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Section for Bioinformatics and Computational Biology

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Christensen, S., Jensen, K., Mailund & Kristensen, L. M. (2001). State space methods for coloured Petri nets. In Proceedings of the 2nd international colloquium on Petri net technologies for modelling communication based systems (pp. 14-15)

Christensen, S., Kristensen, L. M. & Mailund (2001). A Sweep-Line Method for State Space Exploration. In Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2001) (pp. 450-464)

Christensen, S., Kristensen, L. M. & Mailund (2001). Condensed State Spaces for Timed Petri Nets. In Proceedings of International Conference on Application and Theory of Petri Nets (ICATPN 2001) (pp. 101-120)

Christensen, O. F., Hobolth, A. & Jensen, J. L. (2005). Pseudo-likelihood analysis of codon substitution models with neighbor dependent rates. Journal of Computational Biology, 12, 1166-1182.

Christensen, O. F., Roberts, G. & Rosenthal, J. (2005). Scaling limits for the transient phase of local Metropolis-Hastings algorithms. Journal of the Royal Statistical Society, Series B, 67, 253-268.

Christensen, S., Schöller, S., Schierup, M. H., Vestergaard, B. F. & Mordhorst, C. H. (2002). Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains. APMIS, 110, 113-122.

Christensen, O. F., Cassiani, G., Diggle, P. J., Ribeiro, P. J. & Andreotti, G. (2004). Statistical estimation of the relative efficiency of natural attenuation mechanisms in contaminated aquifers. Stochastic environmental research and risk assessment (SERRA), 18, 339-350.

Christensen, O. F., Frydenberg, M., Jensen, J. L. & Pedersen, J. G. (2005). Tests and Confidence Intervals for an Extended Variance Component Using the Modified Likelihood Ratio Statistic.

Christensen, O. F., Roberts, G. & Sköld, M. (2006). Robust Markov chain Monte Carlo methods for spatial generalised linear mixed models. Journal of Computational and Graphical Statistics, 15, 1-17.

Christensen, O. F. (2006). Pseudo-likelihood for non-reversible nucleotide substitution models with neighbour dependent rates. Statistical Applications in Genetics and Molecular Biology, 5(18).

Christensen, L. L., Wikman, F., Wiuf, C., Madsen, B. E., Andersen, C. L. & Ørntoft, T. F. (2007). Genetic Variants in MLH1 and MSH2 are not Associated with the Development of Sporadic Colorectal Cancer in Denmark. Poster session presented at The 2nd Biennial Scientific Meeting of the International Society for Gastrointestinal Hereditary Tumours, Yokohama, Japan.

Christensen, L. L., Wikman, F., Wiuf, C., Madsen, B. E., Overvad, K., Tjønnland, A., Koed, K. & Ørntoft, T. F. (2006). The Association of Missense and Silent Mutations with the Development of sporadic and Familial Breast Cancer in the Danish Population. Poster session presented at 19th Meeting of the European Association for Cancer Research, Budapest, Hungary.

Christensen, O. F., Frydenberg, M., Jensen, J. L. & Pedersen, J. G. (2007). Tests and confidence intervals for an extended variance component using the modified likelihood ratio statistic. Scandinavian Journal of Statistics, 34(2), 347-364. https://doi.org/10.1111/j.1467-9469.2006.00520.x

Christensen, L. L., Madsen, B. E., Wikman, F. P., Wiuf, C., Koed, K., Tjønneland, A., Olsen, A. V., Syvänen, A.-C., Andersen, C. L. & Orntoft, T. F. (2008). The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population. BMC Medical Genetics, 9, 52. https://doi.org/10.1186/1471-2350-9-52

Christensen, D. S., Ahrenfeldt, J., Sokač, M., Kisistók, J., Thomsen, M. K., Maretty, L., McGranahan, N. & Birkbak, N. J. (2022). Treatment Represents a Key Driver of Metastatic Cancer Evolution. Cancer Research, 82(16), 2918-2927. https://doi.org/10.1158/0008-5472.CAN-22-0562

Christensen, M. H., Drue, S. O., Rasmussen, M. H., Frydendahl, A., Lyskjær, I., Demuth, C., Nors, J., Gotschalck, K. A., Iversen, L. H., Andersen, C. L. & Pedersen, J. S. (2023). Dreams: deep read-level error model for sequencing data applied to low-frequency variant calling and circulating tumor DNA detection. Genome Biology, 24(1), 99. Article 99. https://doi.org/10.1186/s13059-023-02920-1

Christensen, D. S. & Birkbak, N. J. (2023). Therapy drives genomic evolution in metastatic cancer. OncoTarget, 14(1), 216-218. https://doi.org/10.18632/oncotarget.28379

Cheng, J. Y. & Mailund, T. (2015). Ancestral population genomics using coalescence hidden Markov models and heuristic optimisation algorithms. Computational Biology and Chemistry, 57, 80-92. https://doi.org/10.1016/j.compbiolchem.2015.02.001

Cheng, J. Y., Mailund, T. & Nielsen, R. (2017). Fast admixture analysis and population tree estimation for SNP and NGS data. Bioinformatics (Online), 33(14), 2148–2155. https://doi.org/10.1093/bioinformatics/btx098

Cheng, J. Y. & Mailund, T. (2020). Ancestral population genomics with Jocx, a coalescent hidden markov model. In J. Y. Dutheil (Ed.), Statistical population genomics (pp. 167-189). Humana Press. https://doi.org/10.1007/978-1-0716-0199-0_8

Cheng, Z., Buggiotti, L., Salavati, M., Marchitelli, C., Palma-Vera, S., Wylie, A., Takeda, H., Tang, L., Crowe, M. A., Wathes, D. C. & GplusE Consortium (2021). Global transcriptomic profiles of circulating leucocytes in early lactation cows with clinical or subclinical mastitis. Molecular Biology Reports, 48, 4611-4623. https://doi.org/10.1007/s11033-021-06494-8

Cheng, Z., Wylie, A., Ferris, C., Ingvartsen, K. L., Wathes, D. C. & GplusE Consortium (2021). Effect of diet and nonesterified fatty acid levels on global transcriptomic profiles in circulating peripheral blood mononuclear cells in early lactation dairy cows. Journal of Dairy Science, 104(9), 10059-10075. https://doi.org/10.3168/jds.2021-20136

Cheng, Z., Palma-Vera, S., Buggiotti, L., Salavati, M., Becker, F., Werling, D., Wathes, D. C. & GplusE Consortium (2022). Transcriptomic analysis of circulating leukocytes obtained during the recovery from clinical mastitis caused by escherichia coli in Holstein dairy cows. Animals, 12(16), 1-22. Article 2146. https://doi.org/10.3390/ani12162146

Cheng, Z., McLaughlin, D. L., Little, M. W., Ferris, C., Salavati, M., Ingvartsen, K. L., Crowe, M. A., Wathes, D. C. & GplusE Consortium (2023). Proportion of Concentrate in the Diet of Early Lactation Dairy Cows Has Contrasting Effects on Circulating Leukocyte Global Transcriptomic Profiles, Health and Fertility According to Parity. International Journal of Molecular Sciences , 24(1), Article 39. https://doi.org/10.3390/ijms24010039

Cheng, Z., Ferris, C., Crowe, M. A., Ingvartsen, K. L., Grelet, C., Vanlierde, A., Foldager, L., Becker, F., Wathes, D. C. & GplusE Consortium (2023). Hepatic global transcriptomic profiles of Holstein cows according to parity reveal age-related changes in early lactation. International Journal of Molecular Sciences , 24(12), Article 9906. https://doi.org/10.3390/ijms24129906

Cheng, Z., Little, M. W., Ferris, C., Takeda, H., Ingvartsen, K. L., Crowe, M. A., Wathes, D. C. & GplusE Consortium (2023). Influence of the concentrate inclusion level in a grass silage-based diet on hepatic transcriptomic profiles in Holstein-Friesian dairy cows in early lactation. Journal of Dairy Science, 106(8), 5805-5824. https://doi.org/10.3168/jds.2022-22860

Cheng, J. Y. (2016). Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics. http://www.jade-cheng.com/au/tmp/thesis/thesis.pdf

Chen, Y., Vanderick, S., Mota, R. R., Grelet, C., GplusE Consortium & Gengler, N. (2021). Estimation of genetic parameters for predicted nitrogen use efficiency and losses in early lactation of Holstein cows. Journal of Dairy Science, 104(4), 4413-4423. https://doi.org/10.3168/jds.2020-18849

Chen, J., Bataillon, T., Glémin, S. & Lascoux, M. (2022). What does the distribution of fitness effects of new mutations reflect? Insights from plants. New Phytologist, 233(4), 1613-1619. https://doi.org/10.1111/nph.17826

Chen, J., Bataillon, T., Glémin, S. & Lascoux, M. (2022). Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations. Genome Biology and Evolution, 14(1), Article evab151. https://doi.org/10.1093/gbe/evab151

Chen, Y., Atashi, H., Mota, R. R., Grelet, C., Vanderick, S., Hu, H., GplusE Consortium & Gengler, N. (2023). Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation. Journal of Animal Breeding and Genetics, 140(6), 695-706. https://doi.org/10.1111/jbg.12819

Chen, Y., Atashi, H., Grelet, C., Mota, R. R., Vanderick, S., Hu, H., GplusE Consortium & Gengler, N. (2023). Genome-wide association study and functional annotation analyses for nitrogen efficiency index and its composition traits in dairy cattle. Journal of Dairy Science, 106(5), 3397-3410. https://doi.org/10.3168/jds.2022-22351

Chen, G., Kobek-Kjeldager, C., Jensen, L. D., Kristensen, J. K., Kaiser, M., Thodberg, K., Zhang, G., Rong, L., Herskin, M. S. & Foldager, L. (2024). Experimental study on temperature difference between the interior and exterior of the vehicle transporting weaner pigs. Biosystems Engineering, 247, 119-131. https://doi.org/10.1016/j.biosystemseng.2024.09.001

Chatwin, H., Holde, K., Yilmaz, Z., Larsen, J. T., Albiñana, C., Vilhjálmsson, B. J., Mortensen, P. B., Thornton, L. M., Bulik, C. M. & Petersen, L. V. (2023). Risk factors for anorexia nervosa: A population-based investigation of sex differences in polygenic risk and early life exposures. International Journal of Eating Disorders, 56(9), 1703-1716. https://doi.org/10.1002/eat.23997

Charmouh, A. P., Bocedi, G. & Hartfield, M. (2023). Inferring the distributions of fitness effects and proportions of strongly deleterious mutations. G3: Genes, Genomes, Genetics, 13(9), Article jkad140. https://doi.org/10.1093/g3journal/jkad140

Charmouh, A. P., Porsborg, P. S., Hansen, L. T., Besenbacher, S., Boeg Winge, S., Almstrup, K., Hobolth, A., Bataillon, T. & Schierup, M. H. (2025). Estimating Gene Conversion Tract Length and Rate From PacBio HiFi Data. Molecular Biology and Evolution, 42(2), Article msaf019. https://doi.org/10.1093/molbev/msaf019

Charlesworth, D., Bartolomé, C., Schierup, M. H. & Mable, B. K. (2003). Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol. Biol. Evol., 20(11), 1741-1753.

Charlesworth, D., Mable, B. K., Schierup, M. H., Bartolomé, C., Awadalla, P. & Schierup, M. H. (2003). Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata. Genetics, 164, 1519-1535.

Chalmer, M. A., Kogelman, L. J. A., Ullum, H., Sørensen, E., Didriksen, M., Mikkelsen, S., Dinh, K. M., Brodersen, T., Nielsen, K. R., Bruun, M. T., Banasik, K., Brunak, S., Erikstrup, C., Pedersen, O. B., Ostrowski, S. R., Olesen, J. & Hansen, T. F. (2023). Population-Based Characterization of Menstrual Migraine and Proposed Diagnostic Criteria. JAMA Network Open, 6(5), e2313235. Article e2313235. https://doi.org/10.1001/jamanetworkopen.2023.13235

Cavassim, M. I. A., Moeskjær, S., Moslemi, C., Fields, B., Bachmann, A., Vilhjálmsson, B. J., Schierup, M. H., W Young, J. P. & Andersen, S. U. (2020). Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex. Microbial Genomics, 6(4), Article 000351. https://doi.org/10.1099/mgen.0.000351

Cavassim, M. I. A., Andersen, S. U., Bataillon, T. & Schierup, M. H. (2021). Recombination facilitates adaptive evolution in rhizobial soil bacteria. Molecular Biology and Evolution, 38(12), 5480-5490. https://doi.org/10.1093/molbev/msab247

Cavassim, M. I. A., Baker, Z., Hoge, C., Schierup, M. H., Schumer, M. & Przeworski, M. (2022). PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. Proceedings of the National Academy of Sciences (PNAS), 119(9), Article e2114401119. https://doi.org/10.1073/pnas.2114401119

Cavassim, M. I. A. (2020). Recombination and horizontal gene transfer through the lens of phylogenomics. [PhD dissertation, Aarhus University]. Aarhus Universitet.

Castric, V., Bechsgaard, J., Schierup, M. H. & Vekemans, X. (2008). Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genetics, 4(8), e1000168. https://doi.org/10.1371/journal.pgen.1000168

Castric, V., Bechsgaard, J. S., Grenier, S., Noureddine, R., Schierup, M. H. & Vekemans, X. (2010). Molecular evolution within and between self-incompatibility specificities. Molecular Biology and Evolution, 27(1), 11-20. https://doi.org/10.1093/molbev/msp224

Castenschiold, C. D. F., Mignani, C., Christiansen, S., Alsved, M., Ickes, L., Tesson, S. V. M., Löndahl, J., Bilde, M., Bataillon, T., Finster, K. & Šantl-Temkiv, T. (2025). Atmospheric Biogenic Ice-Nucleating Particles Link to Microbial Communities in the Arctic Marine Environment in Western Greenland. Environmental Science and Technology, 59(42), 22518-22532. https://doi.org/10.1021/acs.est.5c03650

Castellano, D., James, J. & Eyre-Walker, A. (2018). Nearly Neutral Evolution across the Drosophila melanogaster Genome. Molecular Biology and Evolution, 35(11), 2685-2694. https://doi.org/10.1093/molbev/msy164

Castellano, D., Macià, M. C., Tataru, P., Bataillon, T. & Munch, K. (2019). Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes. Genetics, 213(3), 953-966. https://doi.org/10.1534/genetics.119.302494

Castellano, D., Eyre-Walker, A. & Munch, K. (2019). Impact of mutation rate and selection at linked sites on DNA variation across the genomes of humans and other homininae. Genome Biology and Evolution, 12(1), 3550-3561. https://doi.org/10.1093/gbe/evz215

Castellano, D. & Munch, K. (2020). Population Genomics in the Great Apes. In J. Y. Dutheil (Ed.), Methods in Molecular Biology (pp. 453-463). Springer. https://doi.org/10.1007/978-1-0716-0199-0_19

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