A2: Energy-Aware Optimization of Workflows in Bioinformatics

@article{mohammadi2023mathematical,

title = {A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters},

author = {Somayeh Mohammadi and Latif PourKarimi and Felix Droop and De Mecquenem, Ninon and Ulf Leser and Knut Reinert},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {The Journal of Supercomputing},

pages = {1–30},

publisher = {Springer},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Giurgiu2023.11.15.567169,

title = {Decoil: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data},

author = {Mădălina Giurgiu and Nadine Wittstruck and Elias Rodriguez-Fos and Rocío Chamorro González and Lotte Brückner and Annabell Krienelke-Szymansky and Konstantin Helmsauer and Anne Hartebrodt and Richard P. Koche and Kerstin Haase and Knut Reinert and Anton G. Henssen},

url = {https://www.biorxiv.org/content/early/2023/11/17/2023.11.15.567169},

doi = {10.1101/2023.11.15.567169},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex and contain rearranged DNA sequences derived from multiple chromosome locations. As the structure of ecDNA can impact oncogene regulation and may indicate mechanisms of its formation, disentangling it at high resolution from sequencing data is essential. Even though methods have been developed to identify and reconstruct ecDNA in cancer genome sequencing, it remains challenging to resolve complex ecDNA structures, in particular amplicons with shared genomic footprints. We here introduce Decoil, a computational method which combines a breakpoint-graph approach with LASSO regression to reconstruct complex ecDNA and deconvolve co-occurring ecDNA elements with overlapping genomic footprints from long-read nanopore sequencing. Decoil outperforms de-novo assembly methods in simulated long-read sequencing data for both, simple and complex ecDNAs. Applying Decoil on whole genome sequencing data uncovered different ecDNA topologies and explored ecDNA structure heterogeneity in neuroblastoma tumors and cell lines, indicating that this method may improve ecDNA structural analyzes in cancer.Competing Interest StatementA.G.H. is founder of Econic Biosciences Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/corr/abs-2006-03104,

title = {Portability of Scientific Workflows in NGS Data Analysis: A Case  Study},

author = {Christopher Schiefer and Marc Bux and Jörgen Brandt and Clemens Messerschmidt and Knut Reinert and Dieter Beule and Ulf Leser},

url = {https://arxiv.org/abs/2006.03104},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {CoRR},

volume = {abs/2006.03104},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Lambda3: homology search for protein, nucleotide and bisulfite-converted sequences},

author = {Hannes Hauswedell and Sara Hetzel and Simon G. Gottlieb and Helene Kretzmer and Alexander Meissner and Knut Reinert},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}