Article

Dorney, Ryley, Dhungel, Bijay P., Rasko, John E.J., Hebbard, Lionel, and Schmitz, Ulf (2023) Recent Advances in Cancer Fusion Transcript Detection. Briefings in Bioinformatics, 24 (1). bbac519.

Wong, Alex C.H., Wong, Justin J.-L., Rasko, John E.J., and Schmitz, Ulf (2023) SpliceWiz: Interactive analysis and visualization of alternative splicing in R. Briefings in Bioinformatics, 25 (1).

Sidorczuk, Katarzyna, Gagat, Przemyslaw, Pietluch, Filip, Kala, Jakub, Rafacz, Dominik, Bakala, Laura, Slowik, Jadwiga, Kolenda, Rafal, Rodiger, Stefan, Fingerhut, Legana C.H.W., Cooke, Ira R., Mackiewicz, Pawel, and Burdukiewicz, Michal (2022) Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data. Briefings in Bioinformatics, 23 (5). bbac343.

Chuah, Aaron, Li, Sean, Do, Andrea, Field, Matt, and Andrews, Daniel (2022) StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritize potentially pathogenic genetic variation. Bioinformatics, 38 (17). pp. 4220-4222.

Nauheimer, Lars, Weigner, Nicholas, Joyce, Elizabeth, Crayn, Darren, Clarke, Charles, and Nargar, Katharina (2021) HybPhaser: a workflow for the detection and phasing of hybrids in target capture data sets. Applications in Plant Sciences, 9 (7). e11441.

Wu, Siyuan, Cui, Tiangang, Zhang, Xinan, and Tian, Tianhai (2020) A non-linear reverse-engineering method for inferring genetic regulatory networks. PeerJ, 8. e9065.

Thang, Mike W. C., Chua, Xin-Yi, Price, Gareth, Gorse, Dominique, and Field, Matt A. (2019) MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data [version 2; peer review: 2 approved]. F1000Research, 8. 726.

Field, Matthew A., Burgio, Gaetan, Chuah, Aaron, Al Shekaili, Jalila, Hassan, Batool, Al Sukaiti, Nashat, Foote, Simon J., Cook, Matthew C., and Andrews, Daniel T. (2019) Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics, 20 (Suppl 8). 546.

Lai, Xin, Eberhardt, Martin, Schmitz, Ulf, and Vera, Julio (2019) Systems biology-based investigation of cooperating microRNAs as monotherapy or adjuvant therapy in cancer. Nucleic Acids Research, 47 (15). pp. 7753-7766.

Monteuuis, Geoffray, Wong, Justin J.L., Bailey, Charles G., Schmitz, Ulf, and Rasko, John E.J. (2019) The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Research, 47 (22). pp. 11497-11513.

Vanichkina, Darya P., Schmitz, Ulf, Wong, Justin J.-L., and Rasko, John E.J. (2018) Challenges in defining the role of intron retention in normal biology and disease. Seminars in Cell and Developmental Biology, 75. pp. 40-49.

Lai, Xin, Gupta, Shailendra K., Schmitz, Ulf, Marquardt, Stephan, Knoll, Susanne, Spitschak, Alf, Wolkenhauer, Olaf, Pützer, Brigitte M., and Vera, Julio (2018) MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance. Theranostics, 8 (4). pp. 1106-1120.

Flaherty, Briana R., Talundzic, Eldin, Barratt, Joel, Kines, Kristine J., Olsen, Christian, Lane, Meredith, Sheth, Mili, and Bradbury, Richard S. (2018) Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. Microbiome, 6 (1). 164.

Chambers, Matthew C., Jagtop, Pratik D., Johnson, James E., McGowan, Thomas, Kumar, Praveen, Onsongo, Getiria, Guerrero, Candace R., Barsnes, Harald, Vaudel, Marc, Martens, Lennart, Grüning, Björn, Cooke, Ira, Heydarian, Mohammad, Reddy, Karen L., and Griffin, Timothy J. (2017) An accessible proteogenomics informatics resource for cancer researchers. Cancer Research, 77 (21). E43-E46.

Schmitz, Ulf, Naderi-Meshkin, Hojjat, Gupta, Shailendra K., Wolkenhauer, Olaf, and Vera, Julio (2016) The RNA world in the 21st century-a systems approach to finding non-coding keys to clinical questions. Briefings in Bioinformatics, 17 (3). pp. 380-392.

Wolfien, Markus, Rimmbach, Christian, Schmitz, Ulf, Jung, Julia Jeannine, Krebs, Stefan, Steinhoff, Gustav, David, Robert, and Wolkenhauer, Olaf (2016) TRAPLINE: A standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation. BMC Bioinformatics, 17. 21.

Amirkhah, Raheleh, Farazmand, Ali, Gupta, Shailendra K., Ahmadi, Hamed, Wolkenhauer, Olaf, and Schmitz, Ulf (2015) Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer. Molecular BioSystems, 11. pp. 2126-2134.

Schmitz, Ulf, Lai, Xin, Winter, Felix, Wolkenhauer, Olaf, Vera, Julio, and Gupta, Shailendra (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Research, 42 (12). pp. 7539-7552.

Lai, Xin, Schmitz, Ulf, Gupta, Shailendra K., Bhattacharya, Animesh, Kunz, Manfred, Wolkenhauer, Olaf, and Vera, Julio (2012) Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs. Nucleic Acids Research, 40 (18). pp. 8818-8834.

Gupta, Shailendra K., Gupta, Shishir K., Smita, Suchi, Srivastava, Mugdha, Lai, Xin, Schmitz, Ulf, Rahman, Qamar, Wolkenhauer, Olaf, and Vera, Julio (2011) Computational analysis and modeling the effectiveness of 'Zanamivir' targeting neuraminidase protein in pandemic H1N1 strains. Infection, Genetics and Evolution, 11 (5). pp. 1072-1082.

Raasch, Peter, Schmitz, Ulf, Patenge, Nadja, Vera, Julio, Kreikemeyer, Bernd, and Wolkenhauer, Olaf (2010) Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinformatics, 11. 491.

Book Chapter

Schmitz, Ulf, Monteuuis, Geoffray, Petrova, Veronika, Shah, Jaynish S., and Rasko, John E.J. (2021) Computational methods for intron retention identification and quantification. In: Wolkenhauer, Olaf, Cai, Yudong, and Rozman, Damjana, (eds.) Systems Medicine: integrative, qualitative and computational approaches. Academic Press, London Wall, United Kingdom, pp. 63-74.

Schmitz, Ulf, Gupta, Shailendra K., Vera, Julio, and Wolkenhauer, Olaf (2019) Computational approaches in microRNA biology. In: Narayan, Roger, (ed.) Encyclopedia of Biomedical Engineering. Elsevier, Amsterdam, The Netherlands, pp. 317-330.

Amirkhah, Raheleh, Meshkin, Hojjat Naderi, Farazmand, Ali, Rasko, John E.J., and Schmitz, Ulf (2017) Computational and experimental identification of tissue-specific MicroRNA targets. In: Dalmay, Tamas, (ed.) MicroRNA Detection and Target Identification: methods and protocols. Methods in Molecular Biology, 1580 . Humana Press Inc., New York, NY, USA, pp. 127-147.

Amirkhah, Raheleh, Farazmand, Ali, Wolkenhauer, Olaf, and Schmitz, Ulf (2016) RNA systems biology for cancer: From diagnosis to therapy. In: Scmitz, U., and Wolkenhauer, O., (eds.) Systems Medicine. Methods in Molecular Biology, 1386 . Springer, New York, NY, USA, pp. 305-330.

Vera, Julio, Wolkenhauer, Olaf, and Schmitz, Ulf (2014) Cancer Systems Biology: Current Achievements in – Omics Data Analysis, Network Reconstruction and Mathematical Modelling. In: UNSPECIFIED, (ed.) Encyclopedia of Life Sciences. John Wiley & Sons, Chichester, UK, pp. 1-12.

Conference Item

Gill, Jaskaran, Chetty, Madhu, Shatte, Adrian, and Hallinan, Jennifer (2021) Dynamically Regulated Initialization for S-system Modelling of Genetic Networks. In: Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. From: CIBCB 2021: IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 13-15 October 2021, Melbourne, VIC, Australia.

Gamage, Hasini Nakulugamuwa, Chetty, Madhu, Shatte, Adrian, and Hallinan, Jennifer (2021) An Efficient Boolean Modelling Approach for Genetic Network Inference. In: Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology. From: CIBCB 2021: IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 13-15 October 2021, Melbourne, VIC, Australia.

Gamage, Hasini Nakulugamuwa, Chetty, Madhu, Shatte, Adrian, and Hallinan, Jennifer (2021) Efficient Ensemble Feature Selection Based Boolean Modelling for Genetic Network Inference. In: Supplemental Proceedings Of Short Papers (Non-peer reviewed) of IEEE CIBCB 2021. pp. 19-20. From: CIBCB 2021: 18th IEEE International Conference in Computational Intelligence in Bioinformatics and Computational Biology, 13-15 October 2021, Melbourne, Australia.

Gill, Jaskaran, Chetty, Madhu, Shatte, Adrian, and Hallinan, Jennifer (2021) Use of known gene-gene interactions in S-system based GRN inference. In: Supplemental Proceedings Of Short Papers (Non-peer reviewed) of IEEE CIBCB 2021. pp. 21-22. From: CIBCB 2021: 18th IEEE International Conference in Computational Intelligence in Bioinformatics and Computational Biology, 13-15 October 2021, Melbourne, Australia.