Zobrazeno 1 - 10
of 113
pro vyhledávání: '"Johannes Söding"'
Autor:
Annika Jochheim, Florian A. Jochheim, Alexandra Kolodyazhnaya, Étienne Morice, Martin Steinegger, Johannes Söding
Publikováno v:
Microbiome, Vol 12, Iss 1, Pp 1-19 (2024)
Abstract Background Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due
Externí odkaz:
https://doaj.org/article/ff87eb465f0a445599013d3df6a4b7e0
Autor:
Saikat Banerjee, Franco L. Simonetti, Kira E. Detrois, Anubhav Kaphle, Raktim Mitra, Rahul Nagial, Johannes Söding
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-16 (2021)
Abstract Trans-acting expression quantitative trait loci (trans-eQTLs) account for ≥70% expression heritability and could therefore facilitate uncovering mechanisms underlying the origination of complex diseases. Identifying trans-eQTLs is challeng
Externí odkaz:
https://doaj.org/article/e01619b9538040d6a7f538976c3ee916
Publikováno v:
Microbiome, Vol 8, Iss 1, Pp 1-15 (2020)
Abstract Background Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without th
Externí odkaz:
https://doaj.org/article/36812ff526fc4f96b38c76bd60b22ef7
Autor:
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
Publikováno v:
BMC Bioinformatics, Vol 20, Iss 1, Pp 1-15 (2019)
Abstract Background HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple seque
Externí odkaz:
https://doaj.org/article/59e6cde7518149c596f2e8cd8b7e6c97
Autor:
Tina Ukmar-Godec, Saskia Hutten, Matthew P. Grieshop, Nasrollah Rezaei-Ghaleh, Maria-Sol Cima-Omori, Jacek Biernat, Eckhard Mandelkow, Johannes Söding, Dorothee Dormann, Markus Zweckstetter
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-15 (2019)
Processing bodies (P-bodies) are non-membrane-bound protein/RNA granules in the cytosol. Here the authors combine bioinformatics, NMR and cell based assays and find that lysine is enriched in the disordered regions of P-body-associated proteins and s
Externí odkaz:
https://doaj.org/article/ba5821511fba49e2bd2ace00270992df
Autor:
Jinmi Choi, Kseniia Lysakovskaia, Gregoire Stik, Carina Demel, Johannes Söding, Tian V Tian, Thomas Graf, Patrick Cramer
Publikováno v:
eLife, Vol 10 (2021)
Enhancer activity drives cell differentiation and cell fate determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human leukemia B-cells to macrop
Externí odkaz:
https://doaj.org/article/2e012031dc084c85b1add7b680e595bb
Autor:
Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players consortium, Silvia N. Crivelli
Publikováno v:
Scientific Reports, Vol 8, Iss 1, Pp 1-18 (2018)
Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field
Externí odkaz:
https://doaj.org/article/b0b847aec1154062a3c86bac14d94e55
Autor:
Martin Steinegger, Johannes Söding
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-8 (2018)
Billions of metagenomic and genomic sequences fill up public datasets, which makes similarity clustering an important and time-critical analysis step. Here, the authors develop Linclust, an algorithm with linear time complexity that can cluster over
Externí odkaz:
https://doaj.org/article/01cb78641dc94c18a3dea062537719c0
Publikováno v:
PLoS Genetics, Vol 14, Iss 12, p e1007856 (2018)
Genetic variants in genome-wide association studies (GWAS) are tested for disease association mostly using simple regression, one variant at a time. Standard approaches to improve power in detecting disease-associated SNPs use multiple regression wit
Externí odkaz:
https://doaj.org/article/19cd8f384cb8424685498d32acf48735
Publikováno v:
PLoS Computational Biology, Vol 14, Iss 11, p e1006526 (2018)
Compensatory mutations between protein residues in physical contact can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment (MSA) of the protein family. Conversely, large coupling coefficien
Externí odkaz:
https://doaj.org/article/fad1e05ac1644b48ae6ee52a0177dec7