Andrew Tritt

Data Engineer

Computational Research Division

Phone: 608-438-0386

Biographical Sketch

Andrew is a data engineer in the Performance and Algorithms Research group. He earned his degree in genetics from the University of Wisconsin, Madison. Since completion of his degree, Andrew has been working at the interface of computing and biology. Prior to joining the Computational Research Division, he worked on data and computational problems arising in the processing and analysis of next generation DNA sequencing data. His current interests involve machine learning and high performance computing solutions for analysis of scientific data.

Journal Articles

M Peter, A Kohler, RA Ohm, A Kuo, J Krützmann, E Morin, M Arend, KW Barry, M Binder, C Choi, A Clum, A Copeland, N Grisel, S Haridas, T Kipfer, K Labutti, E Lindquist, A Lipzen, R Maire, B Meier, S Mihaltcheva, V Molinier, C Murat, S Pöggeler, CA Quandt, C Sperisen, A Tritt, E Tisserant, PW Crous, B Henrissat, U Nehls, S Egli, JW Spatafora, IV Grigoriev, FM Martin, "Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum", Nature Communications, 2016, 7, doi: 10.1038/ncomms12662

LG Nagy, R Riley, A Tritt, C Adam, C Daum, D Floudas, H Sun, JS Yadav, J Pangilinan, KH Larsson, K Matsuura, K Barry, K Labutti, R Kuo, RA Ohm, SS Bhattacharya, T Shirouzu, Y Yoshinaga, FM Martin, IV Grigoriev, DS Hibbett, "Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities", Molecular Biology and Evolution, 2016, 33:959--970, doi: 10.1093/molbev/msv337

A Kohler, A Kuo, LG Nagy, E Morin, KW Barry, F Buscot, B Canbäck, C Choi, N Cichocki, A Clum, J Colpaert, A Copeland, MD Costa, J Doré, D Floudas, G Gay, M Girlanda, B Henrissat, S Herrmann, J Hess, N Högberg, T Johansson, HR Khouja, K Labutti, U Lahrmann, A Levasseur, EA Lindquist, A Lipzen, R Marmeisse, E Martino, C Murat, CY Ngan, U Nehls, JM Plett, A Pringle, RA Ohm, S Perotto, M Peter, R Riley, F Rineau, J Ruytinx, A Salamov, F Shah, H Sun, M Tarkka, A Tritt, C Veneault-Fourrey, A Zuccaro, A Tunlid, IV Grigoriev, DS Hibbett, F Martin, "Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists", Nature Genetics, 2015, 47:410--415, doi: 10.1038/ng.3223

D Floudas, BW Held, R Riley, LG Nagy, G Koehler, AS Ransdell, H Younus, J Chow, J Chiniquy, A Lipzen, A Tritt, H Sun, S Haridas, K LaButti, RA Ohm, U Kües, RA Blanchette, IV Grigoriev, RE Minto, DS Hibbett, "Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii", Fungal Genetics and Biology, 2015, 76:78--92, doi: 10.1016/j.fgb.2015.02.002

H Muraguchi, K Umezawa, M Niikura, M Yoshida, T Kozaki, K Ishii, K Sakai, M Shimizu, K Nakahori, Y Sakamoto, C Choi, CY Ngan, E Lindquist, A Lipzen, A Tritt, S Haridas, K Barry, IV Grigoriev, PJ Pukkila, "Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea", PLoS ONE, 2015, 10, doi: 10.1371/journal.pone.0141586

EA Becker, PM Seitzer, A Tritt, D Larsen, M Krusor, AI Yao, D Wu, D Madern, JA Eisen, AE Darling, MT Facciotti, "Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response", PLoS Genetics, 2014, 10, doi: 10.1371/journal.pgen.1004784

M Toome, A Kuo, B Henrissat, A Lipzen, A Tritt, Y Yoshinaga, M Zane, K Barry, IV Grigoriev, JW Spatafora, MC Aime, "Draft genome sequence of a rare smut relative, Tilletiaria anomala UBC 951", Genome Announcements, 2014, 2, doi: 10.1128/genomeA.00539-14

A Tritt, JA Eisen, MT Facciotti, AE Darling, "An Integrated Pipeline for de Novo Assembly of Microbial Genomes", PLoS ONE, 2012, 7, doi: 10.1371/journal.pone.0042304

AE Darling, A Tritt, JA Eisen, MT Facciotti, "Mauve assembly metrics", Bioinformatics, 2011, 27:2756--2757, doi: 10.1093/bioinformatics/btr451

YS Dufour, GE Wesenberg, AJ Tritt, JD Glasner, NT Perna, JC Mitchell, TJ Donohue, "chipD: a web tool to design oligonucleotide probes for high-density tiling arrays", Nucleic Acids Research, 2010, 38:W321--W325, doi: 10.1093/nar/gkq517

Reports

Oliver Rübel, Andrew Tritt, Benjamin Dichter, Thomas Braun, Nicholas Cain, Nathan Clack, Thomas J. Davidson, Max Dougherty, Jean-Christophe Fillion-Robin, Nile Graddis, Michael Grauer, Justin T. Kiggins, Lawrence Niu, Doruk Ozturk, William Schroeder, Ivan Soltesz, Friedrich T. Sommer, Karel Svoboda, Lydia Ng, Loren M. Frank, Kristofer Bouchard, "NWB:N 2.0: An Accessible Data Standard for Neurophysiology", bioRxiv, January 17, 2019, doi: https://doi.org/10.1101/523035