Dr. Cecilia Alsmark

Contact information

• Phone number:
• e-mail adress: cecilia.alsmark (at) fkog.uu.se

Work description

I did my PhD in Uppsala, Sweden, working on comparative genomics of bacteria. The two main projects involved the sequencing of the genomes of Rickettsia prowazeki, the causative agent of typhus and of Bartonella henselae that causes cat scratch disease in humans.

During my time as a post doc I have left both the bacteria and the lab bench and turned to doing bioinformatics on eukaryotic pathogens instead. My main interest has been to identify and evaluate the prokaryote contribution to the gene content of some of the most widespread human parasites. My work has been divided between the development of methods to detect horizontally transferred genes (HGT) on a whole genome scale and then investigation of a few genomes. The software development has been in collaboration with Dr Thomas Sicheritz Ponten, DTU, Copenhagen and the detection of HGTs has been in collaboration with The Institute of Genome Research (TIGR) and the Sanger Centre.

Cecilia has now moved back to Sweden as a post doc in the Department of Medicinal Chemistry, Uppsala University, her new contact details are:

Dr. Cecilia Alsmark

Department of Medicinal Chemistry

Uppsala University

BMC - Biomedical Center, Box 574

S-751 23 Uppsala

Sweden

Cecilia's publications

• Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biol. vol 14 (2013). pubmed
• Alsmark UC, Sicheritz-Ponten T, Foster PG, Hirt RP, Embley TM. Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis. Methods in Molecular Biology. vol 532 p. 489-500 (2009). pubmed
• Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM and Johnson PJ. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. vol 315 p. 207-12 (2007). pubmed
• Clark CG, Alsmark UC, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noel CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T and Hall N. Structure and content of the Entamoeba histolytica genome. Adv Parasitol.. vol 67 p. 51-190 (2007). pubmed
• Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Bohme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE and El-Sayed NM. The genome of the African trypanosome Trypanosoma brucei. Science. vol 309 p. 416-22 (2005). pubmed
• El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE andersson B, Stuart KD and Hall N. Comparative genomics of trypanosomatid parasitic protozoa. Science. vol 309 p. 404-9 (2005). pubmed
• Frank AC, Alsmark CM, Thollesson M and Andersson SG. Functional Divergence and Horizontal Transfer of Type IV Secretion Systems. Mol Biol Evol. vol 22 p. 1325-36 (2005). pubmed
• Loftus B anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM and Hall N. The genome of the protist parasite Entamoeba histolytica. Nature. vol 433 p. 865-8 (2005). pubmed
• Alsmark CM, Frank AC, Karlberg EO, Legault BA, Ardell DH, Canback B, Eriksson AS, Naslund AK, H Andley SA, Huvet M, La Scola B, Holmberg M and Andersson SG. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc Natl Acad Sci U S A. vol 101 p. 9716-21 (2004). pubmed
• Amiri H, Alsmark CM and Andersson SG. Proliferation and deterioration of Rickettsia palindromic elements. Mol Biol Evol. vol 19 p. 1234-43 (2002). pubmed
• Andersson SG, Alsmark C, Canback B, Davids W, Frank C, Karlberg O, Klasson L, Antoine-Legault B, Mira A and Tamas I. Comparative genomics of microbial pathogens and symbionts. Bioinformatics. vol 18 Su p. S17 (2002). pubmed
• Andersson SG, Zomorodipour A andersson JO, Sicheritz-Ponten T, Alsmark UC, Podowski RM, Naslund AK, Eriksson AS, Winkler HH and Kurl and CG. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. vol 396 p. 133-40 (1998). pubmed