Functional Genomics

WAR: webserver for aligning structural RNAs

Þórarinsson, E. & Lindgreen, S., 2008, In: Nucleic Acids Research. 36, Suppl. 2, p. W79-W84 6 p.

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

TopBP1 makes the final call for repair on the verge of cell division

Østergaard, Vibe Hallundbæk & Lisby, Michael, 2016, In: Molecular & Cellular Oncology. 3, 2, 3 p., e1093066.

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

RNF8 and RNF168 but not HERC2 are required for DNA damage-induced ubiquitylation in chicken DT40 cells

Østergaard, Vibe Hallundbæk, Pentzold, C., Pedersen, R. T., Iosif, S., Alpi, A., Bekker-Jensen, Simon Holst, Mailand, Niels & Lisby, Michael, 2012, In: D N A Repair. 11, 11, p. 892–905 14 p.

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

Transcription-replication conflicts at chromosomal fragile sites—consequences in M phase and beyond

Østergaard, Vibe Hallundbæk & Lisby, Michael, Mar 2017, In: Chromosoma. 126, 2, p. 213-222 10 p.

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

Two differentially regulated Arabidopsis genes define a new branch of the DFR superfamily.

Østergaard, L., Lauvergeat, V., Naested, H., Mattsson, O. & Mundy, J., 2001, In: Plant Science. 160, 3, p. 463-472 9 p.

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

Mediastinalt parathyroideacysteadenom--en sjaelden årsag til primaer hyperparatyroidisme

Øgard, C. G., Nielsen, S. L., Jakobsen, H., Leth-Espensen, P., drb459, drb459 & drb459, drb459, 28 Aug 2006, In: Ugeskrift for Laeger. 168, 35, p. 2921-2 2 p.

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

High-throughput screening of Erwinia chrysanthemi pectin methylesterase variants using carbohydrate microarrays

Øbro, J., Sørensen, I., Derkx, P., Madsen, C. T., Drews, M., Willer, M., Mikkelsen, J. D. & Willats, W. G. T., 2009, In: Proteomics - Practical Proteomics. 9, 7, p. 1861-1868

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

Morphological classification of plant cell deaths

van Doorn, W. G., Beers, E. P., Dangl, J. L., Franklin-Tong, V. E., Gallois, P., Hara-Nishimura, I., Jones, A. M., Kawai-Yamada, M., Lam, E., Mundy, J., Mur, L. A. J., Petersen, Morten, Smertenko, A., Taliansky, M., Van Breusegem, F., Wolpert, T., Woltering, E., Zhivotovsky, B. & Bozhkov, P. V., 2011, In: Cell Death and Differentiation. 18, 8, p. 1241-1246 6 p.

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

Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

van Beest, M., Dooijes, D., van De Wetering, M., Kjaerulff, S., Bonvin, A., Nielsen, O., Clevers, H. & Nielsen, Olaf, 1 Sep 2000, In: Journal of Biological Chemistry. 275, 35, p. 27266-73 8 p.

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

ALG-2 participates in recovery of cells after plasma membrane damage by electroporation and digitonin treatment

la Cour, J. M., Gojkovic, P. W., Ambjorner, S. E. B., Bagge, J., Jensen, S. M., Panina, S. & Berchtold, Martin Werner, 2018, In: PLOS ONE. 13, 9, p. 1-13 e0204520.

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

Ciprofloxacin intercalated in fluorohectorite clay: identical pure drug activity and toxicity with higher adsorption and controlled release rate

dos Santos, E. C., Rozynek, Z., Hansen, E. L., Hartmann-Petersen, Rasmus, Klitgaard, R. N., Løbner-Olesen, Anders, Michels, L., Mikkelsen, A., Plivelic, Nunes Bordallo, Heloisa & Fossum, J. O., 17 May 2017, In: R S C Advances. 7, 43, p. 26537-26545

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

The rad52-Y66A allele alters the choice of donor template during spontaneous chromosomal recombination

de Mayolo, A. A., Sunjevaric, I., Reid, R., Mortensen, U. H., Rothstein, R. & Lisby, Michael, 2010, In: DNA Repair. 9, 1, p. 23-32

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

DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices

da Piedade, I., Tang, M. E. & Elemento, O., 2009, In: BMC Bioinformatics. 10, 388, 16 p.

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

The Arabidopsis thaliana mRNA decay factor PAT1 functions in osmotic stress responses and decaps ABA-responsive genes

Zuo, Zhangli Thomsen, Roux, M. E., Sæmundsson, H. P., Müller, M., Bosch, S. M. & Petersen, Morten, 2021, In: FEBS Letters. 595, 2, p. 253-263 11 p.

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

PAT mRNA decapping factors are required for proper development in Arabidopsis

Zuo, Zhangli Thomsen, Roux, M. E., Dagdas, Y. F., Rodriguez, Eleazar & Petersen, Morten, 2024, In: FEBS Letters. 598, 9, p. 1008-1021 14 p.

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

mRNA Decapping Factors LSM1 and PAT Paralogs Are Involved in Turnip Mosaic Virus Viral Infection

Zuo, Zhangli Thomsen, Roux, M., Rodriguez, Eleazar & Petersen, Morten, 2022, In: Molecular plant-microbe interactions : MPMI. 35, 2, p. 125-130 6 p.

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

The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development

Zuo, Zhangli Thomsen, Roux, M. E., Chevalier, J. R., Dagdas, Y. F., Yamashino, T., Højgaard, S. D., Knight, E., Østergaard, L., Rodriguez, Eleazar & Petersen, Morten, 2023, In: Life Science Alliance. 6, 9, 11 p.

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

Comparative Proteomics and Secretomics Revealed Virulence and Antibiotic Resistance-Associated Factors in Vibrio parahaemolyticus Recovered From Commonly Consumed Aquatic Products

Zhu, Z., Yang, L., Yu, P., Wang, Y., Peng, Xu & Chen, L., 2020, In: Frontiers in Microbiology. 11, 31 p., 1453.

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

Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions

Zhu, X., Wirén, M., Sinha, I., Rasmussen, N. N., Linder, T., Holmberg, Steen, Ekwall, K. & Gustafsson, C. M., 2006, In: Molecular Cell. 22, 2, p. 169-78 9 p.

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

A putative ABC transporter is involved in negative regulation of biofilm formation by Listeria monocytogenes.

Zhu, X., Long, F., Chen, Y., Knoechel, Susanne, She, Q. & Shi, X., 2008, In: Applied and Environmental Microbiology. 74, 24, p. 7675-7683

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

Phenotypic, proteomic, and genomic characterization of a putative ABC-transporter permease involved in Listeria monocytogenes biofilm formation

Zhu, X., Liu, W., Lametsch, Rene, Aarestrup, F. M., Shi, C., She, Q., Shi, X. & Knoechel, Susanne, 2011, In: Foodborne Pathogens and Disease. 8, 4, p. 495-501 7 p.

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

Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low-temperature survival

Zhu, C., Sun, B., Liu, T., Zheng, H., Gu, W., He, W., Sun, F., Wang, Y., Yang, M., Bei, W., Peng, Xu, She, Q., Xie, L. & Chen, L., 5 Jun 2017, In: BMC Genomics. 18, 19 p., 436.

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

Dss1 interaction with Brh2 as a regulatory mechanism for recombinational repair.

Zhou, Q., Kojic, M., Cao, Z., Lisby, Michael, Mazloum, N. A. & Holloman, W. K., 2007, In: Molecular and Cellular Biology. 27, 7, p. 2512-26 14 p.

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

Development of a Simvastatin Selection Marker for a Hyperthermophilic Acidophile, Sulfolobus islandicus

Zheng, T., Huang, Q., Zhang, C., Ni, J., She, Q. & Shen, Y., 2012, In: Applied and Environmental Microbiology. 78, 2, p. 568-574 7 p.

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

A Membrane-Associated DHH-DHHA1 Nuclease Degrades Type III CRISPR Second Messenger

Zhao, R., Yang, Y., Zheng, F., Zeng, Z., Feng, W., Jin, X., Wang, J., Yang, K., Liang, Y. X., She, Q. & Han, W., 2020, In: Cell Reports. 32, 11, 16 p., 108133.

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

(p)ppGpp Regulates a Bacterial Nucleosidase by an Allosteric Two-Domain Switch

ZHANG, YONG, Bærentsen, R. L., Fuhrer, T., Sauer, U., Gerdes, K. & Brodersen, D. E., 2019, In: Molecular Cell. 74, 6, p. 1239-1249, e1-e4

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

Novel (p)ppGpp Binding and Metabolizing Proteins of Escherichia coli

ZHANG, YONG, Zbornikova, E., Rejman, D. & Gerdes, K., 2018, In: mBio. 9, 2, 20 p., e02188-17.

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

A bacterial ras-like small GTP-binding protein and its cognate GAP establish a dynamic spatial polarity axis to control directed motility

ZHANG, YONG, Franco, M., Ducret, A. & Mignot, T., Jul 2010, In: PLOS Biology. 8, 7

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

Inactivation of Target RNA Cleavage of a III-B CRISPR-Cas System Induces Robust Autoimmunity in Saccharolobus islandicus

Zhang, Y., Lin, Jinzhong, Tian, X., Wang, Y., Zhao, R., Wu, C., Wang, X., Zhao, P., Bi, X., Yu, Z., Han, W., Peng, N., Liang, Y. X. & She, Q., 2022, In: International Journal of Molecular Sciences . 23, 15, 16 p., 8515.

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

Replication Protein Rep Provides Selective Advantage to Viruses in the Presence of CRISPR-Cas Immunity

Zhang, W., Bhoobalan-Chitty, Y., Zhai, Xichuan, Hui, Y., Hansen, Lars Hestbjerg, Deng, Ling & Peng, Xu, 2023, In: CRISPR Journal. 6, 1, p. 32-42

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

Molecular cloning and antimicrobial activity of enterolysin A and helveticin J of bacteriolysins from metagenome of Chinese traditional fermented foods

Zhang, T., Pan, Y., Li, B., Ou, J., Zhang, J., Chen, Y., Peng, Xu & Chen, L., 2013, In: Food Control. 31, 2, p. 499-507 9 p.

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

Spatial transcriptome unveils a discontinuous inflammatory pattern in proficient mismatch repair colorectal adenocarcinoma

Zhang, R., Feng, Y., Ma, W., Guo, Y., Luo, M., Li, Y., Zang, Y., Dong, X., Lu, S., Guo, Q., Xu, Q., Chen, H., Li, Y., Liu, L., CHEN, Ao, Chen, G. & Xu, X., 2023, In: Fundamental Research. 3, 4, 7 p.

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

STAT3 induces transcription of the DNA methyltransferase 1 gene (DNMT1) in malignant T lymphocytes

Zhang, Q., Wang, H. Y., Woetmann, Anders , Raghunath, P. N., Ødum, Niels & Wasik, M. A., 2006, In: Blood. 108, 3, p. 1058-64 6 p.

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

New locus important for Myxococcus social motility and development

Zhang, C. Y., Cai, K., Liu, H., ZHANG, YONG, Pan, H. W., Wang, B., Wu, Z. H., Hu, W. & Li, Y. Z., Nov 2007, In: Journal of Bacteriology. 189, 21, p. 7937-7941 5 p.

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

Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method

Zhang, C., Guo, L., Deng, L., Wu, Y., Liang, Y., Huang, L. & She, Q., Nov 2010, In: Microbiology. 156, Part 11

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

Genetic manipulation in Sulfolobus islandicus and functional analysis of DNA repair genes

Zhang, C., Tian, B., Li, S., Ao, X., Dalgaard, K., Gökce, S., Liang, Y. & She, Q., 2013, In: Biochemical Society Transactions. 41, 1, p. 405-410 6 p.

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

The apt/6-methylpurine counterselection system and its applications in genetic studies of the hyperthermophilic archaeon Sulfolobus islandicus

Zhang, C., She, Q., Bi, H. & Whitaker, R. J., 2016, In: Applied and Environmental Microbiology. 82, 10, p. 3070-3081 12 p.

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

Phosphatidylserine stimulates ceramide 1-phosphate (C1P) intermembrane transfer by C1P transfer proteins

Zhai, X., Gao, Y., Mishra, S. K., Simanshu, D. K., Boldyrev, I. A., Benson, L. M., Bergen III, H. R., Malinina, L., Mundy, J., Molotkovsky, J. G., Patel, D. J. & Brown, R. E., 10 Feb 2017, In: Journal of Biological Chemistry. 292, 6, p. 2531-2541 11 p.

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

Discovery and characterization of a thermostable and highly halotolerant GH5 cellulase from an Icelandic hot spring isolate

Zarafeta, D., Kissas, D., Sayer, C., Islin, S. R., Ladoukakis, E., Isupov, M. N., Chatziioannou, A., Peng, Xu, Littlechild, J. A., Skretas, G. & Kolisis, F. N., 2016, In: P L o S One. 11, 1, 18 p., e0146454.

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

EstDZ3: a new esterolytic enzyme exhibiting remarkable thermostability

Zarafeta, D., Szabo, Z., Moschidi, D., Phan, Safir Hien, Chrysina, E. D., Peng, Xu, Ingham, C. J., Kolisis, F. N. & Skretas, G., 2016, In: Frontiers in Microbiology. 7, 14 p., 1779.

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

Genomic analysis of Acidianus hospitalis W1 a host for studying crenarchaeal virus and plasmid life cycles

You, X. Y., Liu, C., Wang, S. Y., Jiang, C. Y., Shah, S. A., Prangishvili, D., She, Q., Liu, S. J. & Garrett, Roger Antony, 2011, In: Extremophiles. 15, p. 487-497 11 p.

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

The draft genome of mandrill (Mandrillus sphinx): an Old World monkey

Yin, Y., Yang, T., Liu, Huan, Huang, Z., Zhang, Y., Song, Y., Wang, W., Guang, X., Sahu, S. K. & Kristiansen, Karsten, 2020, In: Scientific Reports. 10, 8 p., 2431.

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

Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants

Yang, T., Sahu, S. K., Yang, L., Liu, Y., Mu, W., Liu, X., Strube, M. L., Liu, Huan & Zhong, B., 2022, In: Frontiers in Plant Science. 13, 13 p., 808156.

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

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis

Yang, Nan, Nesme, Joseph, Røder, Henriette Lyng, Li, Xuan Ji, Zuo, Zhangli Thomsen, Petersen, Morten, Burmølle, Mette & Sørensen, Søren Johannes, 2021, In: npj Biofilms and Microbiomes. 7, 11 p., 82.

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

Prophage-Related Gene VpaChn25_0724 Contributes to Cell Membrane Integrity and Growth of Vibrio parahaemolyticus CHN25

Yang, L., Wang, Y., Yu, P., Ren, S., Zhu, Z., Jin, Y., Yan, J., Peng, Xu & Chen, L., 2020, In: Frontiers in Cellular and Infection Microbiology. 10, 18 p., 595709.

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

Diverse Aquatic Animal Matrices Play a Key Role in Survival and Potential Virulence of Non-O1/O139 Vibrio cholerae Isolates

Yan, L., Jin, Y., Zhang, B., Xu, Y., Peng, Xu, Qin, S. & Chen, L., 2022, In: Frontiers in Microbiology. 13, 21 p., 896767.

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

Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs)

Xu, Y., Wang, S., Li, L., Sahu, S. K., Petersen, Morten, Liu, X., Melkonian, M., Zhang, G. & Liu, Huan, 2019, In: Scientific Reports. 9, 10 p., 12485.

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

The Draft Genome of Hariotina reticulata (Sphaeropleales, Chlorophyta) Provides Insight into the Evolution of Scenedesmaceae

Xu, Y., Li, L., Liang, H., Melkonian, B., Lorenz, M., Friedl, T., Petersen, Morten, Liu, Huan, Melkonian, M. & Wang, S., 2019, In: Protist. 170, 6, 6 p., 125684.

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

An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data

Xu, W., Lin, Y., Zhao, K., Li, H., Tian, Y., Ngatia, J. N., Ma, Y., Sahu, S. K., Guo, H., Guo, X., Xu, Y. C., Liu, Huan, Kristiansen, Karsten, Lan, T. & Zhou, X., 2021, In: Ecology and Evolution. 11, 1, p. 390-401 12 p.

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

A spatiotemporal atlas of mouse liver homeostasis and regeneration

Xu, J., Guo, P., Hao, S., Shangguan, S., Shi, Q., Volpe, G., Huang, K., Zuo, J., An, J., Yuan, Y., Cheng, M., Deng, Q., Zhang, X., Lai, G., Nan, H., Wu, B., Shentu, X., Wu, L., Wei, X., Jiang, Y. & 38 others, Huang, X., Pan, F., Song, Y., Li, R., Wang, Z., Liu, C., Liu, S., Li, Y., Yang, T., Xu, Z., Du, W., Li, L., Ahmed, T., You, K., Dai, Z., Li, L., Qin, B., Li, Y., Lai, L., Qin, D., Chen, J., Fan, R., Li, Y., Hou, J., Ott, M., Sharma, A. D., Cantz, T., Schambach, A., Kristiansen, Karsten, Hutchins, A. P., Göttgens, B., Maxwell, P. H., Hui, L., Xu, X., Liu, L., CHEN, Ao, Lai, Y. & Esteban, M. A., 2024, In: Nature Genetics. 56, p. 953-969 17 p.

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

Survival and Genome Diversity of Vibrio parahaemolyticus Isolated from Edible Aquatic Animals

Xu, D., Peng, Xu, Xie, L. & Chen, L., 2022, In: Diversity. 14, 5, 23 p., 350.

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

Sulfolobus Replication Factor C stimulates the activity of DNA Polymerase B1

Xing, X., Zhang, L., Guo, L., She, Q. & Huang, L., 2014, In: Journal of Bacteriology. 196, 13, p. 2367-2375 9 p.

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

Histone H3 lysine 56 acetylation and the response to DNA replication fork damage

Wurtele, H., Kaiser, G. S., Bacal, J., St-Hilaire, E., Lee, E., Tsao, S., Dorn, J., Maddox, P., Lisby, Michael, Pasero, P. & Verreault, A., 2012, In: Molecular and Cellular Biology. 32, 1, p. 154-172 19 p.

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

Interaction of extremophilic archaeal viruses with human and mouse complement system and viral biodistribution in mice

Wu, L., Uldahl, K. B., Chen, F., Benasutti, H., Logvinski, D., Vu, V., Banda, N. K., Peng, Xu, Simberg, D. & Moghimi, S. M., Oct 2017, In: Molecular Immunology. 90, p. 273-279 7 p.

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

Modeling promoter grammars with evolving hidden Markov models

Won, K., Sandelin, Albin Gustav, Marstrand, T. T. & Krogh, Anders, 2008, In: Bioinformatics. 24, 15, p. 1669-75 6 p.

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

Discovering novel hydrolases from hot environments

Wohlgemuth, R., Littlechild, J., Monti, D., Schnorr, K., van Rossum, T., Siebers, B., Menzel, P., Kublanov, I. V., Rike, A. G., Skretas, G., Szabo, Z., Peng, Xu & Young, M. J., 2018, In: Biotechnology Advances. 36, 8, p. 2077-2100

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

Nonmalignant T cells stimulate growth of T-cell lymphoma cells in the presence of bacterial toxins

Woetmann, Anders , Lovato, P., Eriksen, K. W., Krejsgaard, T., Labuda, T., Zhang, Q., Mathiesen, A., Geisler, Carsten, Svejgaard, A., Wasik, M. A. & Ødum, Niels, 2007, In: Blood. 109, 8, p. 3325-32 7 p.

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

Protein phosphatase 2A (PP2A) regulates interleukin-4-mediated STAT6 signaling

Woetmann, Anders , Brockdorff, J., Lovato, P., Nielsen, M., Leick, V., Rieneck, K., Svejgaard, A., Geisler, Carsten & Ødum, Niels, 2002, In: Journal of Biological Chemistry. 278, 5, p. 2787-91 4 p.

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

Inhibition of protein phosphatase 2A induces serine/threonine phosphorylation, subcellular redistribution, and functional inhibition of STAT3

Woetmann, Anders , Nielsen, M., Christensen, S. T., Brockdorff, J., Kaltoft, K., Engel, A. M., Skov, S., Brender, C., Geisler, Carsten, Svejgaard, A., Rygaard, J., Leick, V. & Odum, N., 1999, In: Proceedings of the National Academy of Science of the United States of America. 96, 19, p. 10620-5 5 p.

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

Where sociality and relatedness diverge: the genetic basis for hierarchical social organization in African elephants

Wittemyer, G., Okello, J. B. A., Rasmussen, H. B., Arctander, P., Nyakaana, S., Douglas-Hamilton, I. & Siegismund, Hans Redlef, 2009, In: PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-CONTAINING PAPERS OF A BIOLOGICAL CHARACTER. 276, 1672, p. 3513-3521

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

Analysis of RNA metabolism in fission yeast

Wise, J. A. & Nielsen, Olaf, May 2017, In: Cold Spring Harbor Protocols. 2017, 5, p. 365-372 8 p.

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

Activation of the Stringent Response by Loading of RelA-tRNA Complexes at the Ribosomal A-Site

Winther, K. S., Roghanian, Mohammad & Gerdes, K., 2018, In: Molecular Cell. 70, 1, p. 95-105, e1-e4 15 p.

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

VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation

Winther, K. S., Tree, J. J., Tollervey, D. & Gerdes, K., 2016, In: Nucleic Acids Research. 44, 20, p. 9860-9871 12 p.

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

Diversity of Holocene life forms in fossil glacier ice

Willerslev, Eske, Hansen, Anders Johannes, Christensen, B., Steffensen, Jørgen Peder & Arctander, P., 1999, In: Proceedings of the National Academy of Science of the United States of America. 96, 14, p. 8017-21

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

Two-step activation of meiosis by the mat1 locus in Schizosaccharomyces pombe

Willer, M., Hoffmann, U., Styrkársdóttir, U., Egel, Richard, Davey, W. J., Nielsen, O. & Nielsen, Olaf, 1 Sep 1995, In: Molecular and Cellular Biology. 15, 9, p. 4964-70 7 p.

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

Crosslinking of Dam methyltransferase with S-adenosyl-methionine

Wenzel, C., Moulard, M., Løbner-Olesen, Anders & Guschlbauer, W., 11 Mar 1991, In: FEBS Letters. 280, 1, p. 147-51 5 p.

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

New vectors in fission yeast: application for cloning the his2 gene

Weilguny, D., Praetorius, M., Carr, A., Egel, Richard, Nielsen, O. & Nielsen, Olaf, 1 Mar 1991, In: Gene. 99, 1, p. 47-54 8 p.

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

Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration

Wei, X., Fu, S., Li, H., Liu, Y., Wang, S., Feng, W., Yang, Y., Liu, X., Zeng, Y-Y., Cheng, M., Lai, Y., Qiu, X., Wu, L., Zhang, N., Jiang, Y., Xu, J., Su, X., Peng, C., Han, L., Lou, W. P-K. & 16 others, Liu, C., Yuan, Y., Ma, K., Yang, T., Pan, X., Gao, S., CHEN, Ao, Esteban, M. A., Yang, H., Wang, J., Fan, G., Liu, L., Chen, L., Xu, X., Fei, J. & Gu, Y., 2022, In: Science. 377, 6610, 10 p., eabp9444.

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

Structured RNAs in the ENCODE selected regions of the human genome.

Washietl, S., Pedersen, J. S., Korbel, J. O., Stocsits, C., Gruber, A. R., Hackermüller, J., Hertel, J., Lindemeyer, M., Reiche, K., Tanzer, A., Ucla, C., Wyss, C., Antonarakis, S. E., Denoeud, F., Lagarde, J., Drenkow, J., Kapranov, P., Gingeras, T. R., Guigó, R., Snyder, M. & 4 others, Gerstein, M. B., Reymond, A., Hofacker, I. L. & Stadler, P. F., 2007, In: Genome Research. 17, 6, p. 852-64 12 p.

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

A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus

Wang, Y., Duan, Z., Zhu, H., Guo, X., Wang, Z., Zhou, J., She, Q. & Huang, L., 2007, In: Virology. 363, 1, p. 124-33 9 p.

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

Genomes of early-diverging streptophyte algae shed light on plant terrestrialization

Wang, S., Li, L., Li, H., Sahu, S. K., Wang, H., Xu, Y., Xian, W., Song, B., Liang, H., Cheng, S., Chang, Y., Song, Y., Çebi, Z., Wittek, S., Reder, T., Peterson, M., Yang, H., Wang, J., Melkonian, B., Van de Peer, Y. & 5 others, Xu, X., Wong, G. K., Melkonian, M., Liu, Huan & Liu, X., 2020, In: Nature Plants. 6, 2, p. 95-106

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

Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

Wang, S., Liang, H., Xu, Y., Li, L., Wang, H., Sahu, D. N., Petersen, Morten, Melkonian, M., Sahu, S. K. & Liu, Huan, 2021, In: Communications Biology . 4, 11 p., 412.

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

The chromosome-scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation

Wang, S., Liang, H., Wang, H., Li, L., Xu, Y., Liu, Y., Liu, M., Wei, J., Ma, T., Le, C., Yang, J., He, C., Liu, J., Zhao, J., Zhao, Y., Lisby, Michael, Sahu, S. K. & Liu, H., 2022, In: Plant Biotechnology Journal. 20, 3, p. 538-553 16 p.

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

The Draft Genome of the Small, Spineless Green Alga Desmodesmus costato-granulatus (Sphaeropleales, Chlorophyta)

Wang, S., Li, L., Xu, Y., Melkonian, B., Lorenz, M., Friedl, T., Petersen, Morten, Sahu, S. K., Melkonian, M. & Liu, Huan, 2019, In: Protist. 170, 6, 5 p., 125697.

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

A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway

Wang, J., Xie, J., Chen, H., Qiu, X., Cui, H., Liu, Y., Sahu, S. K., Fang, D., Li, T., Wang, M., Chen, Y., Liu, Huan, Zhang, J. & Wang, B., 2022, In: Communications Biology . 5, 12 p., 1294.

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

Comparative transcriptomic analyses of chlorogenic acid and luteolosides biosynthesis pathways at different flowering stages of diploid and tetraploid Lonicera japonica

Wang, H., Li, Y., Wang, S., Kong, D., Sahu, S. K., Bai, M., Li, H., Li, L., Xu, Y., Liang, H., Liu, Huan & Wu, H., 2020, In: PeerJ. 8, 24 p., e8690.

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

Archaeal extrachromosomal genetic elements

Wang, H., Peng, N., Shah, S. A., Huang, L. & She, Q., 2015, In: Microbiology and Molecular Biology Reviews. 79, 1, p. 117-152 36 p.

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

Global, regional, and national under-5 mortality, adult mortality, age-specific mortality, and life expectancy, 1970-2016: A systematic analysis for the Global Burden of Disease Study 2016

Wang, H., Abajobir, A. A., Abate, K. H., Abbafati, C., Abbas, K. M., Abd-Allah, F., Abera, S. F., Abraha, H. N., Abu-Raddad, L. J., Abu-Rmeileh, N. M. E., Adedeji, I. A., Adedoyin, R. A., Adetifa, I. M. O., Adetokunboh, O., Afshin, A., Aggarwal, R., Agrawal, A., Agrawal, S., Ahmad Kiadaliri, A., Ahmed, M. B. & 31 others, Aichour, A. N., Aichour, I., Aichour, M. T. E., Aiyar, S., Akanda, A. S., Akinyemiju, T. F., Akseer, N., Al-Eyadhy, A., Al Lami, F. H., Alabed, S., Alahdab, F., Al-Aly, Z., Alam, K., Alam, N., Alasfoor, D., Aldridge, R. W., Alene, K. A., Bjerregaard, P., Christensen, H., De Courten, B., Havmoeller, R., He, F., Iburg, K. M., Larsson, A., McGrath, J. J., Mengistie, M. A., Singh, Prashant, Sobngwi, E., Truelsen, Thomas Clement, Wang, Y. & GBD 2016 Mortality Collaborators, G. 2. M. C., 2017, In: The Lancet. 390, 10100, p. 1084-1150 67 p.

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

Yeast transcriptional regulator Leu3p: Self-masking, specificity of masking, and evidence for regulation by the intracellular level of Leu3p

Wang, D., Zheng, F., Holmberg, Steen & Kohlhaw, G. B., 1999, In: The Journal of Biological Chemistry. 274 (27), p. 19017-19024

Research output: Contribution to journal › Journal article › Research

Common Chromosomal Fragile Sites - Conserved Failure Stories

Voutsinos, Vasileios, Munk, S. H. N. & Østergaard, Vibe Hallundbæk, 2018, In: Genes. 9, 12, p. 1-16 580.

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

Ethanol exposure increases mutation rate through error-prone polymerases

Voordeckers, K., S.Colding-Christensen, Camilla, Grasso, L., Pardo, B., Hoes, L., Kominek, J., Gielens, K., Dekoster, K., Gordon, J., Van der Zande, E., Bircham, P., Swings, T., Michiels, J., Van Loo, P., Nuyts, S., Pasero, P., Lisby, Michael & Verstrepen, K. J., 2020, In: Nature Communications. 11, 16 p., 3664.

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

In vivo and in vitro protein imaging in thermophilic archaea by exploiting a novel protein tag

Visone, V., Han, W., Perugino, G., del Monaco, G., She, Q., Rossi, M., Valenti, A. & Ciaramella, M., 3 Oct 2017, In: PLoS ONE. 12, 10, 19 p., e0185791.

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

Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ

Vischer, N. O. E., Verheul, J., Postma, M., van Saparoea, B. V. D. B., Galli, E., Natale, P., Gerdes, K., Luirink, J., Vollmer, W., Vicente, M. & den Blaauwen, T., 2015, In: Frontiers in Microbiology. 6, 18 p., 586.

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

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture.

Vinther, Jeppe, Hedegaard, M. M., Gardner, P. P., Andersen, J. S. & Arctander, P., 2006, In: Nucleic Acids Research. 34, 16, p. e107

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

The 3' region of human papillomavirus type 16 early mRNAs decrease expression

Vinther, Jeppe, Rosenstierne, M. W., Kristiansen, K. & Norrild, B., 2005, In: BMC Infectious Diseases. 5, p. 83

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

RNA-binding IMPs promote cell adhesion and invadopodia formation.

Vikesaa, J., Hansen, T. V. O., Jønson, L., Borup, R., Wewer, Ulla M., Christiansen, Jan & Nielsen, Finn Cilius, 2006, In: EMBO Journal. 25, 7, p. 1456-68 12 p.

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

CRISPR adaptive immune systems of Archaea

Vestergaard, G. A., Garrett, Roger Antony & Shah, S. A., 2014, In: R N A Biology. 11, 2, p. 157-168 12 p.

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

A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus

Vestergaard, G. A., Häring, M., Peng, Xu, Rachel, R., Garrett, Roger Antony & Prangishvili, D., 2005, In: Virology. 336, 1, p. 83-92 10 p.

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

Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system

Vestergaard, G. A., Shah, S. A., Bize, A., Reitberger, W., Reuter, M., Phan, H., Briegel, A., Rachel, R., Garrett, Roger Antony & Prangishvili, D., 2008, In: Journal of Bacteriology. 190, 20, p. 6837-6845 8 p.

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

Structure of the acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses

Vestergaard, G. A., Aramayo, R., Basta, T., Häring, M., Peng, Xu, Brügger, K., Chen, L., Rachel, R., Boisset, N., Garrett, Roger Antony & Prangishvili, D., 2008, In: Journal of Virology. 82, 1, p. 371-381 11 p.

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

Schizosaccharomyces pombe Mms1 channels repair of perturbed replication into Rhp51 independent homologous recombination

Vejrup-Hansen, R., Mizuno, K., Miyabe, I., Fleck, O., Holmberg, Christian, Murray, J. M., Carr, A. M. & Nielsen, Olaf, 2011, In: DNA Repair. 10, 3, p. 283-95 13 p.

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

Spd2 assists Spd1 in the modulation of ribonucleotide reductase architecture but does not regulate deoxynucleotide pools

Vejrup-Hansen, R., Fleck, O., Landvad, K., Fahnøe, Ulrik, Broendum, S. S., Schreurs, A., Kragelund, Birthe Brandt, Carr, A. M., Holmberg, Christian & Nielsen, Olaf, 2014, In: Journal of Cell Science. 127, p. 2460-2470 11 p.

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

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE

Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M-H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M. & 4 others, Hayashizaki, Y., Gustincich, S., Sandelin, Albin Gustav & Carninci, P., 2009, In: Genome Research. 19, 2, p. 255-65 10 p.

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

Discovery of regulatory elements is improved by a discriminatory approach

Valen, E., Sandelin, Albin Gustav, Winther, Ole & Krogh, Anders, 2009, In: PLoS Computational Biology. 5, 11, p. e1000562

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

Emerging roles of the CIP2A–TopBP1 complex in genome integrity

Ummethum, Henning Ole, Li, Jiayi, Lisby, Michael & Østergaard, Vibe Hallundbæk, 2023, In: NAR Cancer. 5, 4, 6 p.

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

Recognition of extremophilic archaeal viruses by eukaryotic cells: a promising nanoplatform from the third domain of life

Uldahl, K. B., Wu, L., Hall, A., Papathanasiou, P., Peng, Xu & Moghimi, S. M., 2016, In: Scientific Reports. 6, 37966.

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

Life cycle characterization of Sulfolobus monocaudavirus 1, an extremophilic spindle-shaped virus with extracellular tail development

Uldahl, K. B., Jensen, S. B., Bhoobalan, Yuvaraj, Martinez Alvarez, Laura, Papathanasiou, P. & Peng, Xu, Jun 2016, In: Journal of Virology. 90, 12, p. 5693-5699 7 p.

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

Ekstremernes herrer

Uldahl, K. B. & Peng, Xu, 2012, In: Aktuel Naturvidenskab. 2012, 05, p. 28-29 2 p.

Research output: Contribution to journal › Journal article › Research

SMV1, an extremely stable thermophilic virus platform for nanoparticle trafficking in the mammalian GI tract

Uldahl, K. B., Walk, S. T., Olshefsky, S. C., Young, M. J. & Peng, Xu, Nov 2017, In: Journal of Applied Microbiology. 123, 5, p. 1286-1297 12 p.

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

The fission yeast heterochromatin protein Rik1 is required for telomere clustering during meiosis

Tuzon, C. T., Borgstrøm, B., Weilguny, D., Egel, Richard, Cooper, J. P. & Nielsen, Olaf, 2004, In: Journal of Cell Biology. 165, 6, p. 759-65 6 p.

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

Intramolecular Interactions Dominate the Autoregulation of Escherichia coli Stringent Factor RelA

Turnbull, K. J., Dzhygyr, I., Lindemose, Søren, Hauryliuk, V. & Roghanian, Mohammad, 2019, In: Frontiers in Microbiology. 10, 12 p., 1966.

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

HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin

Turnbull, K. & Gerdes, K., Jun 2017, In: Molecular Microbiology. 104, 5, p. 781-792 12 p.

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

Analysis of Escherichia coli mutants with altered DNA content

Trun, N. J., Gottesman, S. & Løbner-Olesen, Anders, 1991, In: Cold Spring Harbor Symposia on Quantitative Biology. 56, p. 353-8 6 p.

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

Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

Toteva, T., Mason, B., Kanoh, Y., Brøgger, P., Green, D., Hansen, J. V., Masai, H. & Thon, Genevieve, 31 Jan 2017, In: Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. 1093-1098 6 p.

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

Anaphase onset before complete DNA replication with intact checkpoint responses.

Torres-Rosell, J., De Piccoli, G., Cordon-Preciado, V., Farmer, S., Jarmuz, A., Machin, F., Pasero, P., Lisby, Michael, Haber, J. E. & Aragón, L., 2007, In: Science. 315, 5817, p. 1411-5 4 p.

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

The Smc5-Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus.

Torres-Rosell, J., Sunjevaric, I., De Piccoli, G., Sacher, M., Eckert-Boulet, N., Reid, R., Jentsch, S., Rothstein, R., Aragón, L. & Lisby, Michael, 2007, In: Nature Cell Biology. 9, 8, p. 923-31 8 p.

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

Synchronized switching of multiple toxin-antitoxin modules by (p)ppGpp fluctuation

Tian, C., Semsey, S. & Mitarai, Namiko, 21 Aug 2017, In: Nucleic Acids Research. 45, 14, p. 8180-8189 10 p.

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

Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases

Tian, C., Roghanian, Mohammad, Jørgensen, M. G., Sneppen, Kim, Sørensen, Michael Askvad, Gerdes, K. & Mitarai, Namiko, Jul 2016, In: Journal of Bacteriology. 198, 14, p. 1918-1926

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

Organization and expression of genes in the genomic region surrounding the glutamine synthetase gene Gln1 from Lotus japonicus

Thykjaer, T., Danielsen, D., She, Q. & Stougaard, J., 1997, In: Molecular Genetics and Genomics. 255, 6, p. 628-36 8 p.

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

Mediator regulates non-coding RNA transcription at fission yeast centromeres

Thorsen, M., Hansen, H., Venturi, M., Holmberg, Steen & Thon, Genevieve, 2012, In: Epigenetics & Chromatin. 5, p. 1-10 10 p.

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

The clr1 locus regulates the expression of the cryptic mating-type loci of fission yeast

Thon, Genevieve & Klar, A., 1992, In: Genetics. 131, 2, p. 287-296 10 p.

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

Directionality of fission yeast mating-type interconversion is controlled by the location of the donor loci

Thon, Genevieve, 1993, In: Genetics. 134, 4, p. 1045-1054 10 p.

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

Histone modifications: Cycling with chromosomal replication

Thon, Genevieve, 2008, In: Current Biology. 18, 9, p. 380-382 3 p.

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

Antigenic diversity by the recombination of pseudogenes

Thon, Genevieve, Baltz, T. & Eisen, H., 1989, In: Genes & Development. 3, 8, p. 1247-1254 8 p.

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

Mating-type switching by homology-directed recombinational repair: a matter of choice

Thon, Genevieve, Maki, T., Haber, J. E. & Iwasaki, H., 2019, In: Current Genetics. 65, 2, p. 351-362

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

Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe

Thon, Genevieve, Cohen, A. & Klar, A., 1994, In: Genetics. 138, 1, p. 29-38 10 p.

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

Trypanosome variable surface glycoproteins: composite genes and order of expression

Thon, Genevieve, Baltz, T., Giroud, C. & Eisen, H., 1990, In: Genes & Development. 4, 8, p. 1374-1383 10 p.

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

Competing to destroy: a fight between two RNA-degradation systems

Thon, Genevieve, 2008, In: Nature Structural and Molecular Biology. 15, 10, p. 1001-2 2 p.

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

The lantibiotic NAI-107 efficiently rescues Drosophila melanogaster from infection with methicillin-resistant Staphylococcus aureus USA300

Thomsen, T. T., Mojsoska, B., Cruz, J. C. S., Donadio, S., Jenssen, H., Løbner-Olesen, Anders & Rewitz, Kim, 2016, In: Antimicrobial Agents and Chemotherapy. 60, 9, p. 5427-5436 10 p.

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

Analogues of a Cyclic Antimicrobial Peptide with a Flexible Linker Show Promising Activity Against Pseudomonas aeruginosa and Staphylococcus aureus

Thomsen, T. T., Mendel, H. C., Al-Mansour, W., Oddo, A., Løbner-Olesen, Anders & Hansen, Paul Robert, 2020, In: Antibiotics. 9, 7, 13 p., 366.

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

Rapid selection of Plasmodium falciparum chloroquine resistance transporter gene and multidrug resistance gene-1 haplotypes associated with past chloroquine and present artemether-lumefantrine use in Inhambane District, southern Mozambique

Thomsen, T. T., Madsen, L. B., Hansson, Helle Smedegaard, Tomás, E. V. E., Charlwood, D., Bygbjerg, Ib Christian & Alifrangis, Michael, Mar 2013, In: American Journal of Tropical Medicine and Hygiene. 88, 3, p. 536-41 6 p.

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

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

Escherichia coli belonging to ST131 rarely transfers bla_ctx-m-15 to fecal Escherichia coli

Thingholm, K. R., Hertz, F. B., Løbner-Olesen, Anders, Frimodt-Møller, N. & Nielsen, K. L., 2019, In: Infection and Drug Resistance. 12, p. 2429-2435

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

KBERG: KnowledgeBase for Estrogen Responsive Genes.

Tang, S., Zhang, Z., Tan, S. L., Tang, M. E., Kumar, A. P., Ramadoss, S. K. & Bajic, V. B., 2007, In: Nucleic Acids Research. 35, Database issue, p. D732-6

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

Computational method for discovery of estrogen responsive genes.

Tang, S., Tan, S. L., Ramadoss, S. K., Kumar, A. P., Tang, M. E. & Bajic, V. B., 2004, In: Nucleic Acids Research. 32, 21, p. 6212-7 5 p.

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

BayesMD: Flexible Biological Modeling for Motif Discovery

Tang, M. E., Krogh, Anders & Winther, Ole, 2008, In: Journal of Computational Biology. 15, 10, p. 1347-63 16 p.

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

Spironolactone induces apoptosis and inhibits NF-kappaB independent of the mineralocorticoid receptor

Sønder, S. U. S., Woetmann, Anders , Ødum, Niels & Bendtzen, K., 2006, In: Apoptosis. 11, 12, p. 2159-65 7 p.

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

CRP Interacts Specifically With Sxy to Activate Transcription in Escherichia coli

Søndberg, E., Sinha, A. K., Gerdes, K. & Semsey, S., 2019, In: Frontiers in Microbiology. 10, 8 p., 2053.

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

Salmonella Typhimurium undergoes distinct genetic adaption during chronic infections of mice

Søndberg, E. & Jelsbak, L., 2016, In: BMC Microbiology. 16, 11 p., 30.

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

Mechanisms and regulation of mitotic recombination in Saccharomyces cerevisiae

Symington, L. S., Rothstein, R. & Lisby, Michael, 2014, In: Genetics (Print). 198, 3, p. 795-835 41 p.

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

Novel method for quantitative estimation of biofilms

Syal, K., Oct 2017, In: Current Microbiology. 74, 10, p. 1194-1199 6 p.

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

Gene Expression Changes with Minor Effects on the Population Average Have Major Effects on the Occurrence of Cells with Extreme Protein Concentrations

Svenningsen, Mikkel Skjoldan, Semsey, S. & Mitarai, Namiko, 2019, In: mSphere. 4, 1, p. 1-6 e00575-18.

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

Birth and Resuscitation of (p)ppGpp Induced Antibiotic Tolerant Persister Cells

Svenningsen, Mikkel Skjoldan, Veress, A., Harms, A., Mitarai, Namiko & Semsey, S., 15 Apr 2019, In: Scientific Reports. 9, 13 p., 6056.

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

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

Suzuki, H., Forrest, A. R. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M. & 31 others, Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Björkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engström, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Jacobsen, A., Krogh, Anders, Nygaard, S., Sandelin, Albin Gustav, Valen, E., Winther, Ole & Riken Omics Science Center, R. O. S. C., 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.

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

Insights into Vibrio parahaemolyticus CHN25 response to artificial gastric fluid stress by transcriptomic analysis

Sun, X., Liu, T., Peng, Xu & Chen, L., 2014, In: International Journal of Molecular Sciences (Online). 15, 12, p. 22539-22562 24 p.

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

An Orc1/Cdc6 ortholog functions as a key regulator in the DNA damage response in Archaea

Sun, M., Feng, X., Liu, Z., Han, W., Liang, Y. X. & She, Q., 2018, In: Nucleic Acids Research. 46, 13, p. 6697-6711

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

Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

Suarez Rodriguez, M. C., Edsgärd, D., Hussain, S. S., Alquezar Planas, D. E., Rasmussen, M., Gilbert, M Thomas P, Nielsen, B. H., Bartels, D. & Mundy, J., Jul 2010, In: The Plant Journal. 63, 2, p. 212-228 17 p.

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

The Interplay Between Immune Response and Bacterial Infection in COPD: Focus Upon Non-typeable Haemophilus influenzae

Su, Y., Jalalvand, F., Thegerström, J. & Riesbeck, K., 2018, In: Frontiers in Immunology. 9, p. 1-26 2530.

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

Functional conservation between Schizosaccharomyces pombe ste8 and Saccharomyces cerevisiae STE11 protein kinases in yeast signal transduction

Styrkársdóttir, U., Egel, Richard, Nielsen, O. & Nielsen, Olaf, 1 Oct 1992, In: Molecular and General Genetics MGG. 235, 1, p. 122-30 9 p.

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

The smt-0 mutation which abolishes mating-type switching in fission yeast is a deletion

Styrkársdóttir, U., Egel, Richard, Nielsen, O. & Nielsen, Olaf, 1 Feb 1993, In: Current Genetics. 23, 2, p. 184-6 3 p.

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

The RNA-splicing factor PSF/p54(nrb) controls DNA-topoisomerase I activity by a direct interaction

Straub, T., Grue, P., Uhse, A., Lisby, Michael, Knudsen, B. R., Tange, T., Westergaard, O. & Boege, F., 9 Oct 1998, In: Journal of Biological Chemistry. 273, 41, p. 26261-26264 4 p.

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

The extraordinary thermal stability of EstA from S. islandicus is independent of post translational modifications

Stiefler-Jensen, D., Schwarz-Linnet, T., de Lichtenberg, C., Nguyen, T. T. T. N., Rand, Kasper Dyrberg, Huang, L., She, Q. & Teilum, Kaare, Sep 2017, In: Protein Science. 26, 9, p. 1819-1827 9 p.

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

Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia

Stephens, N. A., Gallagher, I. J., Rooyackers, O., Skipworth, R. J., Tan, B. H., Marstrand, T. T., Ross, J. A., Guttridge, D. C., Lundell, L., Fearon, K. C. & Timmons, J. A., 2010, In: Genome Medicine. 2, 12 p., 1.

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

Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2

Stedman, K. M., She, Q., Phan, H., Arnold, H. P., Holz, I., Garrett, Roger Antony & Zillig, W., 2003, In: Research in Microbiology. 154, 4, p. 295-302 7 p.

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

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Harvard FlyBase curators, Berkeley Drosophila Genome Project, Hodges, E., Hinrichs, A. S., Caspi, A., Paten, B., Park, S-W., Han, M. V. & 26 others, Maeder, M. L., Polansky, B. J., Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M. W., Park, Y., Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J., Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M. & Kellis, M., 2007, In: Nature. 450, 7167, p. 219-32 13 p.

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

Analysis of Schizosaccharomyces pombe mediator reveals a set of essential subunits conserved between yeast and metazoan cells

Spåhr, H., Samuelsen, C. O., Baraznenok, V., Ernest, I., Huylebroeck, D., Remacle, J. E., Samuelsson, T., Kieselbach, T., Holmberg, Steen & Gustafsson, C. M., 2001, In: Proceedings of the National Academy of Science of the United States of America. 98, 21, p. 11985-11990 5 p.

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

A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination

Song, J., Klümper, U., Riber, Leise, Dechesne, A., Smets, B. F., Sørensen, Søren Johannes & Brandt, Kristian Koefoed, 2020, In: FEMS Microbiology Ecology. 96, 11, 10 p., fiaa200.

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

In vivo activation of STAT3 in cutaneous T-cell lymphoma. Evidence for an antiapoptotic function of STAT3.

Sommer, V. H., Clemmensen, O. J., Nielsen, O., Wasik, M., Lovato, P., Brender, C., Eriksen, K. W., Woetmann, Anders , Kaestel, C. G., Nissen, Mogens Holst, Ropke, C., Skov, Søren & Ødum, Niels, 2004, In: Leukemia. 18, 7, p. 1288-95 7 p.

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

Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas

Sofos, N., Feng, M., Stella, S., Pape, T., Fuglsang, Anders, Lin, Jinzhong, Huang, Q., Li, Y., She, Q. & Montoya, Guillermo, 2020, In: Molecular Cell. 79, 5, p. 741-757

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

Sulfolobus Turreted Icosahedral Virus c92 Protein Responsible for the Formation of Pyramid-Like Cellular Lysis Structures

Snyder, J. C., Brumfield, S. K., Peng, N., She, Q. & Young, M. J., 2011, In: Journal of Virology. 85, 13, p. 6287-92 6 p.

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

Cancer cells become susceptible to natural killer cell killing after exposure to histone deacetylase inhibitors due to glycogen synthase kinase-3-dependent expression of MHC class I-related chain A and B

Skov, Søren, Pedersen, M. T., Andresen, Lars, Straten, P. T., Woetmann, Anders & Ødum, Niels, 2005, In: Cancer Research. 65, 23, p. 11136-45 9 p.

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

A human topoisomerase IIα heterodimer with only one ATP binding site can go through successive catalytic cycles

Skouboe, C., Bjergbaek, L., Østergaard, Vibe Hallundbæk, Larsen, M. K., Knudsen, B. R. & Andersen, A. H., 21 Feb 2003, In: Journal of Biological Chemistry. 278, 8, p. 5768-5774 7 p.

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

The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD⁺

Skjerning, R. B., Senissar, M., Winther, K. S., Gerdes, K. & Brodersen, D. E., 2019, In: Molecular Microbiology. 111, 1, p. 221-236

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

Alarmone (p)ppGpp regulates the transition from pathogenicity to mutualism in Photorhabdus luminescens

Skjerning, R. B., Roghanian, Mohammad, Gerdes, K. & Clarke, D. J., 2016, In: Molecular Microbiology. 100, 4, p. 735-747 13 p.

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

Initiation of DNA replication in Escherichia coli after overproduction of the DnaA protein

Skarstad, K., Løbner-Olesen, Anders, Atlung, T., von Meyenburg, K. & Boye, E., Jul 1989, In: Molecular General Genetics. 218, 1, p. 50-6 7 p.

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

Neuropsychological assessment of chronic non-malignant pain patients treated in a multidisciplinary pain centre

Sjøgren, P., Christrup, Lona Louring, Petersen, Morten & Højsted, J., Aug 2005, In: European Journal of Pain. 9, 4, p. 453-62 10 p.

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

In silico evolution of lysis-lysogeny strategies reproduces observed lysogeny propensities in temperate bacteriophages

Sinha, V., Goyal, A., Svenningsen, Sine Lo, Semsey, S. & Krishna, S., 26 Jul 2017, In: Frontiers in Microbiology. 8, 11 p., 1386.

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

The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis

Sinha, A. K. & Winther, K. S., 2021, In: Communications Biology . 4, 10 p., 434.

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

Fatty acid starvation activates RelA by depleting lysine precursor pyruvate

Sinha, A. K., Winther, K. S., Roghanian, Mohammad & Gerdes, K., 2019, In: Molecular Microbiology. 112, 4, p. 1339-1349

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

The Roles of Bacterial DNA Double-Strand Break Repair Proteins in Chromosomal DNA Replication

Sinha, A. K., Possoz, C. & Leach, D. R. F., 2020, In: FEMS Microbiology Reviews. 44, 3, p. 351-368

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

Bacterial Chromosome Replication and DNA Repair During the Stringent Response

Sinha, A. K., Løbner-Olesen, Anders & Riber, Leise, 2020, In: Frontiers in Microbiology. 11, 9 p., 582113.

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

RAD18-independent ubiquitination of proliferating-cell nuclear antigen in the avian cell line DT40

Simpson, L. J., Ross, A. L., Szüts, D., Alviani, C. A., Østergaard, Vibe Hallundbæk, Patel, K. J. & Sale, J. E., 1 Sep 2006, In: EMBO Reports. 7, 9, p. 927-932 6 p.

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

Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

Simonsen, Bo Thisted, Siegismund, Hans Redlef & Arctander, P., 1998, In: Molecular Ecology. 7, 2, p. 225-37 12 p.

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

Arabidopsis accelerated cell death 11, ACD11, is a ceramide-1-phosphate transfer protein and intermediary regulator of phytoceramide levels

Simanshu, D. K., Zhai, X., Munch, D., Hofius, D., Markham, J. E., Bielawski, J., Bielawska, A., Malinina, L., Molotkovsky, J. G., Mundy, J. W., Patel, D. J. & Brown, R. E., 2014, In: Cell Reports. 6, 2, p. 388-399 12 p.

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

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Siepel, A., Bejerano, G., Pedersen, Jakob Skou, Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., Weinstock, G. M., Wilson, R. K., Gibbs, R. A., Kent, W. J., Miller, W. & Haussler, D., 2005, In: Genome Research. 15, 8, p. 1034-50 16 p.

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

Structure of African elephant populations

Siegismund, Hans Redlef & Arctander, P., 1996, In: Journal of Heredity. 86, 6, p. 467-9 2 p.

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

Molecular cloning of a novel bioH gene from an environmental metagenome encoding a carboxylesterase with exceptional tolerance to organic solvents

Shi, Y., Pan, Y., Li, B., He, W., She, Q. & Chen, L., 2013, In: B M C Biotechnology. 13, 11 p., 13.

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

Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP

Sheppard, C., Blombach, F., Belsom, A., Schulz, S., Daviter, T., Smollett, K., Mahieu, E., Erdmann, S., Tinnefeld, P., Garrett, Roger Antony, Grohmann, D., Rappsilber, J. & Werner, F., 2016, In: Nature Communications. 7, 13 p., 13595.

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

Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus

She, Q., Zhang, C., Deng, L., Peng, N., Chen, Z. & Liang, Y. X., 2009, In: Biochemical Society Transactions. 37, Pt 1, p. 92-6 4 p.

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

Archaea and CRISPR biology

She, Q. & Han, W., 17 Aug 2017, In: Microbiology Today. 44, 3, p. 122-125 4 p.

Research output: Contribution to journal › Journal article › Communication

Minimal enhancer elements of the leghemoglobin lba and lbc3 gene promoters from Glycine max L. have different properties

She, Q., Lauridsen, P., Stougaard, J. & Marcker, K. A., 1993, In: Plant Molecular Biology. 22, 6, p. 945-56 11 p.

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

Comparative sequence analysis of cis elements present in Glycine max L. leghemoglobin lba and lbc3 genes

She, Q., Sandal, N. N., Stougaard, J. & Marcker, K. A., 1993, In: Plant Molecular Biology. 22, 5, p. 931-5 4 p.

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

A distinct role for recombination repair factors in an early cellular response to transcription-replication conflicts

Shao, Xin, Joergensen, A. M., Howlett, N. G., Lisby, Michael & Østergaard, Vibe Hallundbæk, 2020, In: Nucleic Acids Research. 48, 10, p. 5467-5484 18 p.

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

Comparative proteomics and secretomics revealed virulence, and coresistance-related factors in non O1/O139 Vibrio cholerae recovered from 16 species of consumable aquatic animals

Shan, X., Fu, J., Li, X., Peng, Xu & Chen, L., 2022, In: Journal of Proteomics. 251, 15 p., 104408.

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

CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems

Shah, S. A. & Garrett, Roger Antony, 2011, In: Research in Microbiology. 162, 1, p. 27-38 12 p.

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

Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

Shah, S. A., Hansen, Niels Richard & Garrett, Roger Antony, 2009, In: Biochemical Society Transactions. 37, Pt 1, p. 23-8 5 p.

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