Search Results - "Tanzer, Andrea"

GENCODE: the reference human genome annotation for The ENCODE Project by Harrow, Jennifer, Frankish, Adam, Gonzalez, Jose M, Tapanari, Electra, Diekhans, Mark, Kokocinski, Felix, Aken, Bronwen L, Barrell, Daniel, Zadissa, Amonida, Searle, Stephen, Barnes, If, Bignell, Alexandra, Boychenko, Veronika, Hunt, Toby, Kay, Mike, Mukherjee, Gaurab, Rajan, Jeena, Despacio-Reyes, Gloria, Saunders, Gary, Steward, Charles, Harte, Rachel, Lin, Michael, Howald, Cédric, Tanzer, Andrea, Derrien, Thomas, Chrast, Jacqueline, Walters, Nathalie, Balasubramanian, Suganthi, Pei, Baikang, Tress, Michael, Rodriguez, Jose Manuel, Ezkurdia, Iakes, van Baren, Jeltje, Brent, Michael, Haussler, David, Kellis, Manolis, Valencia, Alfonso, Reymond, Alexandre, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J

“…The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and…”
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RNA modifications in structure prediction – Status quo and future challenges by Tanzer, Andrea, Hofacker, Ivo L., Lorenz, Ronny

“…•Review on RNA modifications (I,Y,m6A) in the light of RNA structures.•Modification requires substrate structures.•Consequences of RNA modification on…”
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multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection by Hoffmann, Steve, Otto, Christian, Doose, Gero, Tanzer, Andrea, Langenberger, David, Christ, Sabina, Kunz, Manfred, Holdt, Lesca M, Teupser, Daniel, Hackermüller, Jörg, Stadler, Peter F

“…Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through…”
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Predicting RNA secondary structures from sequence and probing data by Lorenz, Ronny, Wolfinger, Michael T., Tanzer, Andrea, Hofacker, Ivo L.

“…•An introduction to algorithms for the prediction of RNA secondary structures is given.•State of the art methods for consensus structures, RNA-RNA…”
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Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs by Deforges, Jules, Reis, Rodrigo S, Jacquet, Philippe, Sheppard, Shaoline, Gadekar, Veerendra P, Hart-Smith, Gene, Tanzer, Andrea, Hofacker, Ivo L, Iseli, Christian, Xenarios, Ioannis, Poirier, Yves

“…Cis-Natural Antisense Transcripts (cis-NATs), which overlap protein coding genes and are transcribed from the opposite DNA strand, constitute an important…”
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Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution by Sedlyarov, Vitaly, Fallmann, Jörg, Ebner, Florian, Huemer, Jakob, Sneezum, Lucy, Ivin, Masa, Kreiner, Kristina, Tanzer, Andrea, Vogl, Claus, Hofacker, Ivo, Kovarik, Pavel

“…Precise regulation of mRNA decay is fundamental for robust yet not exaggerated inflammatory responses to pathogens. However, a global model integrating…”
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Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome by Korbel, Jan O, Urban, Alexander Eckehart, Affourtit, Jason P, Godwin, Brian, Grubert, Fabian, Simons, Jan Fredrik, Kim, Philip M, Palejev, Dean, Carriero, Nicholas J, Du, Lei, Taillon, Bruce E, Chen, Zhoutao, Tanzer, Andrea, Saunders, A.C. Eugenia, Chi, Jianxiang, Yang, Fengtang, Carter, Nigel P, Hurles, Matthew E, Weissman, Sherman M, Harkins, Timothy T, Gerstein, Mark B, Egholm, Michael, Snyder, Michael

“…Structural variation of the genome involves kilobase- to megabase-sized deletions, duplications, insertions, inversions, and complex combinations of…”
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Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq) by Lagarde, Julien, Uszczynska-Ratajczak, Barbara, Santoyo-Lopez, Javier, Gonzalez, Jose Manuel, Tapanari, Electra, Mudge, Jonathan M., Steward, Charles A., Wilming, Laurens, Tanzer, Andrea, Howald, Cédric, Chrast, Jacqueline, Vela-Boza, Alicia, Rueda, Antonio, Lopez-Domingo, Francisco J., Dopazo, Joaquin, Reymond, Alexandre, Guigó, Roderic, Harrow, Jennifer

“…Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a…”
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A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation by Hess, Lena, Moos, Verena, Lauber, Arnel A, Reiter, Wolfgang, Schuster, Michael, Hartl, Natascha, Lackner, Daniel, Boenke, Thorina, Koren, Anna, Guzzardo, Paloma M, Gundacker, Brigitte, Riegler, Anna, Vician, Petra, Miccolo, Claudia, Leiter, Susanna, Chandrasekharan, Mahesh B, Vcelkova, Terezia, Tanzer, Andrea, Jun, Jun Qi, Bradner, James, Brosch, Gerald, Hartl, Markus, Bock, Christoph, Bürckstümmer, Tilmann, Kubicek, Stefan, Chiocca, Susanna, Bhaskara, Srividya, Seiser, Christian

“…The class I histone deacetylases are essential regulators of cell fate decisions in health and disease. While pan- and class-specific HDAC inhibitors are…”
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Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression by Pervouchine, Dmitri D., Djebali, Sarah, Breschi, Alessandra, Davis, Carrie A., Barja, Pablo Prieto, Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Zaleski, Chris, See, Lei-Hoon, Fastuca, Meagan, Drenkow, Jorg, Wang, Huaien, Bussotti, Giovanni, Pei, Baikang, Balasubramanian, Suganthi, Monlong, Jean, Harmanci, Arif, Gerstein, Mark, Beer, Michael A., Notredame, Cedric, Guigó, Roderic, Gingeras, Thomas R.

“…Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of a large and…”
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Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library by Korbel, Jan O, Gerstein, Mark B, Lam, Hugo Y K, Mu, Xinmeng Jasmine, Stütz, Adrian M, Tanzer, Andrea, Cayting, Philip D, Snyder, Michael, Kim, Philip M

“…Sequencing a person's genome may reveal large DNA insertions and other structural rearrangements, but assessing their effects requires pinpointing them to…”
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Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells by Hölzer, Martin, Krähling, Verena, Amman, Fabian, Barth, Emanuel, Bernhart, Stephan H., Carmelo, Victor A. O., Collatz, Maximilian, Doose, Gero, Eggenhofer, Florian, Ewald, Jan, Fallmann, Jörg, Feldhahn, Lasse M., Fricke, Markus, Gebauer, Juliane, Gruber, Andreas J., Hufsky, Franziska, Indrischek, Henrike, Kanton, Sabina, Linde, Jörg, Mostajo, Nelly, Ochsenreiter, Roman, Riege, Konstantin, Rivarola-Duarte, Lorena, Sahyoun, Abdullah H., Saunders, Sita J., Seemann, Stefan E., Tanzer, Andrea, Vogel, Bertram, Wehner, Stefanie, Wolfinger, Michael T., Backofen, Rolf, Gorodkin, Jan, Grosse, Ivo, Hofacker, Ivo, Hoffmann, Steve, Kaleta, Christoph, Stadler, Peter F., Becker, Stephan, Marz, Manja

“…The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the…”
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The expansion of the metazoan microRNA repertoire by Hertel, Jana, Lindemeyer, Manuela, Missal, Kristin, Fried, Claudia, Tanzer, Andrea, Flamm, Christoph, Hofacker, Ivo L, Stadler, Peter F

“…MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA…”
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Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals by Lynch, Vincent J, Tanzer, Andrea, Wang, Yajun, Leung, Frederick C, Gellersen, Birgit, Emera, Deena, Wagner, Gunter P

“…Evolutionary change in gene regulation can result from changes in cis-regulatory elements, leading to differences in the temporal and spatial expression of…”
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Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome by Howald, Cédric, Tanzer, Andrea, Chrast, Jacqueline, Kokocinski, Felix, Derrien, Thomas, Walters, Nathalie, Gonzalez, Jose M, Frankish, Adam, Aken, Bronwen L, Hourlier, Thibaut, Vogel, Jan-Hinnerk, White, Simon, Searle, Stephen, Harrow, Jennifer, Hubbard, Tim J, Guigó, Roderic, Reymond, Alexandre

“…Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome…”
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Evolution of microRNAs located within Hox gene clusters by Tanzer, Andrea, Amemiya, Chris T., Kim, Chang-Bae, Stadler, Peter F.

“…MicroRNAs (miRNAs) form an abundant class of non‐coding RNA genes that have an important function in post‐transcriptional gene regulation and in particular…”
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Animal snoRNAs and scaRNAs with exceptional structures by Marz, Manja, Gruber, Andreas R., Höner zu Siederdissen, Christian, Amman, Fabian, Badelt, Stefan, Bartschat, Sebastian, Bernhart, Stephan H., Beyer, Wolfgang, Kehr, Stephanie, Lorenz, Ronny, Tanzer, Andrea, Yusuf, Dilmurat, Tafer, Hakim, Hofacker, Ivo L., Stadler, Peter F.

“…The overwhelming majority of small nucleolar RNAs (snoRNAs) fall into two clearly defined classes characterized by distinctive secondary structures and sequence…”
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RNAs everywhere: genome-wide annotation of structured RNAs by Backofen, Rolf, Bernhart, Stephan H., Flamm, Christoph, Fried, Claudia, Fritzsch, Guido, Hackermüller, Jörg, Hertel, Jana, Hofacker, Ivo L., Missal, Kristin, Mosig, Axel, Prohaska, Sonja J., Rose, Dominic, Stadler, Peter F., Tanzer, Andrea, Washietl, Stefan, Will, Sebastian

“…Starting with the discovery of microRNAs and the advent of genome‐wide transcriptomics, non‐protein‐coding transcripts have moved from a fringe topic to a…”
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Comparative promoter region analysis powered by CORG by Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, Vingron, Martin

“…Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription…”
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AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements by Fallmann, Jörg, Sedlyarov, Vitaly, Tanzer, Andrea, Kovarik, Pavel, Hofacker, Ivo L

“…AREsite2 represents an update for AREsite, an on-line resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3'UTR sequences. The new…”
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