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Bioinformatics (Oxford, England), ISSN 1367-4803, 07/2019
Sequence alignment remains fundamental in bioinformatics. Pair-wise alignment is traditionally based on ad hoc scores for substitutions, insertions, and... 
Journal Article
Genome Biology, ISSN 1474-7596, 03/2019, Volume 20, Issue 1, pp. 58 - 17
Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report... 
Repeat diseases | Long-read sequencing | Nanopore | Tandem repeat | PacBio | LOCALIZATION | CTG REPEAT | GENOME | ALIGNMENT | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | MYOTONIC-DYSTROPHY | TRINUCLEOTIDE REPEAT | Proteins | Disease | Cell division | Genomes | Mutation | Localization | Bioinformatics | Deoxyribonucleic acid--DNA | Methods | Genotypes
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 02/2018, Volume 46, Issue 4, pp. 1661 - 1673
Abstract Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what... 
IONIZING-RADIATION FORMATION | ALIGNMENT | DATABASE | SINGLE-MOLECULE | BIOCHEMISTRY & MOLECULAR BIOLOGY | COMPLEX STRUCTURAL VARIATION | DOUBLE-STRAND BREAKS | UPDATE | CHROMOTHRIPSIS | HUMAN-GENOME | INVERSIONS | Computational Biology
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 03/2011, Volume 39, Issue 4, pp. e23 - e23
Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to... 
DNA-SEQUENCES | ACID SUBSTITUTION MATRICES | DATABASE | COMPARATIVE GENOMICS | BIOCHEMISTRY & MOLECULAR BIOLOGY | Sequence Homology, Amino Acid | DNA - chemistry | Sequence Alignment | Algorithms | Repetitive Sequences, Nucleic Acid | Sequence Analysis, DNA - methods | Sequence Homology, Nucleic Acid | AT Rich Sequence | Methods Online
Journal Article
by Forrest, Alistair R. R and Kawaji, Hideya and Rehli, Michael and Baillie, J. Kenneth and de Hoon, Michiel J. L and Haberle, Vanja and Lassmann, Timo and Kulakovskiy, Ivan V and Lizio, Marina and Itoh, Masayoshi and Andersson, Robin and Mungall, Christopher J and Meehan, Terrence F and Schmeier, Sebastian and Bertin, Nicolas and Jørgensen, Mette and Dimont, Emmanuel and Arner, Erik and Schmidl, Christian and Schaefer, Ulf and Medvedeva, Yulia A and Plessy, Charles and Vitezic, Morana and Severin, Jessica and Semple, Colin A and Ishizu, Yuri and Young, Robert S and Francescatto, Margherita and Alam, Intikhab and Albanese, Davide and Altschuler, Gabriel M and Arakawa, Takahiro and Archer, John A. C and Arner, Peter and Babina, Magda and Rennie, Sarah and Balwierz, Piotr J and Beckhouse, Anthony G and Pradhan-Bhatt, Swati and Blake, Judith A and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessano and Briggs, James and Brombacher, Frank and Burroughs, A. Maxwell and Califano, Anea and Cannistraci, Carlo V and Carbajo, Daniel and Chen, Yun and Chierici, Marco and Ciani, Yari and Clevers, Hans C and Dalla, Emiliano and Davis, Carrie A and Detmar, Michael and Diehl, Alexander D and Dohi, Taeko and bløs, Finn and Edge, Albert S. B and Edinger, Matthias and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and Fagiolini, Michela and Fairbairn, Lynsey and Fang, Hai and Farach-Carson, Mary C and Faulkner, Geoffrey J and Favorov, Alexander V and Fisher, Malcolm E and Frith, Martin C and Fujita, Rie and Fukuda, Shiro and Furlanello, Cesare and Furuno, Masaaki and Furusawa, Jun-ichi and Geijtenbeek, Teunis B and Gibson, Anew P and Gingeras, Thomas and Goldowitz, Daniel and Gough, Julian and Guhl, Sven and Guler, Reto and Gustincich, Stefano and Ha, Thomas J and Hamaguchi, Masahide and Hara, Mitsuko and Harbers, Matthias and Harshbarger, Jayson and Hasegawa, Akira and Hasegawa, Yuki and Hashimoto, Takehiro and Herlyn, Meenhard and Hitchens, Kelly J and Ho Sui, Shannan J and Hofmann, Oliver M and Hoof, Ilka and Hori, Fumi and Huminiecki, Lukasz and ... and FANTOM Consortium and RIKEN PMI CLST DGT and FANTOM Consortium and the RIKEN PMI and CLST (DGT) and The FANTOM Consortium and the RIKEN PMI and CLST (DGT)
Nature, ISSN 0028-0836, 2014, Volume 507, Issue 7493, pp. 462 - +
Journal Article
Nucleic Acids Research, ISSN 1362-4962, 01/2011, Volume 39, Issue 4, pp. 23 - 23
Biological sequences are often analyzed by detecting homologous regions between them. Homology search is confounded by simple repeats, which give rise to... 
Journal Article
Bioinformatics, ISSN 1367-4803, 12/2012, Volume 28, Issue 23, pp. 3144 - 3146
Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the '--add' and '--addfragments' options in the... 
DATABASE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Sequence Alignment - methods | Computational Biology - methods | Software | Algorithms | Phylogeny | Base Sequence | Applications Note
Journal Article
Journal Article
Genome Biology, ISSN 1474-7596, 05/2015, Volume 16, Issue 1, p. 106
Journal Article
Genome Research, ISSN 1088-9051, 03/2011, Volume 21, Issue 3, pp. 487 - 493
Journal Article
Nucleic Acids Research, ISSN 0305-1048, 4/2014, Volume 42, Issue 8, pp. 4823 - 4832
Proximal promoters are fundamental genomic elements for gene expression. They vary in terms of GC percentage, CpG abundance, presence of TATA signal,... 
EVOLUTION | DETERMINANTS | BIOCHEMISTRY & MOLECULAR BIOLOGY | SEQUENCE | GENOME-WIDE ANALYSIS | DIVERSITY | TRANSCRIPTION INITIATION | SELECTION | CPG ISLANDS | EXPRESSION | FEATURES | Promoter Regions, Genetic | Data Interpretation, Statistical | Animals | Humans | Transcription Initiation Site | TATA Box | CpG Islands | Transcription, Genetic | Mice | Computational Biology
Journal Article
by Andersson, Robin and Gebhard, Claudia and Miguel-Escalada, Irene and Hoof, Ilka and Bornholdt, Jette and Boyd, Mette and Chen, Yun and Zhao, Xiaobei and Schmidl, Christian and Suzuki, Takahiro and Ntini, Evgenia and Arner, Erik and Valen, Eivind and Li, Kang and Schwarzfischer, Lucia and Glatz, Dagmar and Raithel, Johanna and Lilje, Berit and Rapin, Nicolas and Bagger, Frederik Otzen and Jørgensen, Mette and Andersen, Peter Refsing and Bertin, Nicolas and Rackham, Owen and Burroughs, A. Maxwell and Baillie, J. Kenneth and Ishizu, Yuri and Shimizu, Yuri and Furuhata, Erina and Maeda, Shiori and Negishi, Yutaka and Mungall, Christopher J and Meehan, Terrence F and Lassmann, Timo and Itoh, Masayoshi and Kawaji, Hideya and Kondo, Naoto and Kawai, Jun and Lennartsson, Aneas and Daub, Carsten O and Heutink, Peter and Hume, David A and Jensen, Torben Heick and Suzuki, Harukazu and Hayashizaki, Yoshihide and Müller, Ferenc and Forrest, Alistair R. R and Carninci, Piero and Rehli, Michael and Sandelin, Albin and de Hoon, Michiel J. L and Haberle, Vanja and Kulakovskiy, Ivan V and Lizio, Marina and Mungall, Christoher J and Schmeier, Sebastian and Dimont, Emmanuel and Schmid, Christian and Schaefer, Ulf and Medvedeva, Yulia A and Plessy, Charles and Vitezic, Morana and Severin, James and Semple, Colin A and Young, Robert S and Francescatto, Margherita and Alam, Intikhab and Albanese, Davide and Altschuler, Gabriel M and Arakawa, Takahiro and Archer, John A. C and Arner, Peter and Babina, Magda and Rennie, Sarah and Balwierz, Piotr J and Beckhouse, Anthony G and Pradhan-Bhatt, Swati and Blake, Judith A and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessano and Briggs, James and Brombacher, Frank and Califano, Anea and Cannistracti, Carlo V and Carbajo, Daniel and Chierici, Marco and Ciani, Yari and Clevers, Hans C and Dalla, Emiliano and Davis, Carrie A and Detmar, Michael and Diehl, Alexander D and Dohi, Taeko and bløs, Finn and Edge, Albert S. B and Edinger, Matthias and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and ... and FANTOM Consortium and The FANTOM Consortium
Nature, ISSN 0028-0836, 2014, Volume 507, Issue 7493, pp. 455 - 461
Journal Article