Biography

• Postdoctoral Research Associate, Department of Biological Sciences & Eck Institute for Global Health, University of Notre Dame, USA 2018 - Present
• Ph.D. in Molecular Epidemiology, Swiss Tropical and Public Health Institute & University of Basel, Switzerland 2018
• M.Sc. in Computer Science, University of Basel, Switzerland 2008
• B.Sc. in Bioinformatics, University of Basel, Switzerland 2006

Projects

• HaplotypR

Publications

First author publications:

• A Lerch, et al. Projecting vaccine demand and impact for emerging zoonotic pathogens. Under review, medRxiv. DOI: http://dx.doi:10.1101/2021.11.09.21266135.
• M Gruenberg, A Lerch et al. Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs. Scientific Reports. 2019; 9(1):17790. DOI: http://dx.doi:10.1038/s41598-019-54203-0.
• A Lerch et al. Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections. Scientific Reports. 2019; 9(1):3333. DOI: http://dx.doi:10.1038/s41598-019-39656-7.
• A Lerch et al. Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections. BMC Genomics. 2017; 18(1):864. DOI: http://dx.doi:10.1186/s12864-017-4260-y.
• D Gaidatzis, A Lerch et al. QuasR: quantification and annotation of short reads in R. Bioinformatics. 2015; 31(7):1130. DOI: http://dx.doi:10.1093/bioinformatics/btu781.

Co-author publications:

• JH Huber, MS Hsiang, N Dlamini, M Murphy, S Vilakati, N Nhlabathi, A Lerch, R Nielsen, N Ntshalintshali, B Greenhouse, TA Perkins. Inferring person-to-person networks of Plasmodium falciparum transmission: are analyses of routine surveillance data up to the task? Malar J. 2022; 21:58. DOI: http://dx.doi:10.1186/s12936-022-04072-2.
• G España, SM Cavany, RJ Oidtman, C Barbera, A Costello, A Lerch, M Poterek, Quan Tran, Annaliese Wieler, SM Moore, TA Perkins. Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA. Epidemics. 2021; 37:100487. DOI: http://dx.doi:10.1016/j.epidem.2021.100487.
• GM Bron, K Strimbu, H Cecilia, A Lerch, SM Moore, Q Tran, TA Perkins,Quirine A. ten Bosch. Over 100 years of Rift Valley Fever: a patchwork of data on pathogen spread and spillover. Pathogens. 2021; 10(6):708. DOI: http://dx.doi:10.3390/pathogens10060708.
• S Jones, K Kay, EM Hodel, M Gruenberg, A Lerch, I Felger, I Hastings. Should Deep-Sequenced Amplicons Become the New Gold Standard for Analyzing Malaria Drug Clinical Trials? Antimicrobial Agents and Chemotherapy. 2021; 65(10). DOI: 10.1128/aac.00437-21.
• TA Perkins, SM Cavany, SM Moore, RJ Oidtman, A Lerch, M Poterek. Estimating unobserved SARS-CoV-2 infections in the United States. PNAS. 2020; 117(36):22597. DOI: http://dx.doi:10.1073/pnas.2005476117.
• 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: http://dx.doi:10.1016/j.ijpara.2019.02.007.
• S Wormald, A Lerch, D Mouradov, L O’Connor. Somatic mutation footprinting reveals a unique tetranucleotide signature associated with intron-exon boundaries in lung cancer. Carcinogenesis. 2018; 39:225. DOI: http://dx.doi:10.1093/carcin/bgx133.
• D Gaidatzis, L Burger, R Murr, A Lerch, S Dessus-Babus, D Schübeler, MB Stadler. DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes. PLoS Genetics, 2014; 10(2):e1004143. DOI: http://dx.doi:10.1371/journal.pgen.1004143.
• P Paysan, M Lüthi, T Albrecht, A Lerch, B Amberg, F Santini, T Vetter. Face reconstruction from skull shapes and physical attributes. Pattern Recognition. DAGM 2009. (DAGM Award). DOI: http://dx.doi:10.1007/978-3-642-03798-6_24.
• M Lüthi, A Lerch, T Albrecht, Z Krol, T Vetter. A hierarchical, multi-resolution approach for model-based skull-segmentation in MRI. Conference Proceedings 3D-Physiological Human, Zermatt Switzerland, December, 2008.
• FS Dietrich, S Voegeli, S Brachat, A Lerch, K Gates, S Steiner, C Mohr, R Pohlmann, …, P Philippsen. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 2004; 304(5668):304. DOI: http://dx.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: http://dx.doi:10.1186/gb-2003-4-7-r45.