Publications of Alexander Herbig

Fellows Yates, J. A.; Velsko, I. M.; Aron, F.; Posth, C.; Hofman, C. A.; Austin, R. M.; Parker, C. E.; Mann, A. E.; Nägele, K.; Arthur, K. W. et al.; Arthur, J. W.; Bauer, C. C.; Crevecoeur, I.; Cupillard, C.; Curtis, M. C.; Dalén, L.; Díaz-Zorita Bonilla, M.; Fernández-Lomana, D.; Carlos, J.; Drucker, D. G.; Escribano Escrivá, E.; Francken, M.; Gibbon, V. E.; Morales, G.; R., M.; Grande Mateu, A.; Harvati, K.; Henry, A. G.; Humphrey, L.; Menéndez, M.; Mihailović, D.; Peresani, M.; Rodríguez Moroder, S.; Roksandic, M.; Rougier, H.; Sázelová, S.; Stock, J. T.; Straus, L. G.; Svoboda, J.; Teßmann, B.; Walker, M. J.; Power, R. C.; Lewis, C. M.; Sankaranarayanan, K.; Guschanski, K.; Wrangham, R. W.; Dewhirst, F. E.; Salazar-García, D. C.; Krause, J.; Herbig, A.; Warinner, C.: The evolution and changing ecology of the African hominid oral microbiome. Proceedings of the National Academy of Sciences of the United States of America 118 (20), e2021655118, pp. 1 - 11 (2021)

Furtwängler, A.; Neukamm, J.; Böhme, L.; Reiter, E.; Vollstedt, M.; Arora, N.; Singh, P.; Cole, S. T.; Knauf, S.; Calvignac-Spencer, S. et al.; Krause-Kyora, B.; Krause, J.; Schuenemann, V. J.; Herbig, A.: Comparison of target enrichment strategies for ancient pathogen DNA. Biotechniques 69 (6), pp. 455 - 459 (2020)

Neukamm, J.; Pfrengle, S.; Molak, M.; Seitz, A.; Francken, M.; Eppenberger, P.; Avanzi, C.; Reiter, E.; Urban, C.; Welte, B. et al.; Stockhammer, P. W.; Teßmann, B.; Herbig, A.; Harvati, K.; Nieselt, K.; Krause, J.; Schuenemann, V. J.: 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biology 18 (1), 108 (2020)

Giffin, K.; Lankapalli, A. K.; Sabin, S.; Spyrou, M. A.; Posth, C.; Kozakaitė, J.; Friedrich, R.; Miliauskienė, Ž.; Jankauskas, R.; Herbig, A. et al.; Bos, K. I.: A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe. Scientific Reports 10 (1), 9499 (2020)

Barquera, R.; Lamnidis, T. C.; Lankapalli, A. K.; Kocher, A.; Hernández-Zaragoza, D. I.; Nelson, E. A.; Zamora-Herrera, A. C.; Perez Ramallo, P.; Bernal-Felipe, N.; Immel, A. et al.; Bos, K.; Acuña-Alonzo, V.; Barbieri, C.; Roberts, P.; Herbig, A.; Kühnert, D.; Márquez-Morfín, L.; Krause, J.: Origin and health status of first-generation Africans from early colonial Mexico. Current Biology 30 (11), 2020.04.002, pp. 2078 - 2091.e11 (2020)

Borry, M.; Cordova, B.; Perri, A.; Wibowo, M.; Honap, T. P.; Ko, J.; Yu, J.; Britton, K.; Girdland-Flink, L.; Power, R. C. et al.; Stuijts, I.; Salazar-García, D. C.; Hofman, C.; Hagan, R.; Kagoné, T. S.; Meda, N.; Carabin, H.; Jacobson, D.; Reinhard, K.; Lewis, C.; Kostic, A.; Jeong, C.; Herbig, A.; Hübner, A.; Warinner, C.: CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ, 8:e9001 (2020)

Key, F. M.; Posth, C.; Esquivel Gomez, L. R.; Hübler, R.; Spyrou, M. A.; Neumann, G. U.; Furtwängler, A.; Sabin, S.; Burri Promerová, M.; Wissgott, A. et al.; Lankapalli, A. K.; Vågene, Å. J.; Meyer, M.; Nagel, S.; Tukhbatova, R.; Khokhlov, A.; Chizhevsky, A.; Hansen, S.; Belinsky, A. B.; Kalmykov, A.; Kantorovich, A. R.; Maslov, V. E.; Stockhammer, P. W.; Vai, S.; Zavattaro, M.; Riga, A.; Caramelli, D.; Skeates, R.; Beckett, J.; Gradoli, M. G.; Steuri, N.; Hafner, A.; Ramstein, M.; Siebke, I.; Lösch, S.; Erdal, Y. S.; Alikhan, N.-F.; Zhou, Z.; Achtman, M.; Bos, K.; Reinhold, S.; Haak, W.; Kühnert, D.; Herbig, A.; Krause, J.: Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nature Ecology & Evolution 4 (3), pp. 324 - 333 (2020)

Nelson, E. A.; Buikstra, J. E.; Herbig, A.; Tung, T. A.; Bos, K. I.: Advances in the molecular detection of tuberculosis in pre-contact Andean South America. International Journey of Paleopathology, 2019.12.006 (2020)

Hübler, R.; Key, F. M.; Warinner, C. G.; Bos, K. I.; Krause, J.; Herbig, A.: HOPS: Automated detection and authentication of pathogen DNA in archaeological remains. Genome Biology 20 (n/a), 280 (2019) (2019)

Spyrou, M. A.; Keller, M.; Tukhbatova, R. I.; Scheib, C. L.; Nelson, E. A.; Andrades Valtueña, A.; Neumann, G.; Walker, D.; Alterauge, A.; Carty, N. et al.; Cessford, C.; Fetz, H.; Gourvennec, M.; Hartle, R.; Henderson, M.; von Heyking, K.; Inskip, S. A.; Kacki, S.; Key, F. M.; Knox, E. L.; Later, C.; Maheshwari-Aplin, P.; Peters, J.; Robb, J. E.; Schreiber, J.; Kivisild, T.; Castex, D.; Lösch, S.; Harbeck, M.; Herbig, A.; Bos, K. I.; Krause, J.: Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes. Nature Communications 10 (1), 4470 (2019)

Bos, K. I.; Kühnert, D.; Herbig, A.; Esquivel Gomez, L. R.; Andrades Valtueña, A.; Barquera Lozano, R. J.; Giffin, K.; Lankapalli, A. K.; Nelson, E. A.; Sabin, S. et al.; Spyrou, M. A.; Krause, J.: Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annual Review of Microbiology 73 (1), pp. 639 - 666 (2019)

Keller, M.; Spyrou, M. A.; Scheib, C. L.; Neumann, G.; Kröpelin, A.; Haas-Gebhard, B.; Päffgen, B.; Haberstroh, J.; Lacomba, A. R.; Raynaud, C. et al.; Cessford, C.; Durand, R.; Stadler, P.; Nägele, K.; Bates, J. S.; Trautmann, B.; Inskip, S. A.; Peters, J.; Robb, J. E.; Kivisild, T.; Castex, D.; McCormick, M.; Bos, K. I.; Harbeck, M.; Herbig, A.; Krause, J.: Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750). Proceedings of the National Academy of Sciences of the United States of America 116 (25), pp. 12363 - 12372 (2019)

Sabin, S.; Herbig, A.; Vagene, A. J.; Ahlström, T.; Bozovic, G.; Arcini, C.; Kuehnert, D.; Bos, K. I.: A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biology: Biology for the Post-Genomic Era 21, 201 (2020) (2019)

Spyrou, M. A.; Bos, K. I.; Herbig, A.; Krause, J.: Ancient pathogen genomics as an emerging tool for infectious disease research. Nature Reviews Genetics 20, pp. 323 - 340 (2019)

Velsko, I. M.; Frantz, L. A. F.; Herbig, A.; Larson, G.; Warinner, C.: Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research. mSystems 3 (4), e00080-18 (2018)

Schuenemann, V. J.; Lankapalli, A. K.; Barquera, R.; Nelson, E. A.; Iraíz Hernández, D.; Acuña Alonzo, V.; Bos, K. I.; Márquez Morfín, L.; Herbig, A.; Krause, J.: Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains. PLOS Neglected Tropical Diseases 12 (6), e0006447 (2018)

Spyrou, M. A.; Tukhbatova, R. I.; Wang, C.-C.; Andrades Valtueña, A.; Lankapalli, A. K.; Kondrashin, V. V.; Tsybin, V. A.; Khokhlov, A.; Kühnert, D.; Herbig, A. et al.; Bos, K. I.; Krause, J.: Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague. Nature Communications 9, 2234 (2018)

Schuenemann, V. J.; Avanzi, C.; Krause-Kyora, B.; Seitz, A.; Herbig, A.; Inskip, S.; Bonazzi, M.; Reiter, E.; Urban, C.; Dangvard Pedersen, D. et al.; Taylor, G. M.; Singh, P.; Stewart, G. R.; Velemínský, P.; Likovsky, J.; Marcsik, A.; Molnár, E.; Pálfi, G.; Mariotti, V.; Riga, A.; Belcastro, M. G.; Boldsen, J. L.; Nebel, A.; Mays, S.; Donoghue, H. D.; Zakrzewski, S.; Benjak, A.; Nieselt, K.; Cole, S. T.; Krause, J.: Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe. PLoS Pathogens 14 (5), pp. 1 - 17 (2018)

Krause-Kyora, B.; Susat, J.; Key, F. M.; Kühnert, D.; Bosse, E.; Immel, A.; Rinne, C.; Kornell, S.-C.; Yepes, D.; Franzenburg, S. et al.; Heyne, H. O.; Meier, T.; Lösch, S.; Meller, H.; Friederich, S.; Nicklisch, N.; Alt, K. W.; Schreiber, S.; Tholey, A.; Herbig, A.; Nebel, A.; Krause, J.: Neolithic and medieval virus genomes reveal complex evolution of Hepatitis B. eLife 7, e36666 (2018)

Vågene, Å. J.; Herbig, A.; Campana, M. G.; García, R.; M., N.; Warinner, C.; Sabin, S.; Spyrou, M. A.; Andrades Valtueña, A.; Huson, D. et al.; Tuross, N.; Bos, K. I.; Krause, J.: Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution 2 (3), pp. 520 - 528 (2018)