Computational and RNA Biology

Physiological and Genetic Adaptations to Diving in Sea Nomads

Ilardo, M. A., Moltke, Ida, Korneliussen, Thorfinn Sand, Cheng, J., Stern, A. J., Racimo, Fernando, Damgaard, P. D. B., Sikora, Martin, Seguin-Orlando, A., Rasmussen, Simon, van den Munckhof, I. C. L., ter Horst, R., Joosten, L. A. B., Netea, M. G., Salingkat, S., Nielsen, Rasmus & Willerslev, Eske, 2018, In: Cell. 173, 3, p. 569-580 12 p., e15.

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

Powerful Inference With the D-Statistic on Low-Coverage Whole-Genome Data

Soraggi, S., Wiuf, Carsten & Albrechtsen, Anders, 2018, In: G3: Genes, Genomes, Genetics (Bethesda). 8, 2, p. 551-566

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

RNA-Seq for Bacterial Gene Expression

Poulsen, L. D. & Vinther, Jeppe, 2018, In: Current Protocols in Nucleic Acid Chemistry. 73, 1, p. 1-12 e55.

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

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

Baillie, J. K., Bretherick, A., Haley, C. S., Clohisey, S., Gray, A., Neyton, L. P. A., Barrett, J., Stahl, E. A., Tenesa, A., Andersson, R., Brown, J. B., Faulkner, G. J., Lizio, M., Schaefer, U., Daub, C., Itoh, M., Kondo, N., Lassmann, T., Kawai, J., Mole, D. & 14 others, Bajic, V. B., Heutink, P., Rehli, M., Kawaji, H., Sandelin, Albin Gustav, Suzuki, H., Satsangi, J., Wells, C. A., Hacohen, N., Freeman, T. C., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & Hume, D. A., 2018, In: PLoS Computational Biology. 14, 3, 24 p., e1005934.

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

SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes

Sidiropoulos, N., Sohi, S. H., Pedersen, T. L., Porse, Bo Torben, Winther, Ole, Rapin, N. & Bagger, F. O., 2018, In: Journal of Computational and Graphical Statistics. 27, 3, p. 673-676 4 p.

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

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Moreno Mayar, J. Víctor, Potter, B. A., Vinner, Lasse, Steinrucken, M., Rasmussen, Simon, Terhorst, J., Kamm, J. A., Albrechtsen, Anders, Malaspinas, A., Sikora, Martin, Reuther, J. D., Irish, J. D., Malhi, R. S., Orlando, L. A. A., Song, Y. S., Nielsen, Rasmus, Meltzer, D. J. & Willerslev, Eske, 2018, In: Nature Genetics. 553, 7687, p. 203-207 5 p.

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

The Muskox Lost a Substantial Part of Its Genetic Diversity on Its Long Road to Greenland

Hansen, C. C. R., Hvilsom, C., Schmidt, N. M., Aastrup, P., de Groot, P. J. V. C., Siegismund, Hans Redlef & Heller, Rasmus, 2018, In: Current Biology. 28, 24, p. 4022-4028, e1-e5

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

The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer

Pastuzyn, E. D., Day, C. E., Kearns, R. B., Kyrke-Smith, M., Taibi, A. V., McCormick, J., Yoder, N., Belnap, D. M., qrc243, qrc243, Morado, D. R., Briggs, J. A. G., Feschotte, C. & Shepherd, J. D., 2018, In: Cell. 172, 1-2, p. 275-288, E18 33 p.

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

The RNA exosome contributes to gene expression regulation during stem cell differentiation

Llinares, M. L., Karadoulama, Evdoxia, Chen, Y., Wojenski, L. A., Villafano, G. J., Lange, Jette Bornholdt, Andersson, Robin, Core, L., Sandelin, Albin Gustav & Jensen, T. H., 2018, In: Nucleic Acids Research. 46, 21, p. 11502-11513

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

The genetic history of whaling in the Cantabrian Sea during the 13th-18th centuries: Were North Atlantic right whales (Eubalaena glacialis) the main target species?

Rey-Iglesia, A., Martinez-Cedeira, J., Lopez, A., Fernandez, R. & Campos, P., 2018, In: Journal of Archaeological Science: Reports. 18, p. 393-398 6 p.

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

Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

Rennie, Sarah, Dalby, M., Lloret-Llinares, M., Bakoulis, Stylianos, Dalager Vaagensø, C., Jensen, T. H. & Andersson, Robin, 2018, In: Nucleic Acids Research. 46, 11, p. 5455-5469 15 p.

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

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

Rennie, Sarah, Dalby, M., van Duin, Lucas & Andersson, Robin, 2018, In: Nature Communications. 9, 16 p., 487.

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

Transfer RNA instability as a stress response in Escherichia coli: rapid dynamics of the tRNA pool as a function of demand

Sørensen, Michael Askvad, Fehler, A. O. & Svenningsen, Sine Lo, 2018, In: RNA Biology. 15, 4/5, p. 586-593 8 p.

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

Genome sequence and effectorome of Moniliophthora perniciosa and Moniliophthora roreri subpopulations

Barbosa, C. S., Rodrigues da Fonseca, Rute Andreia, Batista, T. M., Barreto, M. A., Argolo, C. S., de Carvalho, M. R., Jordao do Amaral, D. O., de Andrade Silva, E. M., Arevalo-Gardini, E., Hidalgo, K. S., Franco, G. R., Pirovani, C. P., Micheli, F. & Gramacho, K. P., 3 Jul 2018, In: BMC Genomics. 19, 12 p., 509.

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

Identification of novel high-impact recessively inherited type 2 diabetes risk variants in the Greenlandic population

Grarup, Niels, Moltke, Ida, Lepola, Mette Andersen, Bjerregaard, P., Larsen, C. V. L., Dahl-Petersen, I. K., Jørsboe, E., Tiwari, H. K., Hopkins, S. E., Wiener, H. W., Boyer, B. B., Linneberg, Allan René, Pedersen, Oluf Borbye, Jørgensen, M. E., Albrechtsen, Anders & Hansen, Torben, 1 Sep 2018, In: Diabetologia. 61, 9, p. 2005–2015

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

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

Møller, H. D., Mohiyuddin, M., Prada Luengo, Inigo, Sailani, M. R., Halling, Jens Frey, Plomgaard, Peter Stendahl, Maretty, L., Hansen, Anders Johannes, Snyder, M. P., Pilegaard, Henriette, Lam, H. Y. K. & Regenberg, Birgitte, 1 Dec 2018, In: Nature Communications. 9, 12 p., 1069.

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

Cohort-wide deep whole genome sequencing and the allelic architecture of complex traits

Gilly, A., Suyeges, D., Kuchenbaecker, K., Pollard, M., Southam, L., Hatzikotoulas, K., Farmaki, A-E., Bjornland, T., Waples, R., Appel, E. V. R., Casalone, E., Melloni, G., Kilian, B., Rayner, N. W., Ntalla, I., Kundu, K., Walter, K., Danesh, J., Butterworth, A., Barroso, I. & 5 others, Tsafantakis, E., Dedoussis, G., Zeggini, E., Moltke, Ida & Zeggini, E., 1 Dec 2018, In: Nature Communications. 9, p. 1-9 4674.

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

A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2

Garland, W., Comet, I., Wu, M., Radzisheuskaya, A., Rib, Leonor, Vitting-Seerup, K., Lloret-Llinares, M., Sandelin, Albin Gustav, Helin, K. & Jensen, T. H., 2019, In: Cell Reports. 29, 7, p. 1800-1811 12 p.

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

A perspective on inverse design of battery interphases using multi-scale modelling, experiments and generative deep learning

Bhowmik, A., Castelli, I. E., Garcia-Lastra, J. M., Bjørn-Jørgensen, P., Winther, Ole & Vegge, T., 2019, In: Energy Storage Materials. 21, p. 446-456

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

Allele frequency-free inference of close familial relationships from genotypes or low-depth sequencing data

Waples, R. K., Albrechtsen, Anders & Moltke, Ida, 2019, In: Molecular Ecology. 28, 1, p. 35-48 14 p.

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

Ancestry-specific association mapping in admixed populations

Skotte, L., Jørsboe, E., Korneliussen, Thorfinn Sand, Moltke, Ida & Albrechtsen, Anders, 2019, In: Genetic Epidemiology. 43, 5, p. 506-521

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

Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus)

Lin, Z., Chen, L., Chen, X., Zhong, Y., Yang, Y., Xia, W., Liu, C., Zhu, W., Wang, H., Yan, B., Yang, Y., Liu, X., Kvie, K. S., Røed, K. H., Wang, K., Xiao, W., Wei, H., Li, G., Heller, R., Gilbert, M. T. P. & 3 others, Qiu, Q., Wang, W. & Li, Z., 2019, In: Science. 364, 6446, p. 1154-+ 7 p., eaav6312.

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

CAGEfightR: analysis of 5'-end data using R/Bioconductor

Thodberg, Malte, Thieffry, A., Vitting-Seerup, K., Andersson, Robin & Sandelin, Albin Gustav, 2019, In: BMC Bioinformatics. 20, 13 p., 487.

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

Catchment properties and the photosynthetic trait composition of freshwater plant communities

Iversen, L. L., Winkel, A., Baastrup-Spohr, L., Hinke, A. B., Alahuhta, J., Baattrup-Pedersen, A., Birk, S., Brodersen, P., Chambers, P. A., Ecke, F., Feldmann, T., Gebler, D., Heino, J., Jespersen, T. S., Moe, S. J., Riis, T., Sass, L., Vestergaard, O., Maberly, S. C., Sand-jensen, K. & 1 others, Pedersen, Ole, 2019, In: Science. 366, 6467, p. 878-881 4 p.

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

Complete Inactivation of Sebum-Producing Genes Parallels the Loss of Sebaceous Glands in Cetacea

Lopes-Marques, M., Machado, A. M., Alves, L. Q., Fonseca, M. M., Barbosa, S., Sinding, M. S., Rasmussen, M. H., Iversen, M. R., Bertelsen, Mads Frost, Campos, P. F., Rodrigues da Fonseca, Rute Andreia, Ruivo, R. & Castro, L. F. C., 2019, In: MOLECULAR BIOLOGY AND EVOLUTION . 36, 6, p. 1270-1280

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

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

Shah, S. A., Alkhnbashi, O. S., Behler, J., Han, W., She, Q., Hess, W. R., Garrett, Roger Antony & Backofen, R., 2019, In: RNA Biology. 16, 4, p. 530-542 13 p.

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

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

Abildgaard, A. B., Stein, Amelie, Nielsen, S. V., Schultz-Knudsen, Katrine, Papaleo, E., Shrikhande, A., Hoffmann, Eva, Bernstein, I., Gerdes, Anne-Marie Axø, Takahashi, M., Ishioka, C., Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2019, In: eLife. 8, 28 p., e49138 .

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

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

Rodrigues da Fonseca, Rute Andreia, Urena, I., Afonso, S., Pires, A. E., Jørsboe, E., Chikhi, L. & Ginja, C., 2019, In: BMC Genomics. 20, p. 1-13 334.

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

DamMet: ancient methylome mapping accounting for errors, true variants, and post-mortem DNA damage

Hanghøj, Kristian Ebbesen, Renaud, Gabriel, Albrechtsen, Anders & Orlando, L., 2019, In: GigaScience. 8, 4, 6 p., giz025.

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

Deconvolution of autoencoders to learn biological regulatory modules from single cell mRNA sequencing data

Kinalis, S., Nielsen, Finn Cilius, Winther, Ole & Bagger, F. O., 2019, In: BMC Bioinformatics. 20, 9 p., 379.

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

Detecting sequence signals in targeting peptides using deep learning

Almagro Armenteros, J. J., Salvatore, Marco, Emanuelsson, O., Winther, Ole, von Heijne, G., Elofsson, A. & Nielsen, H., 2019, In: Life Science Alliance. 2, 5, 14 p., 201900429.

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

Detection of internal N7-methylguanosine (m⁷G) RNA modifications by mutational profiling sequencing

Enroth, Christel Hougård, Poulsen, L. D., Iversen, S., Kirpekar, F., Albrechtsen, Anders & Vinther, Jeppe, 2019, In: Nucleic Acids Research. 47, 20, 13 p., e126.

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

Excess primer degradation by Exo I improves the preparation of 3' cDNA ligation-based sequencing libraries

Enroth, Christel Hougård, Fehler, A. O., Poulsen, L. D. & Vinther, Jeppe, 2019, In: BioTechniques. 67, 3, p. 110-116

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

Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli

Pedersen, Steen, Terkelsen, Thilde Bagger, Eriksen, M., Hauge, M. K., Lund, C. C., Sneppen, Kim & Mitarai, Namiko, 2019, In: Journal of Molecular Biology. 431, 6, p. 1088-1097 10 p.

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

Genetic basis of ruminant headgear and rapid antler regeneration

Wang, Y., Zhang, C., Wang, N., Li, Z., Heller, R., Liu, R., Zhao, Y., Han, J., Pan, X., Zheng, Z., Dai, X., Chen, C., Dou, M., Peng, S., Chen, X., Liu, J., Li, M., Wang, K., Liu, C., Lin, Z. & 18 others, Chen, L., Hao, F., Zhu, W., Song, C., Zhao, C., Zheng, C., Wang, J., Hu, S., Li, C., Yang, H., Jiang, L., Li, G., Liu, M., Sonstegard, T. S., KU, thw266, Jiang, Y., Wang, W. & Qiu, Q., 2019, In: Science. 364, 6446, p. 1153-+ eaav6335.

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

Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites

Colonna, V., D’Agostino, N., Garrison, E., Albrechtsen, Anders, Meisner, Jonas, Facchiano, A., Cardi, T. & Tripodi, P., 2019, In: Scientific Reports. 9, 14 p., 10067.

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

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K., Barr, J. J., Bibby, K., Brouns, S. J. J., Cazares, A., de Jonge, P. A., Desnues, C., Díaz Muñoz, S. L., Fineran, P. C., Kurilshikov, A., Lavigne, R., Mazankova, K. & 97 others, McCarthy, D. T., Nobrega, F. L., Reyes Muñoz, A., Tapia, G., Trefault, N., Tyakht, A. V., Vinuesa, P., Wagemans, J., Zhernakova, A., Aarestrup, F. M., Ahmadov, G., Alassaf, A., Anton, J., Asangba, A., Billings, E. K., Cantu, V. A., Carlton, J. M., Cazares, D., Cho, G., Condeff, T., Cortés, P., Cranfield, M., Cuevas, D. A., De la Iglesia, R., Decewicz, P., Doane, M. P., Dominy, N. J., Dziewit, L., Elwasila, B. M., Eren, A. M., Franz, C., Fu, J., Garcia-Aljaro, C., Ghedin, E., Gulino, K. M., Haggerty, J. M., Head, S. R., Hendriksen, R. S., Hill, C., Hyöty, H., Ilina, E. N., Irwin, M. T., Jeffries, T. C., Jofre, J., Junge, R. E., Kelley, S. T., Khan Mirzaei, M., Kowalewski, M., Kumaresan, D., Leigh, S. R., Lipson, D., Lisitsyna, E. S., Llagostera, M., Maritz, J. M., Marr, L. C., McCann, A., Molshanski-Mor, S., Monteiro, S., Moreira-Grez, B., Morris, M., Mugisha, L., Muniesa, M., Neve, H., Nguyen, N. P., Nigro, O. D., Nilsson, A. S., O’Connell, T., Odeh, R., Oliver, A., Piuri, M., Prussin, A. J., Qimron, U., Quan, Z. X., Rainetova, P., Ramírez-Rojas, A., Raya, R., Reasor, K., Rice, G. A. O., Rossi, A., Santos, R., Shimashita, J., Stachler, E. N., Stene, L. C., Strain, R., Stumpf, R., Torres, P. J., Twaddle, A., Ugochi Ibekwe, M. A., Villagra, N., Wandro, S., White, B., Whiteley, A., Whiteson, K. L., Wijmenga, C., Zambrano, M. M., Zschach, Henrike & Dutilh, B. E., 2019, In: Nature Microbiology. 4, p. 1727-1736

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

IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

Vitting-Seerup, K. & Sandelin, Albin Gustav, 2019, In: Bioinformatics. 35, 21, p. 4469-4471

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

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples

Renaud, Gabriel, Hanghøj, Kristian Ebbesen, Korneliussen, Thorfinn Sand, Willerslev, Eske & Orlando, L., 2019, In: Genetics (Print). 212, 3, p. 587-614 28 p.

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

Lack of the Major Multifunctional Catalase KatA in Pseudomonas aeruginosa Accelerates Evolution of Antibiotic Resistance in Ciprofloxacin-Treated Biofilms

Ahmed, M. N., Porse, A., Abdelsamad, A., Sommer, M., Høiby, Niels & Ciofu, Oana, 2019, In: Antimicrobial Agents and Chemotherapy. 63, 10, 12 p., e00766-19.

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

Langevin diffusions on the torus: estimation and applications

García-Portugués, E., Sørensen, Michael, Mardia, K. V. & Hamelryck, Thomas Wim, 2019, In: Statistics and Computing. 29, 1, p. 1-22 22 p.

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

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Brown, P., Tan, A-C., El-Esawi, M. A., Liehr, T., Blanck, O., Gladue, D. P., Almeida, G. M. F., Cernava, T., Sorzano, C. O., Yeung, A. W. K., Engel, M. S., Chandrasekaran, A. R., Muth, T., Staege, M. S., Daulatabad, S. V., Widera, D., Zhang, J., Meule, A., Honjo, K., Pourret, O. & 1,560 others, Yin, C., Zhang, Z., Cascella, M., Flegel, W. A., Goodyear, C. S., van Raaij, M. J., Bukowy-Bieryllo, Z., Campana, L. G., Kurniawan, N. A., Lalaouna, D., Huttner, F. J., Ammerman, B. A., Ehret, F., Cobine, P. A., Tan, E., Han, H., Xia, W., McCrum, C., Dings, R. P. M., Marinello, F., Nilsson, H., Nixon, B., Voskarides, K., Yang, L., Costa, V. D., Bengtsson-Palme, J., Bradshaw, W., Grimm, D. G., Kumar, N., Martis, E., Prieto, D., Sabnis, S. C., Amer, S. E. D. R., Liew, A. W. C., Perco, P., Rahimi, F., Riva, G., Zhang, C., Devkota, H. P., Ogami, K., Basharat, Z., Fierz, W., Siebers, R., Tan, K., Boehme, K. A., Brenneisen, P., Brown, J. A. L., Dalrymple, B. P., Harvey, D. J., Ng, G., Werten, S., Bleackley, M., Dai, Z., Dhariwal, R., Gelfer, Y., Hartmann, M. D., Miotla, P., Tamaian, R., Govender, P., Gurney-Champion, O. J., Kauppila, J. H., Zhang, X., Echeverria, N., Subhash, S., Sallmon, H., Tofani, M., Bae, T., Bosch, O., Cuiv, P. O., Danchin, A., Diouf, B., Eerola, T., Evangelou, E., Filipp, F. V., Klump, H., Kurgan, L., Smith, S. S., Terrier, O., Tuttle, N., Ascher, D. B., Janga, S. C., Schulte, L. N., Becker, D., Browngardt, C., Bush, S. J., Gaullier, G., Ide, K., Meseko, C., Werner, G. D. A., Zaucha, J., Al-Farha, A. A., Greenwald, N. F., Popoola, S. I., Rahman, M. S., Xu, J., Yang, S. Y., Hiroi, N., Alper, O. M., Baker, C. I., Bitzer, M., Chacko, G., Debrabant, B., Dixon, R., Forano, E., Gilliham, M., Kelly, S., Klempnauer, K., Lidbury, B. A., Lin, M. Z., Lynch, I., Ma, W., Maibach, E. W., Mather, D. E., Nandakumar, K. S., Ohgami, R. S., Parchi, P., Tressoldi, P., Xue, Y., Armitage, C., Barraud, P., Chatzitheochari, S., Coelho, L. P., Diao, J., Doxey, A. C., Gobet, A., Hu, P., Kaiser, S., Mitchell, K. M., Salama, M. F., Shabalin, I. G., Song, H., Stevanovic, D., Yadollahpour, A., Zeng, E., Zinke, K., Alimba, C. G., Beyene, T. J., Cao, Z., Chan, S. S., Gatchell, M., Kleppe, A., Piotrowski, M., Torga, G., Woldesemayat, A. A., Cosacak, M. I., Haston, S., Ross, S. A., Williams, R., Wong, A., Abramowitz, M. K., Effiong, A., Lee, S., Abid, M. B., Agarabi, C., Alaux, C., Albrecht, D. R., Atkins, G. J., Beck, C. R., Bonvin, A. M. J. J., Bourke, E., Brand, T., Braun, R. J., Bull, J. A., Cardoso, P., Carter, D., Delahay, R. M., Ducommun, B., Duijf, P. H. G., Epp, T., Eskelinen, E., Fallah, M., Farber, D. B., Fernandez-Triana, J., Feyerabend, F., Florio, T., Friebe, M., Furuta, S., Gabrielsen, M., Gruber, J., Grybos, M., Han, Q., Heinrich, M., Helantera, H., Huber, M., Jeltsch, A., Jiang, F., Josse, C., Jurman, G., Kamiya, H., de Keersmaecker, K., Kristiansson, E., de Leeuw, F., Li, J., Liang, S., Lopez-Escamez, J. A., Lopez-Ruiz, F. J., Marchbank, K. J., Marschalek, R., Martin, C. S., Miele, A. E., Montagutelli, X., Morcillo, E., Nicoletti, R., Niehof, M., O'Toole, R., Ohtomo, T., Oster, H., Palma, J., Paterson, R., Peifer, M., Portilla, M., Portillo, M. C., Pritchard, A. L., Pusch, S., Raghava, G. P. S., Roberts, N. J., Ross, K., Schuele, B., Sergeant, K., Shen, J., Stella, A., Sukocheva, O., Uversky, V. N., Vanneste, S., Villet, M. H., Viveiros, M., Vorholt, J. A., Weinstock, C., Yamato, M., Zabetakis, I., Zhao, X., Ziegler, A., Aizat, W. M., Atlas, L., Bridges, K. M., Chakraborty, S., Deschodt, M., Domingues, H. S., Esfahlani, S. S., Falk, S., Guisado, J. L., Kane, N. C., Kueberuwa, G., Lau, C. L., Liang, D., Liu, E., Luu, A. M., Ma, C., Ma, L., Moyer, R., Norris, A. D., Panthee, S., Parsons, J. R., Peng, Y., Pinto, I. M., Reschke, C. R., Sillanpaa, E., Stewart, C. J., Uhle, F., Yang, H., Zhou, K., Zhu, S., Ashry, M., Bergsland, N., Berthold, M., Chen, C., Colella, V., Cuypers, M., Eskew, E. 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A., Cuenda, A., Dao, M., Dauga, D., Deng, Z., Devkota, K., Doan, L. V., Elewa, Y. H. A., Fan, D., Faruk, M., Feifei, S., Ferguson, T. S., Fleres, F., Foster, E. J., Foster, C. S., Furer, T., Gao, Y., Garcia-Rivera, E. J., Gazdar, A., George, R. B., Ghosh, S., Gianchecchi, E., Gleason, J. M., Hackshaw, A., Hall, A., Hall, R., Harper, P., Hogg, W. E., Huang, G., Hunter, K. E., IJzerman, A. P., Jesus, C., Jian, G., Lewis, J. S. ,. J., Kanj, S. S., Kaur, H., Kelly, S., Kheir, F., Kichatova, V. S., Kiyani, M., Klein, R., Kovesi, T., Kraschnewski, J. L., Kumar, A. P., Labutin, D., Lazo-Langner, A., Leclercq, G., Li, M., Li, Q., Li, T., Li, Y., Liao, W., Liao, Z., Lin, J., Lizer, J., Lobreglio, G., Lowies, C., Lu, C., Majeed, H., Martin, A., Martinez-Sobrido, L., Meresh, E., Middelveen, M., Mohebbi, A., Mota, J., Mozaheb, Z., Muyaya, L., Nandhakumar, A., Ng, S. H. X., Obeidat, M., Oh, D., Owais, M., Pace-Asciak, P., Panwar, A., Park, C., Patterson, C., Penagos-Tabaree, F., Pianosi, P. T., Pinzi, V., Pridans, C., Psaroulaki, A., Pujala, R. K., Pulido-Arjona, L., Qi, P., Rahman, P., Rai, N. K., Rassaf, T., Refardt, J., Ricciardi, W., Riess, O., Rovas, A., Sacks, F. M., Saleh, S., Sampson, C., Schmutz, A., Sepanski, R., Sharma, N., Singh, M., Spearman, P., Subramaniapillai, M., Swali, R., Tan, C. M., Tellechea, J. I., Thomas, L., Tong, X., Veys, R., Vitriol, V., Wang, H., Wang, J., Wang, J., Waugh, J., Webb, S. A., Williams, B. A., Workman, A. D., Xiang, T., Xie, L., Xu, J., Xu, T., Yang, C., Yoon, J. G., Yuan, C. M., Zaritsky, A., Zhang, Y., Zhao, H., Zuckerman, H., Lyu, R., Pullan, W. & Zhou, Y., 2019, In: Database: The Journal of Biological Databases and Curation. 2019, 66 p., baz085.

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

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Chen, L., Qin, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., Su, W., Liu, G., Li, Q., Fu, W., Pan, X., Liu, C., Yang, J., Zhang, C., Yin, Y., Wang, Y. & 32 others, Zhao, Y., Zhang, C., Wang, Z., Qin, Y., Liu, W., Wang, B., Ren, Y., Zhang, R., Zeng, Y., Rodrigues da Fonseca, Rute Andreia, Wei, B., Li, R., Wan, W., Zhao, R., Zhu, W., Wang, Y., Duan, S., Gao, Y., Zhang, Y. E., Chen, C., Hvilsom, C., Epps, C. W., Chemnick, L. G., Doug, Y., Mirarab, S., Siegismund, Hans Redlef, Ryder, O. A., Gilbert, M Thomas P, Lewin, H. A., KU, thw266, Heller, Rasmus & Wang, W., 2019, In: Science. 364, 6446, p. 1152-

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

More grist for the mill? Species delimitation in the genomic era and its implications for conservation

Stanton, D. W. G., Frandsen, P., Waples, R. K., Heller, Rasmus, Russo, I. M., Orozco-terWengel, P. A., Pedersen, C. T., Siegismund, Hans Redlef & Bruford, M. W., 2019, In: Conservation Genetics. 20, 1, p. 101-113

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

Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML

Jakobsen, J. S., Laursen, L. G., Schuster, Mikkel Bruhn, Pundhir, Sachin, Schoof, E., Ge, Y., d'Altri, T., Vitting-Seerup, K., Rapin, N., Gentil, C., Jendholm, J., Theilgaard-Mønch, Kim, Reckzeh, K., Bullinger, L., Döhner, K., Hokland, P., Fitzgibbon, J. & Porse, Bo Torben, 2019, In: Science Advances. 5, 7, p. 1-16 16 p., eaaw4304.

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

NetSurfP-2.0: improved prediction of protein structural features by integrated deep learning

Klausen, M. S., Jespersen, M. C., Nielsen, H., Jensen, K. K., Jurtz, V. I., Sønderby, C. K., Sommer, M. O. A., Winther, Ole, Nielsen, M., Petersen, Bent & Marcatili, P., 2019, In: Proteins: Structure, Function and Bioinformatics. 87, 6, p. 520-527

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

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells

Agrawal-Singh, S., Lerdrup, Mads, Gomes, A. R., van de Werken, H. J. G., Johansen, Jens Vilstrup, Andersson, Robin, Sandelin, Albin Gustav, Helin, K. & Hansen, K., 2019, In: eLife. 8, p. 1-32 32 p., e40364.

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

Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array

Makarova, K. S., Karamycheva, S., Shah, S. A., Vestergaard, G. A., Garrett, Roger Antony & Koonin, E. V., 2019, In: FEMS Microbiology Letters. 366, 7, 5 p., fnz079.

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

Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads

Prada Luengo, Inigo, Krogh, Anders, Sørensen, L. M. & Regenberg, Birgitte, 2019, In: BMC Bioinformatics. 20, 9 p., 663.

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

Single mRNP Analysis Reveals that Small Cytoplasmic mRNP Granules Represent mRNA Singletons

Mateu-Regué, À., Christiansen, Jan, Bagger, F. O., Winther, O., Hellriegel, C. & Nielsen, Finn Cilius, 2019, In: Cell Reports. 29, 3, p. 736-748, e1-e4

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

Testing for Hardy-Weinberg equilibrium in structured populations using genotype or low-depth next generation sequencing data

Meisner, Jonas & Albrechtsen, Anders, 2019, In: Molecular Ecology Resources. 19, 5, p. 1144-1152 9 p.

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

The epigenetic factor BORIS (CTCFL) controls the androgen receptor regulatory network in ovarian cancer

Salgado-Albarrán, M., González-Barrios, R., Guerra-Calderas, L., Alcaraz, N., Sánchez-Correa, T. E., Castro-Hernández, C., Sánchez-Pérez, Y., Aréchaga-Ocampo, E., García-Carrancá, A., de León, D. C., Herrera, L. A., Baumbach, J. & Soto-Reyes, E., 2019, In: Oncogenesis. 8, 12 p., 41.

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

The splicing factor RBM25 controls MYC activity in acute myeloid leukemia

Ge, Y., Schuster, Mikkel Bruhn, Pundhir, Sachin, Rapin, N., Bagger, F. O., Sidiropoulos, N., Hashem, N. & Porse, Bo Torben, 2019, In: Nature Communications. 10, 1, p. 1-14 14 p., 172.

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

The transmembrane autophagy cargo receptors ATI1 and ATI2 interact with ATG8 through intrinsically disordered regions with distinct biophysical properties

Sjøgaard, Ida Marie Zobbe, Bressendorff, Simon, Prestel, Andreas, Kausika, S., Oksbjerg, Emilie Duus, Kragelund, Birthe Brandt & Brodersen, Peter, 2019, In: Biochemical Journal. 476, 3, p. 449-465 17 p.

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

Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers [version 1; peer review: not peer reviewed]

Shome, S., Parra, R. G., Fatima, N., Monzon, A. M., Cuypers, B., Moosa, Y., Coimbra, N. D. R., Assis, J., Giner-Delgado, C., Dönertaş, H. M., Cuesta-Astroz, Y., Saarunya, G., Allali, I., Gupta, S., Srivastava, A., Kalsan, M., Valdivia, C., Olguin-Orellana, G. J., Papadimitriou, S., Parisi, D. & 22 others, Kristensen, N. P., Rib, Leonor, Guebila, M. B., Bauer, E., Zaffaroni, G., Bekkar, A., Ashano, E., Paladin, L., Necci, M., Moreyra, N. N., Rydén, M., Villalobos-Solís, J., Papadopoulos, N., Rafael, C., Karakulak, T., Kaya, Y., Gladbach, Y., Dhanda, S. K., Šoštarić, N., Alex, A., DeBlasio, D. & Rahman, F., 1 Jan 2019, In: F1000Research. 8, 9 p., 1574.

Research output: Contribution to journal › Editorial › Research

SignalP 5.0 improves signal peptide predictions using deep neural networks

Armenteros, J. J. A., Tsirigos, Konstantinos, Sønderby, C. K., Petersen, T. N., Winther, Ole, Brunak, Søren, von Heijne, G. & Nielsen, H., 18 Feb 2019, In: Nature Biotechnology. 37, 4, p. 420-423

Research output: Contribution to journal › Journal article › Communication

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

Thodberg, Malte, Thieffry, A., Lange, Jette Bornholdt, Boyd, M., Holmberg, Christian, Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, Olaf & Sandelin, Albin Gustav, 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.

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

Multiplex Genome Engineering for Optimizing Bioproduction in Saccharomyces cerevisiae

Auxillos, Jamie Yam, Garcia-Ruiz, E., Jones, S., Li, T., Jiang, S., Dai, J. & Cai, Y., 19 Mar 2019, In: Biochemistry. 58, 11, p. 1492-1500 9 p.

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

Fast and accurate relatedness estimation from high-throughput sequencing data in the presence of inbreeding

Hanghøj, Kristian Ebbesen, Moltke, Ida, Andersen, P. A., Manica, A. & Korneliussen, Thorfinn Sand, May 2019, In: GigaScience. 8, 5, 9 p., giz034.

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

A step-by-step guide to analyzing CAGE data using R/Bioconductor

Thodberg, Malte & Sandelin, Albin Gustav, 18 Jun 2019, In: F1000Research. 8, 49 p., 886.

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

ERG Controls B Cell Development by Promoting Igh V-to-DJ Recombination

Søndergaard, E., Rauch, A., Michaut, Magali, Rapin, N., Rehn, M., Wilhelmson, Anna, Camponeschi, A., Hasemann, M. S., Bagger, F. O., Jendholm, J., Knudsen, K. J., Mandrup, S., Mårtensson, I. L. & Porse, Bo Torben, 26 Nov 2019, In: Cell Reports. 29, 9, p. 2756-2769.e6 21 p.

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

FUT2–ABO epistasis increases the risk of early childhood asthma and Streptococcus pneumoniae respiratory illnesses

Ahluwalia, T. S., Eliasen, A. U., Sevelsted, A., Pedersen, C-E. T., Stokholm, J., Chawes, B., Bork-Jensen, J., Grarup, N., Pedersen, O., Hansen, T., Linneberg, A., Sharma, A., Weiss, S. T., Evans, M. D., Jackson, D. J., Morin, A., Krogfelt, K. A., Schjørring, S., Mortensen, P. B., Hougaard, D. M. & 13 others, Bybjerg-Grauholm, J., Bækvad-Hansen, M., Mors, O., Nordentoft, Merete, Børglum, A. D., Werge, Thomas, Agerbo, E., Gern, J. E., Lemanske, R. F., Ober, C., Pedersen, A. G., Bisgaard, H. & Bønnelykke, Klaus, 2020, In: Nature Communications. 11, 12 p., 6398.

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

Lactobacillus rhamnosus GG Genomic and Phenotypic Stability in an Industrial Production Process

Strickertsson, Marianne Stage, Wichmann, A., Jørgensen, M., Vera-Jimenéz, N. I., Wielje, M., Nielsen, Dennis Sandris, Sandelin, Albin Gustav, Chen, Y. & Baker, A., 2020, In: Applied and Environmental Microbiology. 86, 6, 15 p., e02780-19.

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

A Targeted Multiomics Approach to Identify Biomarkers Associated with Rapid eGFR Decline in Type 1 Diabetes

Limonte, C. P., Valo, E., Montemayor, D., Afshinnia, F., Ahluwalia, T. S., Costacou, T., Darshi, M., Forsblom, C., Hoofnagle, A. N., Groop, P-H., Miller, R. G., Orchard, T. J., Pennathur, S., Rossing, P., Sandholm, N., Snell-Bergeon, J. K., Ye, H., Zhang, J., Natarajan, L., De Boer, I. H. & 1 others, Sharma, K., 2020, In: American Journal of Nephrology. 51, 10, p. 839-848 10 p.

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

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

Wu, G., Schmid, M., Rib, Leonor, Polak, P., Meola, N., Sandelin, Albin Gustav & Jensen, T. H., 2020, In: Cell Reports. 30, 7, p. 2387-2401, e1-e5

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

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations]

Orengo, C., Velankar, S., Wodak, S., Zoete, V., Bonvin, A. M. J. J., Elofsson, A., Feenstra, K. A., Gerloff, D. L., Hamelryck, T., Hancock, J. M., Helmer-Citterich, M., Hospital, A., Orozco, M., Perrakis, A., Rarey, M., Soares, C., Sussman, J. L., Thornton, J. M., Tuffery, P., Tusnady, G. & 3 others, Wierenga, R., Salminen, T. & Schneider, B., 2020, In: F1000Research. 9, 27 p., 278.

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

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

A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data

Moreno-Mayar, J. V., Korneliussen, Thorfinn Sand, Dalal, J., Renaud, Gabriel, Albrechtsen, Anders, Nielsen, Rasmus & Malaspinas, A., 2020, In: Bioinformatics. 36, 3, p. 828-841 14 p.

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

Ancient Genomes Reveal the Evolutionary History and Origin of Cashmere-Producing Goats in China

Cai, Y., Fu, W., Cai, D., Heller, R., Zheng, Z., Wen, J., Li, H., Wang, X., Alshawi, A., Sun, Z., Zhu, S., Wang, J., Yang, M., Hu, S., Li, Y., Yang, Z., Gong, M., Hou, Y., Lan, T., Wu, K. & 3 others, Chen, Y., Jiang, Y. & Wang, X., 2020, In: Molecular Biology and Evolution. 37, 7, p. 2099-2109 11 p.

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

CAncer bioMarker Prediction Pipeline (CAMPP) - A standardized framework for the analysis of quantitative biological data

Terkelsen, T., Krogh, Anders & Papaleo, E., 2020, In: PLOS Computational Biology. 16, 3, 20 p., e1007665.

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

Cancer Cell Acid Adaptation Gene Expression Response is Correlated to Tumor-Specific Tissue Expression Profiles and Patient Survival

Yao, Jiayi, Czaplinska, D., Ialchina, Renata, Schnipper, J., Liu, B., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2020, In: Cancers. 12, 8, 27 p., 2183.

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

Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways

Thieffry, A., Vigh, Maria Louisa, Lange, Jette Bornholdt, Ivanov, M., Brodersen, Peter & Sandelin, Albin Gustav, 2020, In: The Plant Cell. 32, 6, p. 1845-1867 23 p.

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

Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome

Abildgaard, A. B., Gersing, S. K., Larsen-Ledet, Sven, Nielsen, S. V., Stein, Amelie, Lindorff-Larsen, Kresten & Hartmann-Petersen, Rasmus, 2020, In: Biomolecules. 10, 8, 24 p., 1141.

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

Community curation of bioinformatics software and data resources

Ison, J., Ménager, H., Brancotte, B., Jaaniso, E., Salumets, A., Raček, T., Lamprecht, A. L., Palmblad, M., Kalaš, M., Chmura, Piotr Jaroslaw, Hancock, J. M., Schwämmle, V. & Ienasescu, H. I., 2020, In: Briefings in Bioinformatics. 21, 5, p. 1697-1705 9 p.

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

Comparative transcriptomics of primary cells in vertebrates

Alam, T., Agrawal, S., Severin, J., Young, R. S., Andersson, R., Arner, E., Hasegawa, A., Lizio, M., Ramilowski, J. A., Abugessaisa, I., Ishizu, Y., Noma, S., Tarui, H., Taylor, M. S., Lassmann, T., Itoh, M., Kasukawa, T., Kawaji, H., Marchionni, L., Sheng, G. & 5 others, Forrest, A. R. R., Khachigian, L. M., Hayashizaki, Y., Carninci, P. & de Hoon, M. J. L., 2020, In: Genome Research. 30, 7, p. 951-961 11 p.

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

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Feuerborn, Tatiana Richtman, Palkopoulou, E., van der Valk, T., von Seth, J., Munters, A. R., Chrzanová Pecnerová, Patrícia, Dehasque, M., Ureña, I., Ersmark, E., Lagerholm, V. K., Krzewinska, M., Rodríguez-Varela, R., Götherström, A., Dalén, L. & Díez-del-Molino, D., 2020, In: BMC Genomics. 21, 10 p., 844.

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

Cytoplasmic mRNPs revisited: Singletons and condensates

Mateu-Regue, A., Nielsen, Finn Cilius & Christiansen, Jan, 2020, In: BioEssays. 42, 12, 13 p., 2000097.

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

Daily estimates of clinical severity of symptoms in bipolar disorder from smartphone-based self-assessments

Busk, J., Faurholt-Jepsen, M., Frost, M., Bardram, J. E., Kessing, Lars Vedel & Winther, Ole, 2020, In: Translational Psychiatry. 10, 12 p., 194.

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

Deep Learning for Diagnostic Binary Classification of Multiple-Lesion Skin Diseases

Thomsen, K., Christensen, A. L., Iversen, L., Lomholt, H. B. & Winther, Ole, 2020, In: Frontiers in Medicine. 7, 7 p., 574329.

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

Detection of Viable and Total Bacterial Community in the Pit Mud of Chinese Strong-Flavor Liquor Using Propidium Monoazide Combined With Quantitative PCR and 16S rRNA Gene Sequencing

Tan, G., Zhou, R., Zhang, W., Hu, Y., Ruan, Z., Li, J., Zhang, C., Shen, D., Peng, N., Liang, Y. & Zhao, S., 2020, In: Frontiers in Microbiology. 11, 9 p., 896.

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