Thomas Sicheritz-Pontén

Thomas Sicheritz-Pontén

Professor

ORCID: 0000-0001-6615-1141

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  1. Published

    A draft genome sequence of the elusive giant squid, Architeuthis dux

    da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, Â. M., Barrio-Hernandez, I., Hoving, H-J., Tafur-Jimenez, R., Chu, C., Frazão, B., Petersen, B., Peñaloza, F., Musacchia, F., Alexander, G. C. & 24 others, Osório, H., Winkelmann, I., Simakov, O., Rasmussen, Simon, Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., KU, thw266, Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Pontén, Thomas, Nielsen, Rasmus & Gilbert, M Thomas P, 2020, In: GigaScience. 9, 1, 12 p., giz152.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection

    Marcatili, P., Nielsen, M. W., Sicheritz-Pontén, Thomas, Jensen, Tim Kåre, Schafer-Nielsen, C., Boye, M., Nielsen, M. & Schou, K. K., 2016, In: BMC Genomics. 17, 13 p., 987.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria

    Haines, M. E. K., Hodges, F. E., Nale, J. Y., Mahony, J., van Sinderen, D., Kaczorowska, J., Alrashid, B., Akter, M., Brown, N., Sauvageau, D., Sicheritz-Pontén, Thomas, Thanki, A. M., Millard, A. D., Galyov, E. E. & Clokie, M. R. J., 2021, In: Frontiers in Microbiology. 12, 15 p., 613529.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Ancient proteins resolve controversy over the identity of Genyornis eggshell

    Demarchi, B., Stiller, Josefin, Grealy, A., Mackie, Meaghan, Deng, Y., Gilbert, M Thomas P, Clarke, J., Legendre, L. J., Boano, R., Sicheritz-Pontén, Thomas, Magee, J., KU, thw266, Bunce, M., Collins, Matthew James & Miller, G., 2022, In: PNAS. 119, 43, 9 p., e2109326119.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Arctic-adapted dogs emerged at the Pleistocene-Holocene transition

    Sinding, M. H. S., Gopalakrishnan, S., Ramos-Madrigal, J., de Manuel, M., Pitulko, V. V., Kuderna, L., Feuerborn, T. R., Frantz, L. A. F., Vieira, F. G., Niemann, J., Samaniego Castruita, J. A., Carøe, C., Andersen-Ranberg, E. U., Jordan, P. D., Pavlova, E. Y., Nikolskiy, P. A., Kasparov, A. K., Ivanova, V. V., Willerslev, E., Skoglund, P. & 15 others, Fredholm, Merete, Wennerberg, S. E., Heide-Jørgensen, M. P., Dietz, R., Sonne, C., Meldgaard, Morten, Dalén, L., Larson, G., Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, L., Wiig, Ø., Marques-Bonet, T., Hansen, Anders Johannes & Gilbert, M Thomas P, 2020, In: Science (New York, N.Y.). 368, 6498, p. 1495-1499 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Complete Genome Sequence of Salmonella enterica Bacteriophage PRF-SP1

    Mutusamy, P., Jothi, S. J., Lee, S. Y., Petersen, Bent, Sicheritz-Pontén, Thomas, Clokie, M. R. J., Loke, S., Millard, A., Parimannan, Sivachandran & Rajandas, Heera, 2021, In: Microbiology resource announcements. 10, 47, 3 p., e00965-21.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    Complete genome sequence of plant growth-promoting Bacillus stratosphericus AIMST-CREST02 isolated from bulk soil of a paddy field

    Sivaprakasam, S., Khan, N. A. M. A., Fan, T. Y., Kumarasan, Y., Sicheritz-Pontén, Thomas, Petersen, Bent, Hata, E. M., Vadamalai, G., Parimannan, Sivachandran & Rajandas, Heera, 2024, In: Microbiology resource announcements. 13, 4, 3 p., e0113723.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae)

    Haddad, N. J., Al-Nakeeb, K. A. A., Petersen, Bent, Dalén, L., Blom, N. & Sicheritz-Pontén, Thomas, 2017, In: Mitochondrial DNA Part B: Resources. 2, 1, p. 139-140 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

    Asplund, M., Kjartansdóttir, K. R., Mollerup, S., Vinner, L., Fridholm, H., Herrera, J. A. R., Friis-Nielsen, J., Hansen, T. A., Jensen, R. H., Nielsen, I. B., Richter, S. R., Rey-Iglesia, A., Matey-Hernandez, M. L., Alquezar-Planas, D. E., Olsen, P. V. S., Sicheritz-Pontén, T., Willerslev, E., Lund, O., Brunak, S., Mourier, T. & 3 others, Nielsen, L. P., Izarzugaza, J. M. G. & Hansen, Anders Johannes, 2019, In: Clinical Microbiology and Infection. 25, 10, p. 1277-1285

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    Dense sampling of bird diversity increases power of comparative genomics

    Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Hart Reeve, A., Xie, D., Chen, G., Guo, C., Faircloth, B. C., Petersen, B., Wang, Z., Zhou, Q., Diekhans, M., Chen, W., Andreu-Sánchez, S., Margaryan, A., Howard, J. T., Parent, C., Pacheco, G. & 130 others, Sinding, Mikkel Holger Strander, Puetz, Lara Christine, Cavill, Emily Louisa, Ribeiro, Â. M., Eckhart, L., Fjeldså, Jon, Hosner, Peter Andrew, Brumfield, R. T., Christidis, L., Bertelsen, Mads Frost, Sicheritz-Pontén, Thomas, Tietze, D. T., Robertson, B. C., Song, G., Borgia, G., Claramunt, S., Lovette, I. J., Cowen, S. J., Njoroge, P., Dumbacher, J. P., Ryder, O. A., Fuchs, J., Bunce, M., Burt, D. W., Cracraft, J., Meng, G., Hackett, S. J., Ryan, P. G., Jønsson, Knud Andreas, Jamieson, I. G., Rodrigues da Fonseca, Rute Andreia, Braun, E. L., Houde, P., Mirarab, S., Suh, A., Hansson, B., Ponnikas, S., Sigeman, H., Stervander, M., Frandsen, P. B., van der Zwan, H., van der Sluis, R., Visser, C., Balakrishnan, C. N., Clark, A. G., Fitzpatrick, J. W., Bowman, R., Chen, N., Cloutier, A., Sackton, T. B., Edwards, S. V., Foote, D. J., Shakya, S. B., Sheldon, F. H., Vignal, A., Soares, A. E. R., Shapiro, B., González-Solís, J., Ferrer-Obiol, J., Rozas, J., Riutort, M., Tigano, A., Friesen, V., Dalén, L., Urrutia, A. O., Székely, T., Liu, Y., Campana, M. G., Corvelo, A., Fleischer, R. C., Rutherford, K. M., Gemmell, N. J., Dussex, N., Mouritsen, H., Thiele, N., Delmore, K., Liedvogel, M., Franke, A., Hoeppner, M. P., Krone, O., Fudickar, A. M., Milá, B., Ketterson, E. D., Fidler, A. E., Friis, G., Parody-Merino, Á. M., Battley, P. F., Cox, M. P., Lima, N. C. B., Prosdocimi, F., Parchman, T. L., Schlinger, B. A., Loiselle, B. A., Blake, J. G., Lim, H. C., Day, L. B., Fuxjager, M. J., Baldwin, M. W., Braun, M. J., Wirthlin, M., Dikow, R. B., Ryder, T. B., Camenisch, G., Keller, L. F., Dacosta, J. M., Hauber, M. E., Louder, M. I. M., Witt, C. C., McGuire, J. A., Mudge, J., Megna, L. C., Carling, M. D., Wang, B., Taylor, S. A., Del-Rio, G., Aleixo, A., Vasconcelos, A. T. R., Mello, C. V., Weir, J. T., Haussler, D., Li, Q., Yang, H., Wang, J., Lei, F., Rahbek, Carsten, Gilbert, M Thomas P, Graves, G. R., Jarvis, E. D., Paten, B. & KU, thw266, 2020, In: Nature. 587, 7833, p. 252-257

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Development of a Phage Cocktail to Target Salmonella Strains Associated with Swine

    Thanki, A. M., Clavijo, V., Healy, K., Wilkinson, R. C., Sicheritz-Pontén, Thomas, Millard, A. D. & Clokie, M. R. J., 2022, In: Pharmaceuticals. 15, 1, 19 p., 58.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    Distinct life histories impact dikaryotic genome evolution in the rust fungus Puccinia striiformis causing stripe rust in wheat

    Chen, Yan-Jun, Schwessinger, B., Tien, R., Vogt, J. K., Sperschneider, J., Nagar, R., McMullan, M., Sicheritz-Pontén, Thomas, Sørensen, C. K., Hovmøller, M. S., Rathjen, J. P. & Justesen, A. F., 2020, In: Genome Biology and Evolution. 12, 5, p. 597-617

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity

    Andrews, K., Landeryou, T., Sicheritz-Pontén, Thomas & Nale, J. Y., 2024, In: Cells. 13, 6, 17 p., 514.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages

    Nale, J. Y., Thanki, A. M., Rashid, S. J., Shan, J., Vinner, G. K., Dowah, A. S. A., Cheng, J. K. J., Sicheritz-Pontén, Thomas & Clokie, M. R. J., 2022, In: Viruses. 14, 12, 21 p., 2772.

    Research output: Contribution to journal › Review › Research › peer-review

  15. Published

    Evolutionary history of the extinct Sardinian dhole

    Ciucani, M. M., Jensen, J. K., Sinding, M. S., Smith, O., Lucenti, S. B., Rosengren, E., Rook, L., Tuveri, C., Arca, M., Cappellini, Enrico, Galaverni, M., Randi, E., Guo, C., KU, thw266, Sicheritz-Pontén, Thomas, Dalén, L., Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2021, In: Current Biology. 31, 24, p. 5571-5579.e6 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs

    Rangel Piñeros, Guillermo Andres, Millard, A., Michniewski, S., Scanlan, D., Sirén, K., Reyes, A., Petersen, Bent, Clokie, M. R. J. & Sicheritz-Pontén, Thomas, 2021, In: PHAGE: Therapy, Applications, and Research. 2, 4, p. 194-203

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Genome sequence of Talaromyces atroroseus, which produces red colorants for the food industry

    Thrane, U., Rasmussen, K. B., Petersen, Bent, Rasmussen, Simon, Sicheritz-Pontén, Thomas & Mortensen, U. H., 2017, In: Genome Announcements. 5, 9, 2 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages

    Ramos-Madrigal, J., Sinding, M-H. S., Carøe, C., Mak, S. S. T., Niemann, J., Samaniego Castruita, J. A., Fedorov, S., Kandyba, A., Germonpré, M., Bocherens, H., Feuerborn, T. R., Pitulko, V. V., Pavlova, E. Y., Nikolskiy, P. A., Kasparov, A. K., Ivanova, V. V., Larson, G., Frantz, L. A. F., Willerslev, E., Meldgaard, M. & 7 others, Petersen, Bent, Sicheritz-Pontén, Thomas, Bachmann, L., Wiig, Ø., Hansen, Anders Johannes, Gilbert, M Thomas P & Gopalakrishnan, Shyam, 2020, In: Current biology : CB. 31, p. 198-206

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

    Hendriksen, R. S., Munk, P., Njage, P., van Bunnik, B., McNally, L., Lukjancenko, O., Röder, T., Nieuwenhuijse, D., Pedersen, S. K., Kjeldgaard, J., Kaas, R. S., Clausen, P. T. L. C., Vogt, J. K., Leekitcharoenphon, P., van de Schans, M. G. M., Zuidema, T., de Roda Husman, A. M., Rasmussen, S., Petersen, B., Bego, A. & 108 others, Rees, C., Cassar, S., Coventry, K., Collignon, P., Allerberger, F., Rahube, T. O., Oliveira, G., Ivanov, I., Vuthy, Y., Sopheak, T., Yost, C. K., Ke, C., Zheng, H., Baisheng, L., Jiao, X., Donado-Godoy, P., Coulibaly, K. J., Jergović, M., Hrenovic, J., Karpíšková, R., Villacis, J. E., Legesse, M., Eguale, T., Heikinheimo, A., Malania, L., Nitsche, A., Brinkmann, A., Saba, C. K. S., Kocsis, B., Solymosi, N., Thorsteinsdottir, T. R., Hatha, A. M., Alebouyeh, M., Morris, D., Cormican, M., O’Connor, L., Moran-Gilad, J., Alba, P., Battisti, A., Shakenova, Z., Kiiyukia, C., Ng’eno, E., Raka, L., Avsejenko, J., Bērziņš, A., Bartkevics, V., Penny, C., Rajandas, H., Parimannan, S., Haber, M. V., Pal, P., Jeunen, G. J., Gemmell, N., Fashae, K., Holmstad, R., Hasan, R., Shakoor, S., Rojas, M. L. Z., Wasyl, D., Bosevska, G., Kochubovski, M., Radu, C., Gassama, A., Radosavljevic, V., Wuertz, S., Zuniga-Montanez, R., Tay, M. Y. F., Gavačová, D., Pastuchova, K., Truska, P., Trkov, M., Esterhuyse, K., Keddy, K., Cerdà-Cuéllar, M., Pathirage, S., Norrgren, L., Örn, S., Larsson, D. G. J., Heijden, T. V. D., Kumburu, H. H., Sanneh, B., Bidjada, P., Njanpop-Lafourcade, B. M., Nikiema-Pessinaba, S. C., Levent, B., Meschke, J. S., Beck, N. K., Van, C. D., Phuc, N. D., Tran, D. M. N., Kwenda, G., Tabo, D. A., Wester, A. L., Cuadros-Orellana, S., Amid, C., Cochrane, G., Sicheritz-Pontén, Thomas, Schmitt, H., Alvarez, J. R. M., Aidara-Kane, A., Pamp, S. J., Lund, O., Hald, T., Woolhouse, M., Koopmans, M. P., Vigre, H., Petersen, T. N. & Aarestrup, F. M., 2019, In: Nature Communications. 10, 1, 12 p., 1124.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

    Mollerup, S., Asplund, M., Friis-Nielsen, J., Kjartansdóttir, K. R., Fridholm, H., Hansen, T. A., Herrera, J. A. R., Barnes, C. J., Jensen, R. H., Richter, S. R., Nielsen, I. B., Pietroni, C., Alquezar-Planas, D. E., Rey-Iglesia, A., Olsen, P. V. S., Rajpert-De Meyts, E., Groth-Pedersen, L., von Buchwald, C., Jensen, D. H., Gniadecki, R. & 20 others, Høgdall, Estrid Vilma Solyom, Langhoff, J. L., Pete, I., Vereczkey, I., Baranyai, Z., Dybkaer, K., Johnsen, H. E., Steiniche, T., Hokland, P., Rosenberg, Jacob, Baandrup, U., Sicheritz-Pontén, Thomas, Willerslev, Eske, Brunak, Søren, Lund, O., Mourier, T., Vinner, Lasse, Izarzugaza, J. M. G., Nielsen, L. P. & Hansen, Anders Johannes, 15 Oct 2019, In: The Journal of Infectious Diseases. 220, 8, p. 1312-1324

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros

    Sánchez-Barreiro, F., Westbury, Binia De Cahsan, Westbury, Michael Vincent, Sun, Xin, Margaryan, Ashot, Fontsere, Claudia, Bruford, M. W., Russo, I. M., Kalthoff, D. C., Sicheritz-Pontén, Thomas, Petersen, Bent, Dalén, L., KU, thw266, Marquès-Bonet, T., Gilbert, M Thomas P & Moodley, Y., 2023, In: Molecular Biology and Evolution. 40, 9, 19 p., msad180.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

    Sánchez-Barreiro, F., Gopalakrishnan, Shyam, Ramos Madrigal, Jazmin, Westbury, Michael Vincent, de Manuel, M., Margaryan, Ashot, Ciucani, M. M., Vieira, Filipe Garrett, Patramanis, Ioannis, Kalthoff, D. C., Timmons, Z., Sicheritz-Pontén, Thomas, Dalén, L., Ryder, O. A., KU, thw266, Marques-Bonet, T., Moodley, Y. & Gilbert, M Thomas P, 2021, In: Molecular Ecology. 30, 23, p. 6355-6369 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Identification of common bacterial antigenic markers from bovine digital dermatitis lesions using meta-transcriptomics in combination with high-density peptide-microarrays

    Nielsen, M. W., Marcatili, P., Sicheritz-Pontén, Thomas, Jensen, Tim Kåre, Schafer-Nielsen, C., Boye, M., Nielsen, M. & Schou, K. K., 2016.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  24. Published

    InPhocus: Current State and Challenges of Phage Research in Singapore

    Verma, N. K., Tan, S. J., Chen, J., Chen, H., Ismail, M. H., Rice, S. A., Bifani, P., Hariharan, S., Paul, V. D., Sriram, B., Dam, L. C., Chan, C. C., Ho, P., Goh, B. C., Chung, S. J., Goh, K. C. M., Thong, S. H., Kwa, A. L. H., Ostrowski, A., Aung, T. T. & 9 others, Razali, H., Low, S. W. Y., Bhattacharyya, M. S., Gautam, H. K., Lakshminarayanan, R., Sicheritz-Pontén, Thomas, Clokie, M. R. J., Moreira, W. & Van Steensel, M. A. M., 2022, In: PHAGE: Therapy, Applications, and Research. 3, 1, p. 6-11 6 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos

    Sinding, M. S., Ciucani, M. M., Ramos Madrigal, Jazmin, Carmagnini, A., Rasmussen, Jacob Agerbo, Feng, S., Chen, G., Vieira, Filipe Garrett, Mattiangeli, V., Ganjoo, R. K., Larson, G., Sicheritz-Pontén, Thomas, Petersen, Bent, Frantz, L., Gilbert, M Thomas P & Bradley, D. G., 2021, In: iScience. 24, 11, 18 p., 103226.

    Research output: Contribution to journal › Journal article › Research › peer-review

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ID: 202359275