Herve Tettelin, PhD

Complete list of publications in reverse chronological order

Huffman A., Ong E., Hur J., D’Mello A., Tettelin H., and He Y. (2022) COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining, and machine learning. Brief. Bioinform. 23, bbac190.

Kilian M., Husby S., Andersen J., Moldoveanu Z., Skov Sørensen U.B., Reinholdt J., and Tettelin H. (2022) Induction of susceptibility to disseminated infection with IgA1-protease producing encapsulated pathogens Streptococcus pneumoniae, Haemophilus influenzae type b, and Neisseria meningitidis. mBio 13, e0055022.

Im H., Kruckow K.L., D’Mello A., Ganaie F., Martinez E., Luck J.N., Cichos K.H., Riegler A.N., Song X., Ghanem E., Saad J.S., Nahm M.H., Tettelin H., and Orihuela C.J. (2021) Anatomical site-specific carbohydrate availability impacts Streptococcus pneumoniae virulence and fitness during colonization and disease. Infect. Immun. 90, e0045121.

Salerno-Gonçalves R., Rezwan T., Luo D., Tettelin H., and Sztein M.B. (2021) B cells control mucosal-associated invariant T cell responses to Salmonella enterica serovar Typhi infection through the CD85j HLA-G receptor. Front. Immunol. 12, 728685.

Thapa E., Aluvathingal J., Nadendla S., Mehta A., Tettelin H., and Weyand N.J. (2021) Complete genome sequence of Neisseria musculi using Illumina and PacBio sequencing. Microbiol. Resour. Announc. 10, e0045221.

Curreli S., Tettelin H., Benedetti F., Krishnan S., Cocchi F., Reitz M., Gallo R.C., and Zella D. (2021) Analysis of DnaK expression from a strain of Mycoplasma fermentans in infected HCT116 human colon carcinoma cells. Int. J. Mol. Sci. 22, 3885.

Dammann A.N., Chamby A.B., Catomeris A.J., Davidson K.M., Tettelin H., van Pijkeren J.-P., Gopalakrishna K.P., Keith M.F., Elder J.L., Ratner A.J., and Hooven T.A. (2021) Genome-wide fitness analysis of group B Streptococcus in human amniotic fluid reveals a transcription factor that controls multiple virulence traits. PLoS Pathog. 17, e1009116.

Namkoong H., Omae Y., Asakura T., Ishii M., Suzuki S., Morimoto K., Kawai Y., Emoto K., Oler A.J., Szymanski E.P., Yoshida M., Matsuda S., Yagi K., Hase I., Nishimura T., Sasaki Y., Asami T., Shiomi T., Matsubara H., Shimada H., Hamamoto J., Jhun B.W., Kim S.-Y., Huh H.J., Won H.-H., Ato M., Kosaki K., Betsuyaku T., Fukunaga K., Kurashima A., Tettelin H., Yanai H., Mahasirimongkol S., Olivier K.N., Hoshino Y., Koh W.-J., Holland S.M., Tokunaga K., and Hasegawa N. (2021) Genome-wide association study in patients with pulmonary Mycobacterium avium complex disease. Eur. Respir. J. 58: 1902269. doi: 10.1183/13993003.02269-2019.

Luck J, Tettelin H., and Orihuela C.J. (2020) Sugar-coated killer: Serotype 3 pneumococcal disease. Front. Cell. Infect. Microbiol. 10: 613287.

Korol C.B., Shallom S.J., Arora K., Boshoff H.I., Freeman A.F., King A., Jancel T., Kabat J., Ganesan S., Torrero M.N., Daugherty S.C., Sampaio E.P., Barry III C., Holland S.M., Tettelin H., Rosenzweig S.D., Zelazny Z.M. (2020) Tissue specific diversification, virulence and immune response to Mycobacterium bovis BCG in a patient with an IFN-γ R1 deficiency. Virulence 11, 1656-1673.

D’Mello A., Riegler A.N., Martínez E., Beno S.M., Ricketts T.D., Foxman E.F., Orihuela C.J.*, and Tettelin H.* [*These authors contributed equally] (2020) An in vivo atlas of host-pathogen transcriptomes during Streptococcus pneumoniae colonization and disease. Proc. Natl Acad. Sci. USA 117, 33507-33518.

Tettelin H., and Medini D., Editors (2020) The pangenome: diversity, dynamics and evolution of genomes. Cham (CH): Springer Nature. Print ISBN: 978-3-030-38280-3, online ISBN: 978-3-030-38281-0. PMID range: 32633908 to 32633921 (Free Books & Documents).

Medini D., Donati C., Rappuoli R., and Tettelin H. (2020) The pangenome: a data-driven discovery in biology. In The pangenome: diversity, dynamics and evolution of genomes, pp. 3-20, Tettelin H., and Medini D. Eds, Cham (CH): Springer Nature. Print ISBN: 978-3-030-38280-3, online ISBN: 978-3-030-38281-0. PMID: 32633919 (Free Books & Documents).

Salerno-Gonçalves R., Tettelin H., Luo D., Guo Q., Ardito M.T., Martin W.D., De Groot A.S., and Sztein M.B. (2020) Differential functional patterns of the memory CD4⁺ and CD8⁺ T-cells from volunteers immunized with Ty21a typhoid vaccine observed using a recombinant Escherichia coli system expressing S. Typhi proteins. Vaccine 38, 258-270.

D’Mello A., Ahearn C.P., Murphy, T.F., and Tettelin H. (2019) ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. BMC Genomics 20, 981.

Kilian M, and Tettelin H. (2019) Identification of virulence-associated properties by comparative genome analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, three S. oralis subspecies, and S. infantis. mBio 10, e01985-19 (Erratum: e02520-19).

Campo J.J., Le T.Q., Pablo J.V., Hung C., Teng A.A., Tettelin H., Tate A., Hanage W.P., Alderson M.R., Liang X., Malley R., Lipsitch M., Croucher N.J. (2018) Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination. eLife 28, e37015.

Zella D., Curreli S., Benedetti F., Krishnan S., Cocchi F., Latinovic O.S., Denaro F., Romerio F., Djavani M., Charurat M.E., Bryant J.L., Tettelin H., and Gallo R.C. (2018) Mycoplasma promotes malignant transformation in vivo, and its DnaK, a bacterial chaperone protein, has broad oncogenic properties. Proc. Natl Acad. Sci. USA 115, E12005-E12014. Press release.

Murphy T.F., Brauer A.L., Pettigrew M.M., LaFontaine E.R., and Tettelin H. (2018) Persistence of Moraxella catarrhalis in chronic obstructive pulmonary disease and regulation of the Hag/MID adhesin. J. Infect. Dis. 219, 1448-1455.

Chung M., Munro J.B., Tettelin H., and Dunning Hotopp J.C. (2018) Using core genome alignments to assign bacterial species. mSystems 3(6), e00236-18.

Pettigrew M.M., Ahearn C.P., Gent J.F., Kong Y., Gallo M.C., Munro J.B., D’Mello A., Sethi S., Tettelin H.*, and Murphy, T.F.* (2018) Haemophilus influenzae genome evolution during persistence in the human airways in chronic obstructive pulmonary disease.  Proc. Natl. Acad. Sci. USA 115, E3256-E3265. [*These authors contributed equally to this work] Press release.

Hooven T.A., Catomeris A.J., Bonakdar M., Tallon L.J., Santana-Cruz I., Ott S., Daugherty S.C., Tettelin H., and Ratner A.J. (2018) The Streptococcus agalactiae stringent response enhances virulence and persistence in human blood.  Infect. Immun. 86, e00612-17.

Tettelin H., Hooven T.A., Zhao X., Su Q., Sadzewicz L., Tallon L.J., Fraser C.M., and Ratner A.J. (2017) Whole genome sequences of bacteremia isolates of Bordetella holmesii.  Genome Announc. 5, pii: e01023-17.

Salerno-Gonçalves R.*, Tettelin H.*, Lou D., Steiner S., Rezwanul T., Guo Q., Picking W.D., Nene V., and Sztein M.B. (2017) Use of a novel antigen expressing system to study the Salmonella enterica serovar Typhi protein recognition by T cells. PLoS Negl. Trop. Dis. 11, e0005912. [*These authors contributed equally to this work]

Shenoy A.T., Brissac T., Gilley R.P., Kumar N., Wang Y., Brissac T., Gonzalez-Juarbe N., Hinkle W.S., Daugherty S.C., Shetty A.C., Ott S., Tallon L.J., Deshane J., Tettelin H., and Orihuela C.J. (2017) Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing. PLoS Pathog. 13, e1006582.

Le Breton Y., Belew A.T., Freiberg J.A., Sundar G.S., Islam E., Lieberman J., Shirtliff M.E., Tettelin H., El-Sayed N.M., and McIver K.S. (2017) Genome-wide discovery of novel M1T1 group A streptococcal determinants important for fitness and virulence during soft-tissue infection. PLoS Pathog. 13, e1006584.

Chen F., Szymanski E.P., Olivier K.N., Liu X., Tettelin H., Holland S.M., Duggal P. (2017) Whole exome sequencing identifies the 6q12-q16 linkage region and a candidate gene TTK for pulmonary nontuberculous mycobacterial disease. Am. J. Respir. Crit. Care Med. 196, 1599-1604.

Agrawal S., Arze C., Adkins R.S., Crabtree J., Riley D.R., Vangala M., Galens K., Fraser C.M., Tettelin H., White O., Angiuoli S.V., Mahurkar A., Fricke W.F. (2017) CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline. BMC Genomics 18, 332.

Lomholt H.B., Scholz C.F.P., Brüggemann H., Tettelin H., and Kilian M. (2017) A comparative study of Cutibacterium (Propionibacterium) acnes clones from acne patients and healthy controls. Anaerobe 47, 57-63.

Panda A., Nagaraj S., Zhao X., Tettelin H., and DeTolla L.J. (2017) Complete genome sequences of Mycobacterium kansasii strains isolated from rhesus macaques. Genome Announc. 5, pii: e00187-17.

Lizcano A., Suresh Babu R.A., Shenoy A.T., Saville A.M., Kumar N., D’Mello A., Hinojosa C.A., Gilley R.P., Segovia J., Mitchell T.J., Tettelin H., and Orihuela C.J. (2017) Transcriptional organization of pneumococcal psrP-secY2A2 and impact of GtfA and GtfB deletion on PsrP-associated virulence properties. Microbes Infect. 19, 323-333.

Skov Sørensen U.B., Yao K., Yang Y., Tettelin H., and Kilian M. (2016) Capsular polysaccharide expression in commensal Streptococcus species: genetic and antigenic similarities with Streptococcus pneumoniae. mBio 7, e01844-16.

Siena E., D’Aurizio R., Riley D., Tettelin H., Guidotti S., Torricelli G., Moxon E.R., and Medini D. (2016) In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes. BMC Genomics 17, 843.

Blanchette K.A., Shenoy A.T., Milner II J., Gilley R.P., McClure E., Hinojosa C.A., Kumar N., Daugherty S.C., Tallon L.J., Ott S., King S.J., Ferreira D.M., Gordon S.B., Tettelin H., and Orihuela C.J (2016) Neuraminidase-exposed galactose promotes Streptococcus pneumoniae biofilm formation during colonization. Infect. Immun. 84, 2922-2932.

Hooven T.A., Catomeris A.J., Akabas L.H., Randis T.M., Maskell D.J., Peters S.E., Ott S., Santana-Cruz I., Tallon L.J., Tettelin H., and Ratner A.J. (2016) The essential genome of Streptococcus agalactiae. BMC Genomics 17, 406.

Park I.K., Hsu A.P., Tettelin H., Shallom S., Drake S.K., Ding L., Wu U.I., Adamo N., Prevots D.R., Olivier K.N., Holland S.M., Sampaio E.P., and Zelazny A.M. (2015) Clonal diversification and changes in lipid traits and colony morphology in Mycobacterium abscessusclinical isolates. J. Clin. Microbiol. 3, 3438-3447.

Szymanski E.P., Leung J.M., Fowler C.J., Haney C., Hsu A.P., Chen F., Duggal P., Oler A.J., McCormack R., Podack E., Drummond R.A., Lionakis M.S., Browne S.K., Prevots D.R., Knowles M., Cutting G., Liu X., Devine S.E., Fraser C.M., Tettelin H., Olivier K.N., Holland S.M. (2015) Pulmonary nontuberculous mycobacterial infection: a multisystem multigenic disease. Am. J. Respir. Crit. Care Med. 192, 618-628.

Tettelin H., Chancey S., Mitchell T., Denapaite D., Schähle Y., Rieger M., and Hakenbeck R. (2015) Genomics, genetic variation, and regions of differences. In Streptococcus pneumoniae: Molecular Mechanisms of Host-Pathogen Interactions, pp. 81-107, Brown J., Hammerschmidt S, and Orihuela C. Eds, Academic Press (San Diego, CA, USA).

Le Breton Y., Belew A.T., Valdes K.M., Islam E., Curry P., Tettelin H., Shirtliff M.E., El-Sayed N.M., and McIver K.S. (2015) Essential genes in the core genome of the human pathogen Streptococcus pyogenes. Sci. Rep. 5, 9838.

Rosini R., Campisi E., De Chiara M., Tettelin H., Rinaudo D., Toniolo C., Metruccio M., Guidotti S., Skov Sørensen U.B., Kilian M., DEVANI Consortium, Ramirez M., Janulczyk R., Donati C., Grandi G., and Margarit I. (2015) Genomic analysis reveals the molecular basis for capsule loss in group B Streptococcus population. PLoS One 10, e0125985.

Chancey S.T., Agrawal S., Schroeder M.R., Farley M.M., Tettelin H.*, and Stephens D.S.* [*These authors have contributed equally to this work] (2015) Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae. Front. Microbiol. 6, 26.

Chancey S.T., Bai X., Kumar N., Drabek E.F., Daugherty S.C., Colon T., Ott S., Sengamalay N., Sadzewicz L., Tallon L.J., Fraser C.M.,Tettelin H. and Stephens D.S. (2015) Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements. PLoS One 10, e0116254.

Vernikos G., Medini D., Riley D.R., and Tettelin H. (2015) Ten years of pan-genome analyses. Curr. Opin. Microbiol. 23, 148-154.

Hooven T.A., Randis T.M., Daugherty S.C., Narechania A., Planet P.J., Tettelin H.*, and Ratner A.J.* [*These authors have contributed equally to this work] (2014) Complete genome sequence of Streptococcus agalactiae strain CNTC 10/84, a hypervirulent sequence type 26 strain. Genome Announc. 2, e01338-14.

Bessen D.E., McShan W.M., Nguyen S.V., Shetty A., Agrawal S., and Tettelin H. (2014) Molecular epidemiology and genomics of group A Streptococcus. Infect. Genet. Evol. (MEEGID). pii: S1567-1348(14)00382-7.

Kilian M., Riley D.R., Jensen A., Brüggemann H., and Tettelin H. (2014) Parallel evolution of Streptococcus pneumoniae andStreptococcus mitis to pathogenic and mutualistic lifestyles. mBio 5, e01490-14.

Dugan V.G., Emrich S.J., Giraldo-Calderón G.I., Harb O.S., Newman R.M., Pickett B.E., Schriml L.M., Stockwell T.B., Stoeckert C.J. Jr, Sullivan D.E., Singh I., Ward D.V., Yao A., Zheng J., Barrett T., Birren B., Brinkac L., Bruno V.M., Caler E., Chapman S., Collins F.H., Cuomo C.A., Di Francesco V., Durkin S., Eppinger M., Feldgarden M., Fraser C.M., Fricke W.F., Giovanni M., Henn M.R., Hine E., Dunning Hotopp J., Karsch-Mizrachi I., Kissinger J.C., Lee E.M., Mathur P., Mongodin E.F., Murphy C.I., Myers G., Neafsey D.E., Nelson K.E., Nierman W.C., Puzak J., Rasko D., Roos D.S., Sadzewicz L., Silva J.C., Sobral B., Squires R.B., Stevens R.L., Tallon L., Tettelin H., Wentworth D., White O., Will R., Wortman J., Zhang Y., Scheuermann R.H. (2014) Standardized metadata for human pathogen/vector genomic sequences. PLoS One 9, e99979.

Tettelin H., Davidson R.M., Agrawal S., Aitken M., Shallom S., Hasan N.A., Strong M., Calado Nogueira de Moura V., De Groote M.A., Duarte R.S., Hine E., Parankush S., Su Q., Daugherty S.C., Fraser C.M., Brown-Elliott B.A., Wallace Jr. R.J., Holland S.M., Sampaio E.P., Olivier K.N., Jackson M., and Zelazny A.M. (2014) High-level relatedness among Mycobacterium abscessus subsp. massiliense strains from widely separated outbreaks. Emerg. Infect. Dis. 20, 364-371.

Zubair S., de Villiers E.P., Younan M., Andersson G., Tettelin H., Riley D.R., Jores J., Bongcam-Rudloff E., and Bishop R.P. (2013) Genome sequences of two pathogenic Streptococcus agalactiae isolates from the one-humped camel Camelus dromedarius. Genome Announc. 1, e00515-13.

Shallom S.J., Gardina P.J., Myers T.G., Sebastian Y., Conville P., Calhoun L.B., Tettelin H., Olivier K.N., Uzel G., Sampaio E.P., Holland S.M., and Zelazny A.M. (2013) New rapid scheme for distinguishing subspecies of the Mycobacterium abscessus group and identification of Mycobacterium massiliense with inducible clarithromycin resistance. J. Clin. Microbiol. 51, 2943-2949. 

Kimaro Mlacha S.Z., Romero-Steiner S., Dunning Hotopp J.C., Kumar N., Ishmael N., Riley D.R., Farooq U., Creasy T.H., Tallon L.J., Liu X., Goldsmith C.S., Sampson J., Carlone G.M., Hollingshead S.K., Scott J.A.G., and Tettelin H. (2013) Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells. BMC Genomics 14, 383.

Kimaro Mlacha S.Z., Peret T.C., Kumar N., Romero-Steiner S., Dunning Hotopp J.C., Ishmael N., Grinblat-Huse V., Riley D.R., Erdman D.D., Carlone G.M., Sampson J., Scott J.A.G., and Tettelin H. (2013) Transcriptional adaptation of pneumococci and human pharyngeal cells in the presence of a virus infection. BMC Genomics 14, 378.

Klinzing D.C., Ishmael N., Dunning Hotopp J.C., Tettelin H., Shields K.R., Madoff L.C., and Puopolo K.M. (2013) The two-component response regulator LiaR regulates cell wall stress responses, pili expression, and virulence in group B Streptococcus. Microbiology 159,1521-1534.

Le Breton Y., Mistry P., Valdes K., Quigley J., Kumar N., Tettelin H., and McIver K. (2013) Genome-wide identification of genes required for fitness of the group A Streptococcus in human blood. Infect. Immun. 81, 862-875.

Tettelin H., Sampaio E.P., Daugherty S., Hine E., Riley D.R., Sadzewicz L., Sengamalay N., Shefchek K., Su Q., Tallon L.J., Conville P., Olivier K., Holland S.M., Fraser C.M., and Zelazny A.M. (2012) Genomic insights into the emerging human pathogen Mycobacterium massiliense. J. Bacteriol. (Genome Announcement) 194, 5450.

Krauland M.G., Dunning Hotopp J.C., Riley D.R., Daugherty S.C., Marsh J.W., Messonier N.E., Mayer L.W., Tettelin H., and Harrison L.H. (2012) Whole genome sequencing to investigate the emergence of clonal complex 23 Neisseria meningitidis serogroup Y disease in the United States. PLoS One 7, e35699.

Brüggemann H., Lomholt H.B., Tettelin H., and Kilian M. (2012) CRISPR/cas loci of type II Propionibacterium acnes confer immunity against acquisition of mobile elements present in type I P. acnes. PLoS One 7, e34171.

Riley D.R., Angiuoli S.V., Crabtree J., Dunning Hotopp J.C., and Tettelin H. (2012) Using Sybil for interactive comparative genomics of microbes on the web. Bioinformatics 28, 160-166.

Hiller N.L., Eutsey R.A., Powell E., Earl J., Janto B., Martin D., Dawid S., Ahmed A., Longwell M., Dahlgreen M., Ezzo S., Tettelin H., Daugherty S.C., Mitchell T., Hillman T., Buchinsky F., Tomasz A., de Lencastre H., Sá-Leão R., Post J.C., Hu F.Z., and Ehrlich G.D. (2011) Differences in genotype and virulence among four multidrug-resistant Streptococcus pneumoniae isolates belonging to the PMEN1 clone. PLoS One 6, e28850.

Sanchez C.J., Kumar N., Lizcano A., Shivshankar P., Dunning Hotopp J.C., Jorgensen J.H., Tettelin H., and Orihuela C.J. (2011) Streptococcus pneumoniae in biofilms are unable to cause invasive disease due to altered virulence determinant production. PLoS One 6, e28738.

Tettelin H. and Kilian M. (2011) Genomes of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis. In Oral Microbial Communities: Genomic Inquiry and Interspecies Communication, pp. 37-42, Kolenbrander P.E. Ed., ASM Press (Washington, DC, USA).

Poulsen K., Tettelin H. and Kilian M. (2011) The Aggregatibacter actinomycetemcomitans genome: diversity of pathogenic potential. In Oral Microbial Communities: Genomic Inquiry and Interspecies Communication, pp. 103-117, Kolenbrander P.E. Ed., ASM Press (Washington, DC, USA).

Bessen D.E., Kumar N., Hall G.S., Riley D.R., Luo F., Lizano S., Ford C.N., McShan W.M., Nguyen S.V., Dunning Hotopp J.C., and Tettelin H. (2011) Whole genome association study on tissue tropism phenotypes in group A Streptococcus. J. Bacteriol. 193, 6651-6663.

Lee A.W., Tettelin H., and Chancey S. (2011) Genomic analyses of clonal isolates provide clues to the evolution of Streptococcus pneumoniae (Commentary). Front. Microbio. 2, 63.

Angiuoli S.V., Dunning Hotopp J.C., Salzberg S.L., and Tettelin H. (2011) Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinformatics 12, 272.

Budroni S., Siena E., Dunning Hotopp J.C., Seib K.L., Serruto D., Nofroni C., Comanducci M., Riley D.R., Daugherty S.C., Angiuoli S.V., Covacci A., Pizza M., Rappuoli R., Moxon R., Tettelin H.*, and Medini D.* [*These authors have contributed equally to this work] (2011) Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination. Proc. Natl. Acad. Sci. USA 108, 4494-4499.

Donati C., Hiller N.L., Tettelin H., Muzzi A., Croucher N.J., Angiuoli S.V., Oggioni M., Dunning Hotopp J.C., Hu F.Z., Riley D., Covacci A., Mitchell T.J., Bentley S.D., Kilian M., Ehrlich G.D., Rappuoli R., Moxon E.R., and Masignani V. (2010) Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol. 11, R107.

Bottacini F., Medini D., Pavesi A., Turroni F., Foroni E., Riley D., Giubellini D., Tettelin H., van Sinderen D., and Ventura M. (2010) Comparative genomics of the genus Bifidobacterium. Microbiology 156, 3243-3254.

Janulczyk R., Masignani V., Maione D., Tettelin H., Grandi G., and Telford J. (2010) Simple sequence repeats and genome plasticity inStreptococcus agalactiae. J. Bacteriol. 192, 3990-4000.

Gomes Moriel D., Bertoldi I., Spagnuolo A., Marchi S., Rosini R., Nesta B., Pastorello I., Mariani Corea V.A., Torricelli G., Cartocci E., Savino S., Scarselli M., Dobrindt U., Hacker J., Tettelin H., Tallon L.J., Sullivan S., Wieler L.H., Ewerse C., Pickard D., Dougan G., Rita Fontana M., Rappuoli R., Pizza M., and Serino L. (2010) Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 107, 9072-9077.

van Schaik W., Top J., Riley D.R., Boekhorst J., Vrijenhoek J.E., Schapendonk C.M., Hendrickx A.P., Nijman I.J., Bonten M.J., Tettelin H., and Willems R.J. (2010) Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faeciumand identification of a large transferable pathogenicity island. BMC Genomics 11, 239.

Schoen C., Tettelin H., Parkhill J., and Frosch M. (2009) Genome flexibility in Neisseria meningitidis. Vaccine 27 supplement 2, B103-B111.

Ishmael N., Dunning Hotopp J.C., Ioannidis P., Biber S., Sakamoto J., Siozios S., Nene V., Werren J., Bourtzis K., Bordenstein S.R.,Tettelin H. (2009) Extensive Genomic Diversity of Closely Related Wolbachia Strains. Microbiology 155, 2211-2222.

Bordenstein S.R., Paraskevopoulos C., Dunning Hotopp J.C., Sapountzis P., Lo N., Bandi C., Tettelin H., Werren J.H., and Bourtzis K. (2009) Parasitism and mutualism in Wolbachia: what the phylogenomic trees can and can not say. Mol. Biol. Evol. 26, 231-241.

Tettelin H. and Feldblyum T. (2009) Bacterial genome sequencing. In Methods in Molecular Biology 551: Molecular Epidemiology of Microorganisms, pp. 231-247, Caugant D.A. Ed., Humana Press Inc. (Clifton, NJ, USA).

Tettelin H. (2009) The bacterial pan-genome and reverse vaccinology. In Genome Dynamics 6: Microbial Pathogenomics, pp. 35-47, de Reuse H. and Bereswill S. Eds, Karger (Basel, Switzerland).

Kilian M., Poulsen K., Blomqvist T., Håvarstein L.S., Bek-Thomsen M., Tettelin H., and Sørensen U.B.S. (2008) Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS ONE 3(7), e2683.

Tettelin H., Riley D., Cattuto C., and Medini D. (2008) Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol. 11: 472-477.

Valdes J., Pedroso I., Quatrini R., Dodson R.J., Tettelin H., Blake R. II, Eisen J.A., and Holmes, D.S. (2008) Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9, 597.

Bek-Thomsen M., Tettelin H., Hance I., Nelson K.E., and Kilian M. (2008) Population diversity and dynamics of Streptococcus mitis,Streptococcus oralis and Streptococcus infantis in the upper respiratory tract of adults determined by a non-culture strategy. Infect. Immun., 76, 1889-1896. Epub 2008 Mar 3.

Jiang S.-M., Ishmael N., Dunning Hotopp J., Puliti M., Tissi 3., Kumar n., Cieslewicz M.J., Tettelin H., and Wessels M.R. (2008) Variation in the group B Streptococcus CsrRS regulon and effects on pathogenicity. J. Bacteriol. 190, 1956-1965. Epub 2008 Jan. 18.

Masignani V., Tettelin H., and Rappuoli R. (2007) Vaccines against infectious diseases: a biotechnology-driven evolution. In Genomic and Personalized Medicine, Willard H.F. and Ginsburg G.S. Eds, Elsevier/Academic Press (San Diego, CA, USA), vol. 1; pp: 562-570.

Raghavan N., Tettelin H., Miller A., Hostetler J., Tallon L., and Knight M. (2007) Nimbus (BgI): An active non-LTR retrotransposon of theSchistosoma mansoni snail host Biomphalaria glabrata. Int. J. Parasitol. 37, 1307-1318.

Dunning Hotopp J.C., Clark M.E., Oliveira D.C.S.G., Foster J.M., Fischer P., Mun~oz Torres M.C., Giebel J.D., Kumar N., Ishmael N., Wang S., Ingram J., Nene R.V., Shepard J., Tomkins J., Richards S., Spiro D.J., Ghedin E., Slatko B.E., Tettelin H.*, and Werren J. H.* [*These authors have contributed equally to this work] (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317, 1753-1756.

Tettelin H., Rappuoli R., and Fraser-Liggett C.M. (2007) Using genomics to identify novel vaccine candidates against pathogens. In The Jordan Report, Accelerated Development of Vaccines 2007, U.S. Department of Health and Human Services, pp. 37-42.

Myers G.S.A., Parker D., Al-Hasani K., Kennan R.M., Seemann T., Ren Q., Badger J.H., Selengut J.D., DeBoy R.T., Tettelin H., Boyce J.D., McCarl V.P., Han X., Nelson W., Madupu R., Mohamoud Y., Holley T., Fedorova N., Khouri H., Bottomley S.P, Whittington R.J., Adler B., Songer J.G., Rood J.I., and Paulsen I.T. (2007) Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nat. Biotechnol. 25, 569-575.

Lanie J.A., Ng W-L, Kazmierczak K.M., Andrzejewski T.M., Davidsen T.M., Wayne K.J., Tettelin H., Glass J.I., and Winkler M. (2006) Genome sequence of Avery's virulent serotype 2 strain D39 of Streptococcus pneumoniae and comparison with that of unencapsulated laboratory strain R6. J. Bacteriol. 189, 38-51.

Tettelin H., Medini D., Donati C., and Masignani V. (2006) Towards a universal group B Streptococcus vaccine using multi-strain genome analysis. Expert Rev. Vaccines 5, 687-694.

Dunning Hotopp J.C., Grifantini R., Kumar N., Tzeng Y.L., Fouts D., Frigimelica E., Draghi M., Giuliani M.M., Rappuoli R., Stephens D.S., Grandi G., and Tettelin H. (2006) Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen specific genes. Microbiology 152, 3733-3749. Featured in Microbiology Today.

Savard J., Tautz D., Richards S., Weinstock G.M., Gibbs R.A., Werren J.H., Tettelin H., and Lercher M.J. (2006) Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of holometabolous insects. Genome Res. 16, 1334-1338.

Baldo L., Dunning Hotopp J.C., Jolley K.A., Bordenstein S.R., Biber S.A., Choudhury R.R., Hayashi C., Maiden M.C.J., Tettelin H., and Werren J.H. (2006) A multilocus sequence typing system for the endosymbiont Wolbachia. Appl. Environ. Microbiol. 72, 7098-7110.

Ramaswamy S.V., Ferrieri P., Madoff L.C., Flores A.E., Kumar N., Tettelin H., and Paoletti L.C. (2006) Identification of novel cps locus polymorphisms in nontypeable group B Streptococcus. J. Med. Microbiol. 55, 775-783.

Dunning Hotopp J.C., Lin M., Madupu R., Crabtree J., Angiuoli S.V., Eisen J., Seshadri R., Ren Q., Wu M., Utterback T.R., Smith S., Lewis M.R., Khouri H., Zhang C., Hua N., Lin Q., Ohashi N., Zhi N., Nelson W., Brinkac L.M., Dodson R.J., Rosovitz M.J., Sundaram J., Daugherty S.C., Davidsen T., Durkin A.S., Gwinn M.L., Haft D.H., Selengut J.D., Sullivan S.A., Zafar N., Zhou L., Benahmed F., Forberger H., Halpin R., Mulligan S., Robinson J., White O., Rikihisa Y., and Tettelin H. (2006) Comparative genomics of emerging human ehrlichiosis agents. PLoS Genet. 2, e21. Featured in Nature Reviews Microbiology.

Medini D., Donati C., Tettelin H., Masignani V., and Rappuoli R. (2005) The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589-594.

Tettelin H., Masignani M., Cieslewicz M.J., Donati C., Medini D., Ward N.L., Angiuoli S.V., Crabtree J., Jones A., Durkin A.S., DeBoy R.T., Davidsen T.M., Mora M., Scarselli M., Margarit y Ros I., Peterson J.D., Hauser C.R., Sundaram J.P., Nelson W.C., Madupu R., Brinkac L.M., Dodson R.J., Rosovitz M.J., Sullivan S.A., Daugherty S.C., Haft D.H., Selengut J., Gwinn M.L., Zhou L., Zafar N., Khouri H., Radune D., Dimitrov G., Watkins K., O'Connor K.J.B., Smith S., Utterback T.R., White O., Rubens C.E., Grandi G., Madoff L.C., Kasper D.L., Telford J.L., Wessels M.R., Rappuoli R., and Fraser C.M. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome." Proc. Natl. Acad. Sci. USA 102, 13950-13955. Erratum in: Proc. Natl. Acad. Sci. USA102, 16530. Featured in Nature Reviews Microbiology. Featured in The Scientist.

Maione D., Margarit I., Rinaudo C.D., Masignani V., Mora M., Scarselli M., Tettelin H., Brettoni C., Iacobini E.T., Rosini R., D'Agostino N., Miorin L., Buccato S., Mariani M., Galli G., Nogarotto R., Nardi Dei G., Vegni F., Fraser C.M., Mancuso G., Teti G., Madoff L.C., Paoletti L.C., Rappuoli R., Kasper D.L., Telford J.L., and Grandi G. (2005) Identification of a universal Group B Streptococcus vaccine by multiple genome screen. Science 309, 148-150. Featured in The Scientist.

Tettelin H. (2004) Streptococcal genomes provide food for thought (News and Views). Nat. Biotechnol. 22, 1523-1524.

Ward N., Larsen Ø., Sakwa J., Bruseth L., Khouri H., Durkin A.S., Dimitrov G., Jiang L., Scanlan D., Kang K., Lewis M., Nelson K.E., Methé B., Wu M., Heidelberg J.F., Paulsen I.T., Fouts D., Ravel J., Tettelin H., Ren Q., Read T., DeBoy R., Seshadri R., Salzberg S.L., Jensen H.B., Kåre Birkeland N., Nelson W., Dodson R.J., Grindhaug S.H., Holt I., Eidhammer I., Jonasen I., Vanaken S., Utterback T., Feldblyum T.V., Lillehaug J., Fraser C.M., and Eisen J.A. (2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath). PLoS Biol. 2, 1616-1628 [2(10): e303].

Tettelin H. and Parkhill J. (2004) The use of genome annotation data and its impact on biological conclusions (correspondence letter). Nature Genetics 36, 1028-1029.

Nierman W., DeShazer D., Kim H., Tettelin H., Nelson K, Feldblyum T., Ulrich R., Ronning C., Brinkac L., Daugherty S., Davidsen T., DeBoy R., Dimitrov G., Dodson R., Durkin S., Gwinn M., Haft D., Khouri H., Kolonay J., Madupu R., Mohammoud Y., Nelson W., Radune D., Romero C., Sarria S., Selengut J., Shamblin C., Sullivan S., White O., Yu Y., Zafar N., Zhou L., and Fraser C.M. (2004) Structural Flexibility in the Burkholderia mallei Genome. Proc. Natl. Acad. Sci. USA 101, 14246-14251.

Tettelin H. and Hollingshead S.K. (2004) Comparative genomics of S. pneumoniae: intra-strain diversity and genome plasticity. In The pneumococcus, pp. 15-29, Tuomanen E., Mitchell T., Morrison D. and Spratt B. Eds. ASM Press (Washington, DC, USA).

Seshadri R., Myers G.S.A., Tettelin H., Eisen J.A., Heidelberg J.F., Davidsen T.M., Dodson R.J., Deboy R.T., Fouts D.E., Haft D.H., Selengut J., Ren Q., Brinkac L.M., Madupu R., Kolonay J.F., Durkin A.S., Daugherty S.C., Shetty J., Shvartsbeyn A., Gebregeorgis E., Geer K., Tsegaye G., Malek J., Ayodeji B., Shatsman S., McLeod M.P., Majs D., Howell J.K., Pal S., Amin A., Vashisth P., McNeill T.Z., Weinstock G.M., Norris S.J., Fraser C.M., and Paulsen I.T. (2004) Comparison of the genome of the oral pathogen, Treponema denticola, with other spirochete genomes. Proc. Natl. Acad. Sci. USA 101, 5646-5651.

Wu M., Sun L.V., Vamathevan J., Riegler M., DeBoy R., Brownlie J.C., McGraw E.A., Martin W., Esser C., Ahmadinejad N., Wiegand C., Madupu R., Beanan M.J., Brinkac L.M., Daugherty S.C., Durkin A.S., Kolonay J.F., Nelson W.C., Mohamoud Y., Lee P., Berry K., Young M.B., Utterback T., Weidman J., Nierman W.C., Paulsen I.T., Nelson K.E., Tettelin H., O'Neill S.L., and Eisen J.A. (2004) Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2: 327-341.

Radune D. and Tettelin H. (2004) Optimized multiplex polymerase chain reaction, an effective method for rapid gap closure. In Methods in Molecular Biology 255: Bacterial Artificial Chromosomes, pp. 309-318, Zhao S. and Stodolsky M. Eds, Humana Press Inc. (Totowa, NJ, USA).

Tettelin H. and Feldblyum T. (2004) Genome sequencing and analysis. In Genomics, Proteomics and Vaccines, pp. 45-73, Grandi G. Ed., John Wiley and Sons Ltd (London, United Kingdom).

Telford J.L., Margarit y Ros I., Maione D., Masignani V., Tettelin H., Bensi G., and Grandi G. (2004) Vaccines against pathogenic streptococci. In Genomics, Proteomics and Vaccines, pp. 205-222, Grandi G. Ed., John Wiley and Sons Ltd (London, United Kingdom).

Nelson K.E., Fleischmann R.D., DeBoy R.T., Paulsen I.T., Fouts D.E., Eisen J.A., Daugherty S.C., Dodson R.J., Durkin A.S., Gwinn M., Haft D.H., Kolonay J.F., Nelson W.C., Mason T., Tallon L., Gray J., Granger D., Tettelin H., Dong H., Galvin J.L., Duncan M.J., Dewhirst F.E., and Fraser C.M. (2003) Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83. J. Bacteriology 185, 5591-5601.

Read T.D., Peterson S.N., Tourasse N., Baillie L.W., Paulsen I.T., Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R., Holtzapple E.K., Økstad O.A., Helgason E., Rilstone J., Wu M., Kolonay J.F., Beanan M.J., Dodson R.J., Brinkac L.M., Gwinn M., DeBoy R.T., Madupu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C., Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y., Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M., Watkins K.L., Nierman W.C., Hazen A., Cline R., Redmond C., Thwaite J.E., White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M., Hanna P.C., Kolstø A-B., and Fraser C.M. (2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423, 81-86.

Seshadri R., Paulsen I.T., Eisen J.A., Read T.D., Nelson K.E., Nelson W.C., Ward N.L., Tettelin H., Davidsen T.M., Beanan M.J., Deboy R.T., Daugherty S.C., Brinkac L.M., Madupu R., Dodson R.J., Khouri H.M., Lee K.H., Carty H.A., Scanlan D., Heinzen R.A., Thompson H.A., Samuel J.E., Fraser C.M., and Heidelberg J.F. (2003) Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proc. Natl. Acad. Sci. USA 100, 5455-5460.

Paulsen I.T., Banerjei L., Myers G.S.A., Nelson K.E., Seshadri R., Read T.D., Fouts D.E., Eisen J.A., Gill S.R., Heidelberg J.F., Tettelin H.,Dodson R.J., Umayam L., Brinkac L., Beanan M., Daugherty S., DeBoy R.T., Durkin S., Kolonay J., Madupu R., Nelson W., Vamathevan J., Tran B., Upton J., Hansen T., Shetty J., Khouri H., Utterback T., Radune D., Ketchum K.A., Dougherty B.A., and Fraser C.M. (2003) Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis. Science 299, 2071-2074.

Paulsen I.T., Seshadri R., Nelson K.E., Eisen J.A., Heidelberg J.F., Read T.D., Dodson R.J., Umayam L., Brinkac L.M., Beanan M.J., Daugherty S.C., Deboy R.T., Durkin A.S., Kolonay J.F., Madupu R., Nelson W.C., Ayodeji B., Kraul M., Shetty J., Malek J., Van Aken S.E., Riedmuller S., Tettelin H., Gill S.R., White O., Salzberg S.L., Hoover D.L., Lindler L.E., Halling S.M., Boyle S.M., and Fraser C.M. (2002) The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. Natl. Acad. Sci. USA 99: 13148-13153.

Tettelin H., Masignani V., Cieslewicz M.J., Eisen J.A., Peterson S., Wessels M.R., Paulsen I.T., Nelson K.E., Margarit I., Read T.D., Madoff L.C., Wolf A.M., Beanan M.J., Brinkac L.M., Daugherty S.C., DeBoy R.T., Durkin A.S., Kolonay J.F., Madupu R., Lewis M.R., Radune D., Fedorova N.B., Scanlan D., Khouri H., Mulligan S., Carty H.A., Cline R.T., Van Aken S.E., Gill J., Scarselli M., Mora M., Iacobini E.T., Brettoni C., Galli G., Mariani M., Vegni F., Maione D., Rinaudo D., Rappuoli R., Telford J.L., Kasper D.L., Grandi G., and Fraser C.M. (2002) Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc. Natl. Acad. Sci. USA 99: 12391-12396.

Grifantini R., Bartolini E., Muzzi A., Draghi M., Frigimelica E., Berger J., Ratti G., Petracca R., Galli G., Agnusdei M., Giuliani M.M., Santini L., Brunelli B., Tettelin H., Rappuoli R., Randazzo F., and Grandi G. (2002) Previously unrecognized vaccine candidates against Group B meningococcus identified by DNA microarrays. Nat. Biotechnol. 20: 914-921.

Eisen J.A., Nelson K.E., Paulsen I.T., Heidelberg J.F., Wu M., Dodson R.J., DeBoy R., Gwinn M.L., Nelson W.C., Haft D.H., Hickey E.K., Peterson J.D., Durkin A.S., Kolonay J.L., Yang F., Holt I., Umayam L.A., Mason T., Brenner M., Shea T.P., Parksey D., Nierman W.C., Feldblyum T.V., Hansen C.L., Craven M.B., Radune D., Vamathevan J., Khouri H., White O., Gruber T.M., Ketchum K.A., Venter J.C.,Tettelin H., Bryant D.A., and Fraser C.M. (2002) The complete genome sequence of Cholorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc. Natl. Acad. Sci. USA 90, 9509-9514.

Read T.D., Gill S.R., Tettelin H., and Dougherty B.A. (2001) Finding drug targets in microbial genomes. Drug Discovery Today 6, 887-892.

Tettelin H., Nelson K.E., Paulsen I.T., Eisen J.A., Read T.D., Peterson S., Heidelberg J., DeBoy R.T., Haft D.H., Dodson R.J., Durkin A.S., Gwinn M., Kolonay J.F., Nelson W.C., Peterson J.D., Umayam L.A., White O., Salzberg S.L., Lewis M.R., Radune D., Holtzapple E., Khouri H., Wolf A.M., Utterback T.R., Hansen C.L., McDonald L.A., Feldblyum T.V., Angiuoli S., Dickinson T., Hickey E.K., Holt I.E., Loftus B.J., Yang F., Smith H.O., Venter J.C., Dougherty B.A., Morrison D.A., Hollingshead S.K., and Fraser C.M. (2001) Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293, 498-506. Fast Breaking Paper. Hot paper 1. Hot paper 2.

Masignani V., Giuliani M.M., Tettelin H., Commanducci M., Rappuoli R., and Scarlato V. (2001) A Mu-like prophage in serogroup BNeisseria meningitidis coding for surface-exposed antigens. Infection and Immunity 69, 2580-2588.

Peterson S., Cline R.T., Tettelin H., Sharov V., and Morrison D.A. (2000) Gene expression analysis of the Streptococcus pneumoniaecompetence regulons by use DNA microarrays. J. Bacteriology 182, 6192-6202.

Saunders N.J., Jeffries A.C., Peden J.F., Hood D.W., Tettelin H., Rappuoli R., and Moxon E.R. (2000) Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58. Mol. Microbiol. 37, 207-215.

Heidelberg J., Eisen J.A., Nelson W.C., Clayton R., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L., Gill S.R., Nelson K.E., Read T.D., Tettelin H., Richardson D., Ermolaeva M.D., Vamathevan J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L., Utterback T., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., Smith H.O., Colwell R.R., Mekalanos J., Venter J.C., and Fraser C.M. (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477-484.

Tettelin H., Saunders N.J., Heidelberg J., Jeffries A.C., Nelson K.E., Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C., Gwinn M.L., DeBoy R., Peterson J.D., Hickey E.K., Haft D.H., Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T., Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D., Utterback T.R., Khouri H., Qin H., Vamathevan J., Gill J., Scarlato V., Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M., Moxon E.R., Rappuoli R., and Venter J.C. (2000) Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287, 1809-1815. Hot Paper in The Scientist.

Pizza M., Scarlato V., Masignani V., Giuliani M.M., Arica B., Comanducci M., Jennings G.T., Baldi L., Bartolini E., Capecchi B., Galeotti C.L., Luzzi E., Manetti R., Marchetti E., Mora M., Nuti S., Ratti G., Santini L., Savino S., Scarselli M., Storni E., Zuo P., Broeker M., Hundt E., Knapp B., Blair E., Mason T., Tettelin H., Hood D.W., Jeffries A.C., Saunders N.J., Granoff D.M., Venter J.C., Moxon E.R., Grandi G., and Rappuoli R. (2000) Whole genome sequencing to identify vaccine candidates against serogroup B meningococcus. Science 287, 1816-1820.

Tettelin H., Radune D., Kasif S., Khouri H., and Salzberg S.L. (1999) Optimized multiplex PCR: efficiently closing a whole genome shotgun sequencing project. Genomics 62, 500-507.

Salzberg S.L., Pertea M., Delcher A.L., Gardner M.J., and Tettelin H. (1999) Interpolated markov models for eukaryotic gene finding. Genomics 59, 24-31.

Gardner M.J., Tettelin H., Carucci D.J., Cummings L.M., Smith H.O., Fraser C.M., Venter J.C., and Hoffman S.L. (1999) The malaria genome sequencing project: complete sequence of P. falciparum chromosome 2. Parassitologia 41, 69-75.

Jing J., Lai Z., Aston C., Lin J., Carucci D.J., Gardner M.J., Mishra B., Anantharaman T.S., Tettelin H., Cummings L.M., Hoffman S.L., Venter J.C., and Schwartz D.C. (1999) Optical mapping of Plasmodium falciparum chromosome 2. Genome Research 9, 175-181.

Gardner M.J., Tettelin H., Carucci D.J., Cummings L.M., Aravind L., Koonin E.V., Shallom S., Mason T., Yu K., Fujii C., Pedersen J., Shen K., Jing J., Aston C., Lai Z., Schwartz D.C., Pertea M., Salzberg S., Zhou L., Sutton G.G., Clayton R.L., White O., Smith H.O., Fraser C.M., Adams M.D., Venter J.C., and Hoffman S.L. (1998) Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science 282, 1126-1132.

Carucci D.J., Gardner M.J., Tettelin H., Cummings L.M., Smith H.O., Adams M.D., Venter J.C., and Hoffman S.L. (1998) Sequencing the genome of Plasmodium falciparum. Current Opinion in Infectious Diseases 11, 531-534.

Carucci D.J., Gardner M.J., Tettelin H., Cummings L.M., Smith H.O., Adams M.D., Hoffman S.L., and Venter J.C. (1998) The malaria genome sequencing project. Expert Rev. Mol. Med. 1998, 1-9.

Gardner M.J., Tettelin H., Carucci D.J., Cummings L.M., Adams M.D., Smith H.O., Venter J.C., and Hoffman S.L. (1998) The malaria genome sequencing project. Protist 149, 109-112.

Tettelin H., Thierry A., Goffeau A., and Dujon B. (1998) Physical mapping of chromosomes VII and XV of Saccharomyces cerevisiae at 3.5 kb average resolution to allow their complete sequencing. Yeast 14, 601-616.

Caro L.H.P., Tettelin H., Vossen J.H., Ram A.F.J., van den Ende H., and Klis F.M. (1997) In silicio identification of glycosyl-phosphatidylinositol-anchored plasma membrane and cell wall proteins of Saccharomyces cerevisiae. Yeast 13, 1477-1489.

Tettelin H., ..., and Kleine K. (115 authors) (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome VII. Nature 387 supplement, 81-84.

Dujon B., ..., Tettelin H., ..., and Kleine K. (97 authors) (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature 387 supplement, 98-102.

Bussey H., ..., Tettelin H., ..., and Hani J. (124 authors) (1997) The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 387 supplement, 103-105.

Van Dyck L., Tettelin H., Purnelle B., and Goffeau A. (1997) An 18.3 kb DNA fragment from yeast chromosome VII carries four unknown open reading frames, the gene for an Asn synthetase, remnants of Ty and three tRNA genes. Yeast 13, 171-176.

Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., Galibert F., Hoheisel J.D., Jacq C., Johnston M., Louis E.J., Mewes H.W., Murakami Y, Philippsen P., Tettelin H., and Oliver S.G. (1996) Life with 6000 genes. Science 274, 546-567.

Dujon B., ..., Tettelin H., ..., and Mewes H.W. (108 authors) (1994) Complete DNA sequence of yeast chromosome XI. Nature 369, 371-378.

Purnelle B., Tettelin H., Van Dyck L., Skala J., and Goffeau A. (1993) The sequence of a 17.5 kb DNA fragment on the left arm of yeast chromosome XI identifies the protein kinase gene ELM1, the DNA primase gene PRI2, a new gene encoding a putative histone and seven new open reading frames. Yeast 9, 1379-1384.

1.     Pathogen genomic diversity in colonization and disease. I have been in the genomics field for over 30 years, since the beginning of my B.Sc. in 1991. I have led the genome sequencing and analysis of many organisms, starting with eukaryotic chromosomes then shifting towards bacterial pathogens. I was the lead author on the first published whole genome sequences of Neisseria meningitidis (a), Streptococcus pneumoniae (b) and Streptococcus agalactiae. Over time, I have made use of the rapidly evolving genome sequencing technologies, from Sanger sequencing to 454, Illumina, and Pacific Biosciences. I have conducted in-depth comparative genomics analyses of isolates of nontypeable Haemophilus influenzae (NTHi) that are critical to the pathogenesis of chronic obstructive pulmonary disease (COPD). We conducted whole-genome sequencing of 269 longitudinally collected cleared and persistent NTHi from a 15-y prospective study of adults with COPD (c,d). We elucidated the phylogeny of NTHi isolates, identified genomic changes that occur with persistence in the human airways, and evaluated the effect of selective pressure on candidate vaccine antigens. Slipped-strand mispairing, mediated by changes in simple sequence repeats in multiple genes during persistence, was found to regulate expression of critical virulence functions and to be a major mechanism for survival in the hostile environment of the human airways. Our results advanced our understanding of how a bacterial pathogen that plays a critical role in COPD adapts to survival in the human respiratory tract.

a.     Tettelin H, Saunders NJ, Heidelberg J, et al. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science. 2000 Mar 10;287(5459):1809-15. PubMed PMID: 10710307.

b.     Tettelin H, Nelson KE, Paulsen IT, Eisen JA, et al. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science. 2001 Jul 20;293(5529):498-506. PubMed PMID: 11463916.

c.     Pettigrew M.M., Ahearn C.P., Gent J.F., Kong Y., Gallo M.C., Munro J.B., D’Mello A., Sethi S., Tettelin H.*, and Murphy, T.F.* [*These authors contributed equally to this work] Haemophilus influenzae genome evolution during persistence in the human airways in chronic obstructive pulmonary disease. Proc. Natl. Acad. Sci. U S A 2018 115(14): E3256-E3265. PubMed PMID: 29555745. PMCID: PMC5889651 (available October 3, 2018).

d.     Murphy TF, Kirkham C, D’Mello A, Sethi S, Pettigrew MM, Tettelin H. Adaptation of nontypeable Haemophilus influenzaein human airways in COPD: genome rearrangements and modulation of expression of HMW1 and HMW2. mBio, 2023 Mar 16:e0014023. PubMed PMID: 36927061; PMCID: PMC10127715.

2.   Translational studies: reverse vaccinology and diagnostics. I have a long track record of developing computational and analytical approaches to support translational efforts aimed at developing new vaccines and therapeutics. In collaboration with the team of Dr. Rino Rappuoli (former Chiron Vaccines, Novartis Vaccines and Diagnostics, and GSK Vaccines), I leveraged bacterial genome information to pioneer the Reverse Vaccinology approach that identifies and prioritizes novel vaccine candidates using whole genome sequencing (a,b). We applied it to Neisseria meningitidisserogroup B for which no broadly protective vaccine candidates had been identified after decades of classical vaccinology. We identified all predicted surface-exposed proteins from serogroup B N. meningitidis in silico based on various protein motifs and these proteins were expressed and screened in high-throughput experiments by Dr. Rappuoli’s vaccine research group (a). For the first time in 35 years, 7 novel protective and conserved vaccine candidates were identified. A subset of these candidates has been shown to provide immune protection in human clinical trials and the 4CMenB vaccine is now on the market. I directed further developments of our reverse vaccinology pipeline for improved vaccine candidate antigen prioritization (d). In another study, I performed comparative genomics of Mycobacterium abscessus subsp. massiliense isolates from outbreaks in cystic fibrosis centers in the USA and UK. Strains from the two cystic fibrosis outbreaks showed high-level relatedness with each other despite their geographical distance. We identified unique SNPs and genomic traits in outbreak strains and designed two PCR-based diagnostic strategies for use in the clinical setting (c). Our findings highlighted the necessity of identifying M.abscessus to the subspecies level and screening all cystic fibrosis isolates for relatedness to these outbreak strains.

a.     Pizza M, Scarlato V, Masignani V, Giuliani MM, Aricò B, et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science. 2000 Mar 10;287(5459):1816-20. PubMed PMID: 10710308.

b.     Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, et al. Identification of a universal Group B Streptococcus vaccine by multiple genome screen. Science. 2005 Jul 1;309(5731):148-50. PubMed PMID: 15994562; PMCID: PMC1351092.

c.     Tettelin H, Davidson RM, Agrawal S, Aitken ML, Shallom S, et al. High-level relatedness among Mycobacterium abscessus subsp. massiliense strains from widely separated outbreaks. Emerg Infect Dis. 2014 Mar;20(3):364-71. PubMed PMID: 24565502; PMCID: PMC3944860.

d.     D’Mello A, Ahearn CP, Murphy TF, Tettelin H. ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. BMC Genomics 2019 Dec 16;20(1):981. PubMed PMID: 31842745. PMCID: PMC6916091.

3.  Large-scale bioinformatics. A significant fraction of my effort is dedicated towards the development, optimization, and use of bioinformatics tools and pipelines. I led the most recent developments of the Sybil comparative genomics package (c). Sybil is an open-source web-based software package for bacterial comparative genomics. It provides a rich set of web interfaces at varying levels of resolution from the whole genome scale down to single genes. The visualizations in Sybil include over 20 interactive interfaces for mining genome conservation and variation. Sybil relies on the construction of paralogous and orthologous protein families for the detection of syntenic regions. I also developed the whole genome multiple alignment-based Mugsy-Annotator tool for identification of clusters of syntenic orthologs (b). Nucleotide alignments make the approach more robust in presence of annotation discrepancies and overcome challenges associated with identification of orthologs based on protein sequence similarity. Finally, I have applied large-scale comparative genomics to the study of bacterial diversity, virulence and evolution. Recent examples include the identification of restriction-modification systems that drive the separation of Neisseria meningitidis isolates into distinct clades (a) and the characterization of the parallel evolution of pathogenic and commensal streptococci (d).

a.     Budroni S, Siena E, Dunning Hotopp JC, et al. Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination. Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4494-9. PubMed PMID: 21368196; PMCID: PMC3060241.

b.     Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H. Improving pan-genome annotation using whole genome multiple alignment. BMC Bioinformatics. 2011 Jun 30;12:272. PubMed PMID: 21718539; PMCID: PMC3142524.

c.     Riley DR, Angiuoli SV, Crabtree J, Dunning Hotopp JC, Tettelin H. Using Sybil for interactive comparative genomics of microbes on the web. Bioinformatics. 2012 Jan 15;28(2):160-6. PubMed PMID: 22121156; PMCID: PMC3259440.

d.     Kilian M, Tettelin H. Identification of virulence-associated properties by comparative genome analysis of Streptococcus pneumoniae, S. pseudopneumoniae, S. mitis, three S. oralis subspecies, and S. infantis. mBio. 2019 Oct 15;10(5). pii: e01985-19 (Erratum: e02520-19). PubMed PMID: 31481387. PMCID: PMC6722419.

4.   Bacterial virulence studies using genome-wide transcriptional profiling. I have extensive experience in studying the genome-wide transcriptional response of bacterial and human cells or organs under various growth conditions, including host-pathogen interactions, using spotted microarrays (a), Illumina-based RNA deep sequencing (RNA-seq)(b-d), and more recently the NanoString probe-based technology. In particular, in collaboration with Dr. Carlos Orihuela at the University of Alabama at Birmingham, I have performed dual RNA-seq profiling of the host-pathogen interplay during colonization and disseminated Streptococcus pneumoniae infection in a mouse model. We generated an in vivo atlas of bacterial and mouse gene responses using whole infected or uninfected organs, as well as infected or uninfected blood. These studies led to the identification of novel anatomical site-specific expression of determinants of pneumococcal pathogenesis, gave insights into their mechanism of interaction with the host, provided key information on currently considered and future protein candidates for vaccine development, and revealed pathways of host response that could lead to new interventions (c).

a.     Kimaro Mlacha SZ, Romero-Steiner S, Hotopp JC, et al. Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells. BMC Genomics. 2013 Jun 9;14:383. PubMed PMID: 23758733; PMCID: PMC3708772.

b.     Shenoy AT, Brissac T, Gilley RP, Kumar N, Wang Y, Brissac T, Gonzalez-Juarbe N, Hinkle WS, Daugherty SC, Shetty AC, Ott S, Tallon LJ, Deshane J, Tettelin H, and Orihuela CJ. Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing. PLoS Pathog. 2017 Aug 25;13(8):e1006582. PMID: 28841717. PMCID: PMC5589263.

c.     D’Mello A, Riegler AN, Martínez E, Beno SM, Ricketts TD, Foxman EF, Orihuela CJ*, and Tettelin H* [*These authors contributed equally] An in vivo atlas of host-pathogen transcriptomes during Streptococcus pneumoniae colonization and disease. Proc. Natl Acad. Sci. U S A 2020 Dec 29;117(52):33507-33518. PubMed PMID: 33318198. Open access.

d.     Potter AD, Edwards VL, D’Mello A, Gray MC, Shetty AC, Forehand AL, Westlake CS, Lamb ER, Zhao X, Ragland SA, Criss AK*, Tettelin H* [*These authors contributed equally]. Dual species transcriptomics reveals conserved metabolic and immunologic processes in interactions between human neutrophils and Neisseria gonorrhoeae. PLoS Pathog. 2024 Jul 8;20(7):e1012369. PubMed PMID: 38976720; PMCID: PMC11257400.

5.    The bacterial species pangenome concept. Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pangenome analyses are now widely applied, including for eukaryotic microbes, and provide a framework for estimating the genomic diversity of the dataset at hand. I pioneered the concept of the bacterial species pangenome while studying genomes of Streptococcus agalactiae (group B Streptococcus) (a). We determined that a pangenome is composed of a conserved core genome surrounded by varying degrees of genomic diversity. We demonstrated that for many bacteria, including many human pathogens, this intra-species diversity results in a pangenome much larger than any individual genome (a-d), and therefore no single genome is fully representative of the species, one of my motivations for modern reference-free comparative genomics. Along with Duccio Medini (at the time GSK Vaccines), I was the editor of the first book on the pangenome that was published by Springer in the spring of 2020 (d).

a.     Tettelin H, Masignani V, Cieslewicz MJ, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13950-5. PubMed PMID: 16172379; PMCID: PMC1216834.

b.     Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol. 2008 Oct;11(5):472-7. PubMed PMID: 19086349.

c.     Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol. 2015 Feb;23C:148-154. PubMed PMID: 25483351.

d.     Tettelin H., and Medini D., Editors (2020) The pangenome: diversity, dynamics and evolution of genomes. Cham (CH): Springer Nature. Print ISBN: 978-3-030-38280-3, online ISBN: 978-3-030-38281-0. PMID range: 32633908 to 32633921 (Free Books & Documents).

Affiliate, Federation of European Microbiological Societies (FEMS)

Member, American Society for Microbiology (ASM)

R01 AI019641                                                    Murphy (PI)                          07/01/19–06/30/25

Genome evolution during bacterial persistence in the human airways in COPD

Chronic obstructive pulmonary disease (COPD) is a chronic debilitating disease that afflicts ~24 million Americans and is the fourth leading cause of death in the US and in the world. We will elucidate the evolutionary dynamics of bacterial pathogens in human COPD airways by analyzing the genomes of serial isolates of strains of nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) that have persisted for months to years. We will also examine transcriptional profiles of serial isolates of persistent strains. Guided by dynamic changes in genomes and transcriptomes in human airways, we will elucidate mechanisms that mediate persistence of NTHi and Mcat using relevant model systems.

Role: Co-Investigator

R01 AI114800                                                    Orihuela (PI)          12/10/19–11/30/24 (renewal pending)

Cardiac microlesion formation during invasive pneumococcal disease

One-in-four adults hospitalized for community-acquired pneumonia experience an adverse cardiac event. This is, in part, the result of Streptococcus pneumoniae invasion of cardiomyocytes. We will determine how glucose limitation experienced by intracellular pneumococci enhances their production of cytotoxic pneumolysin and hydrogen peroxide. SpxB-derived H₂O₂ and pneumolysin are both required for S. pneumoniae killing of cardiomyocytes, while each alone is insufficient. At the Institute for Genome Sciences, we will apply RNA-seq based transcriptional profiling of bacteria-cardiomyocyte interactions and integrate results with associated metabolomics data.

Role: Co-Investigator (MPI on renewal)

R01 AI155476                                                     Ratner (PI)                            06/08/2021–05/31/26

Capsular serotype in group B Streptococcus colonization and disease

Despite widespread screening and routine intrapartum antimicrobial prophylaxis, Group B Streptococcus (GBS) remains a major cause of infectious morbidity and mortality among infants. The goal of this project is to gain a detailed understanding of the role of serotype-specific and serotype-independent factors in GBS colonization and pathogenesis. This will be achieved through whole genome sequencing of isolates with evidence of capsule switching. Knowledge gained will provide a very important foundation for formulating GBS vaccine policy and guiding post-licensure surveillance.

R21 AI156226                                                      Bessen (PI)                           07/01/21–06/30/25

Macrolide resistance transfer in Streptococcus pyogenes

Group A Streptococcus (GAS) is a strict human pathogen that primarily infects the epithelia at the throat or skin. Antibiotic-resistance is increasing and elevated GAS to the status of “concerning threat” in the CDC’s Antibiotic Resistance Threats Report of 2019. The proposed study seeks a deeper understanding of the biological causes and clinical consequences of the acquisition by GAS of mobile genetic elements harboring macrolide-resistance genes.

07/28/01    New Scientist piece about Dr. Tettelin’s publication of the first Streptococcus pneumoniae genome in the journal Science:

https://www.newscientist.com/article/mg17123014-300-sweet-killer/

04/01/03    EMBO Reports piece that quotes Dr. Tettelin and Dr. Rino Rappuoli on reverse vaccinology:

http://www.ncbi.nlm.nih.gov/pubmed/12671675

01/28/11    Dr. Tettelin was interviewed and cited by MIT's Technology Review about the publication of a large-scale Streptococcus pneumoniae genomics study in the journal Science:

http://www.technologyreview.com/biomedicine/32231/

06/20/11    Dr. Tettelin was interviewed by the Biotechnology Industry Organization (BIO) for a podcast on reverse vaccinology and the pan-genome concept. He also discussed how DNA sequencing is evolving and how that impacts vaccine development:

http://www.biotech-now.org/health/2011/06/podcast-dr-herve-tettelin-on-vaccine-development

12/01/16    Dr. Tettelin was interviewed by The Scientist on the pan-genome concept.

http://www.the-scientist.com/?articles.view/articleNo/47510/title/The-Pangenome--Are-Single-Reference-Genomes-Dead-/

03/22/18    Press release and press coverage of Dr. Tettelin’s 2018 PNAS paper on COPD pathogens:

http://www.medschool.umaryland.edu/news/2018/With-Big-Data-Researchers-Identify-New-Targets-for-Lung-Disease-Treatments.html

https://www.rdmag.com/news/2018/03/big-data-researchers-identify-new-targets-lung-disease-treatments

http://publichealth.yale.edu/article.aspx?id=16956

https://www.buffalo.edu/ubnow/stories/2018/03/murphy-copd-pathogen.html

http://www.buffalo.edu/news/releases/2018/03/025.html

http://www.infosalus.com/salud-investigacion/noticia-nuevos-objetivos-tratamientos-enfermedades-pulmonares-20180321072931.html

12/04/18    Press release and metrics of Dr. Tettelin’s 2018 PNAS paper on bacteria and cancer:

http://www.ihv.org/news/2018/Institute-of-Human-Virology-Researchers-Discover-That-a-Bacterial-Protein-Promotes-Cancer.html

https://pnas.altmetric.com/details/52149379/news

07/25/19    Press release on Drs Murphy and Tettelin’s new 5-year R01 award on COPD pathogens:

http://www.buffalo.edu/news/releases/2019/07/030.html

12/14/20    Press releases and metrics of Dr. Tettelin’s 2020 PNAS paper on S. pneumoniae transcriptomics of host-pathogen interactions:

https://pnas.altmetric.com/details/95992463/news

https://www.igs.umaryland.edu/doc/PNAS_Strep_pneumo_fin_IGS_HT.pdf

https://www.medschool.umaryland.edu/news/2020/University-of-Maryland-School-of-Medicine-Researchers-Create-Extensive-Gene-Expression-Database-to-Gain-New-Insights-into-Pneumococcal-Infections.html

https://www.uab.edu/news/research/item/11757-an-atlas-of-s-pneumoniae-and-host-gene-expression-during-colonization-and-disease

https://www.eurekalert.org/pub_releases/2020-12/uoms-rcg121420.php ; https://www.newswise.com/articles/researchers-create-extensive-gene-expression-database-to-gain-new-insights-into-pneumococcal-infections

11/30/21    Press release from the University of Puerto Rico School of Medicine quoting Dr. Tettelin about the selection of Marielisa Cabrera-Sánchez as a finalist of the American Medical Association’s National Research Challenge:

https://www.facebook.com/176928629036688/posts/4779896872073151/?d=n

Pre-finals podcast. Finals AMA event. Post-final AMA interview of the winner: Marielisa Cabrera-Sánchez.

University at Buffalo press release.

Examples of Sybil comparative genomics websites

Comparative Genomics of Streptococcus pneumoniae

Comparative Genomics of Cutibacterium (formerly Propionibacterium) acnes

Comparative genomics of nontypeable Haemophilus inflenzae