKBIL2 polymorphisms and susceptibility to pneumococcal disease: a genetic association study.

Chapman SJ, Khor CC, Vannberg FO, Rautanen A, Walley A, Segal S, Moore CE, Davies RJ, Day NP, Peshu N, Crook DW, Berkley JA, Williams TN, Scott JA, Hill AV.

Crit Care. 2010;14(6):R227. doi: 10.1186/cc9377. Epub 2010 Dec 20.

17.

Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.

Thye T, Vannberg FO, Wong SH, Owusu-Dabo E, Osei I, Gyapong J, Sirugo G, Sisay-Joof F, Enimil A, Chinbuah MA, Floyd S, Warndorff DK, Sichali L, Malema S, Crampin AC, Ngwira B, Teo YY, Small K, Rockett K, Kwiatkowski D, Fine PE, Hill PC, Newport M, Lienhardt C, Adegbola RA, Corrah T, Ziegler A; African TB Genetics Consortium; Wellcome Trust Case Control Consortium, Morris AP, Meyer CG, Horstmann RD, Hill AVS.

Nat Genet. 2010 Sep;42(9):739-741. doi: 10.1038/ng.639. Epub 2010 Aug 8. Erratum in: Nat Genet. 2011 Oct;43(10):1040.

18.

Leprosy and the adaptation of human toll-like receptor 1.

Wong SH, Gochhait S, Malhotra D, Pettersson FH, Teo YY, Khor CC, Rautanen A, Chapman SJ, Mills TC, Srivastava A, Rudko A, Freidin MB, Puzyrev VP, Ali S, Aggarwal S, Chopra R, Reddy BS, Garg VK, Roy S, Meisner S, Hazra SK, Saha B, Floyd S, Keating BJ, Kim C, Fairfax BP, Knight JC, Hill PC, Adegbola RA, Hakonarson H, Fine PE, Pitchappan RM, Bamezai RN, Hill AV, Vannberg FO.

PLoS Pathog. 2010 Jul 1;6:e1000979. doi: 10.1371/journal.ppat.1000979.

19.

CISH and susceptibility to infectious diseases.

Khor CC, Vannberg FO, Chapman SJ, Guo H, Wong SH, Walley AJ, Vukcevic D, Rautanen A, Mills TC, Chang KC, Kam KM, Crampin AC, Ngwira B, Leung CC, Tam CM, Chan CY, Sung JJ, Yew WW, Toh KY, Tay SK, Kwiatkowski D, Lienhardt C, Hien TT, Day NP, Peshu N, Marsh K, Maitland K, Scott JA, Williams TN, Berkley JA, Floyd S, Tang NL, Fine PE, Goh DL, Hill AV.

N Engl J Med. 2010 Jun 3;362(22):2092-101. doi: 10.1056/NEJMoa0905606. Epub 2010 May 19.

20.

Genomewide association study of leprosy.

Wong SH, Hill AV, Vannberg FO; India-Africa-United Kingdom Leprosy Genetics Consortium.

N Engl J Med. 2010 Apr 15;362(15):1446-7; author reply 1447-8. doi: 10.1056/NEJMc1001451. No abstract available.

PMID:
20393182
21.

Comment on "CRTAM confers late-stage activation of CD8+ T cells to regulate retention within lymph node".

Wong SH, Vannberg FO, Spencer AJ, van der Weyden L, Hill AV, Wyllie DH.

J Immunol. 2010 Apr 15;184(8):4052-3. doi: 10.4049/jimmunol.1090017. No abstract available.

22.

Mannose-binding lectin genotypes: lack of association with susceptibility to thoracic empyema.

Chapman SJ, Vannberg FO, Khor CC, Rautanen A, Maskell NA, Davies CW, Moore CE, Day NP, Crook DW, Davies RJ, Hill AV.

BMC Med Genet. 2010 Jan 15;11:5. doi: 10.1186/1471-2350-11-5.

23.

An integrated expression phenotype mapping approach defines common variants in LEP, ALOX15 and CAPNS1 associated with induction of IL-6.

Fairfax BP, Vannberg FO, Radhakrishnan J, Hakonarson H, Keating BJ, Hill AV, Knight JC.

Hum Mol Genet. 2010 Feb 15;19(4):720-30. doi: 10.1093/hmg/ddp530. Epub 2009 Nov 26.

24.

NFKBIZ polymorphisms and susceptibility to pneumococcal disease in European and African populations.

Chapman SJ, Khor CC, Vannberg FO, Rautanen A, Segal S, Moore CE, Davies RJ, Day NP, Peshu N, Crook DW, Berkley JA, Williams TN, Scott JA, Hill AV.

Genes Immun. 2010 Jun;11(4):319-25. doi: 10.1038/gene.2009.76. Epub 2009 Oct 1.

25.

CD209 genetic polymorphism and tuberculosis disease.

Vannberg FO, Chapman SJ, Khor CC, Tosh K, Floyd S, Jackson-Sillah D, Crampin A, Sichali L, Bah B, Gustafson P, Aaby P, McAdam KP, Bah-Sow O, Lienhardt C, Sirugo G, Fine P, Hill AV.

PLoS One. 2008 Jan 2;3(1):e1388. doi: 10.1371/journal.pone.0001388.

26.

Positive replication and linkage disequilibrium mapping of the chromosome 21q22.1 malaria susceptibility locus.

Khor CC, Vannberg FO, Chapman SJ, Walley A, Aucan C, Loke H, White NJ, Peto T, Khor LK, Kwiatkowski D, Day N, Scott A, Berkley JA, Marsh K, Peshu N, Maitland K, Williams TN, Hill AV.

Genes Immun. 2007 Oct;8(7):570-6. Epub 2007 Aug 16.

27.

IkappaB genetic polymorphisms and invasive pneumococcal disease.

Chapman SJ, Khor CC, Vannberg FO, Frodsham A, Walley A, Maskell NA, Davies CW, Segal S, Moore CE, Gillespie SH, Denny P, Day NP, Crook DW, Davies RJ, Hill AV.

Am J Respir Crit Care Med. 2007 Jul 15;176(2):181-7. Epub 2007 Apr 26.

PMID:
17463416
28.

Functional polymorphisms in the FCN2 gene are not associated with invasive pneumococcal disease.

Chapman SJ, Vannberg FO, Khor CC, Segal S, Moore CE, Knox K, Day NP, Davies RJ, Crook DW, Hill AV.

Mol Immunol. 2007 May;44(12):3267-70. Epub 2007 Mar 26.

PMID:
17382393
29.

A Mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosis.

Khor CC, Chapman SJ, Vannberg FO, Dunne A, Murphy C, Ling EY, Frodsham AJ, Walley AJ, Kyrieleis O, Khan A, Aucan C, Segal S, Moore CE, Knox K, Campbell SJ, Lienhardt C, Scott A, Aaby P, Sow OY, Grignani RT, Sillah J, Sirugo G, Peshu N, Williams TN, Maitland K, Davies RJ, Kwiatkowski DP, Day NP, Yala D, Crook DW, Marsh K, Berkley JA, O'Neill LA, Hill AV.

Nat Genet. 2007 Apr;39(4):523-8. Epub 2007 Feb 25.

30.

PTPN22 and invasive bacterial disease.

Chapman SJ, Khor CC, Vannberg FO, Maskell NA, Davies CW, Hedley EL, Segal S, Moore CE, Knox K, Day NP, Gillespie SH, Crook DW, Davies RJ, Hill AV.

Nat Genet. 2006 May;38(5):499-500. No abstract available.

PMID:
16642008
31.

Identification of genes differentially expressed in Mycobacterium tuberculosis by differential display PCR.

Rivera-Marrero CA, Burroughs MA, Masse RA, Vannberg FO, Leimbach DL, Roman J, Murtagh JJ Jr.

Microb Pathog. 1998 Dec;25(6):307-16.

PMID:
9895269
32.

Detailed analysis of a 17q21 microdissection library by sequence bioinformatics and isolation of region-specific clones.

Bentley KL, Li WL, VannBerg FO, Choi JY, Yu J, Kao FT, Ruaño G.

Somat Cell Mol Genet. 1997 Sep;23(5):353-65.

PMID:
9580249

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