Anita Lerch Assistant Research Professor

Research Interests:

Our research focuses on analyzing genomic and transcriptomic data of vector-borne diseases, in particular Plasmodium and Trypanosoma, to study the development of the pathogen in the host and the population dynamics of the pathogen and its vector.

Biography:

• Assistant Research Professor, Department of Biological Science, University of Notre Dame IN. 2023-Present
• Postdoctoral Research Associate, Department of Biological Sciences, University of Notre Dame, USA, 2018-2023
• Ph.D. Student, Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute Basel, Switzerland, 2013-2018
• Bioinformatician, Dept. Systems Biology and Personalised Medicine, Walter & Eliza Hall Institute Melbourne, Australia, 2012-2013
• Bioinformatician, Computational Biology Group, Friedrich Miescher Institute Basel, Switzerland, 2011-2012
• Assistant in medical image processing, Department of Computer Science, University of Basel, Switzerland, 2008-2011
• Laboratory technician, Department of Applied Microbiology, Biozentrum, University of Basel, Switzerland, 1999-2003

Education:

• Ph.D., Molecular Epidemiology. University of Basel, Switzerland, March 2018
• M.S., Computer Science. University of Basel, Switzerland, July 2008
• B.S., Computer Science. University of Basel, Switzerland, July 2006
• Biological Laboratory Technician, Hoffmann - La Roche Basel, Switzerland, July 1997

Recent Papers:

• A Holzschuh, A Lerch, I Gerlovina, BS Fakih, AH Al-mafazy, EJ Reaves, A Ali, F Abbas, MH Ali, MA Ali, MW Hetzel, J Yukich, C Koepfli. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nature Communication. 14, 3699 (2023). DOI: 10.1038/s41467-023-39417-1.
• A Lerch, QA ten Bosch, M L’Azou Jackson, AA Bettis, M Bernuzzi, GAV Murphy, QM Tran, JH Huber, AS Siraj, GM Bron, M Elliott, CS Hartlage, S Koh, K Strimbu, M Walters, TA Perkins, SM Moore. Projecting vaccine demand and impact for emerging zoonotic pathogens. BMC Medicine. 2022;20:202. DOI: 10.1186/s12916-022-02405-1.
• Vivax Sporozoite Consortium. Transcriptome and histone epigenome of Plasmodium vivax salivary-gland sporozoites point to tight regulatory control and mechanisms for liver-stage differentiation in relapsing malaria. Int J Parasitol. 2019; 49(7):501. DOI: 10.1016/j.ijpara.2019.02.007.
• M Gruenberg*, A Lerch*, HP Beck, I Felger. Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs. Scientific Reports. 2019; 9(1):17790. DOI: 10.1038/s41598-019-54203-0.
• A Lerch, C Koepfli, NE Hofmann, JH Kattenberg, A Rosanas-Urgell, I Betuela, I Mueller, I Felger. Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections. Scientific Reports. 2019; 9(1):3333. DOI: 10.1038/s41598-019-39656-7.
• A Lerch, C Koepfli, N Hofmann, C Messerli, S Wilcox, JH Kattenberg, I Betuela, L O’Connor, I Mueller, I Felger. Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections. BMC Genomics. 2017; 18(1):864. DOI: 10.1186/s12864-017-4260-y. 
• D Gaidatzis*, A Lerch*, F Hahne, MB Stadler. QuasR: quantification and annotation of short reads in R. Bioinformatics. 2015; 31(7):1130. DOI: 10.1093/bioinformatics/btu781.
• FS Dietrich, S Voegeli, S Brachat, A Lerch, K Gates, S Steiner, C Mohr, R Pohlmann, P Luedi, S Choi, RA Wing, A Flavier, TD Gaffney, P Philippsen. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004; 304(5668):304. DOI: 10.1126/science.1095781.
• S Brachat, FS Dietrich, S Voegeli, Z Zhang, L Stuart, A Lerch, K Gates, T Gaffney, P Philippsen. Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. Genome Biology. 2003; 4(7):R45. DOI: 10.1186/gb-2003-4-7-r45.