Computational identification of new structured cis-regulatory elements in the 3′-untranslated region of human protein coding genes

Por Chen, Xiaowei Sylvia, Brown, Chris M.
Publicado em 2012

Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes

Por Donath, Alexander, Jühling, Frank, Al-Arab, Marwa, Bernhart, Stephan H, Reinhardt, Franziska, Stadler, Peter F, Middendorf, Martin, Bernt, Matthias
Publicado no Nucleic Acids Res (2019)

BlastR—fast and accurate database searches for non-coding RNAs

Por Bussotti, Giovanni, Raineri, Emanuele, Erb, Ionas, Zytnicki, Matthias, Wilm, Andreas, Beaudoing, Emmanuel, Bucher, Philipp, Notredame, Cedric
Publicado em 2011

Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data

Por Ragan, Chikako, Mowry, Bryan J., Bauer, Denis C.
Publicado em 2012

Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation

Por Xing, Chuanhua, Bitzer, Donald L., Alexander, Winser E., Vouk, Mladen A., Stomp, Anne-Marie
Publicado em 2009

Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA

Por Boivin, Vincent, Reulet, Gaspard, Boisvert, Olivier, Couture, Sonia, Elela, Sherif Abou, Scott, Michelle S
Publicado no Nucleic Acids Res (2020)

A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential

Por Hill, Steven T, Kuintzle, Rachael, Teegarden, Amy, Merrill, Erich, Danaee, Padideh, Hendrix, David A
Publicado no Nucleic Acids Res (2018)

A new computational method for the detection of horizontal gene transfer events

Por Tsirigos, Aristotelis, Rigoutsos, Isidore
Publicado em 2005

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

Por Philippe, Nicolas, Bou Samra, Elias, Boureux, Anthony, Mancheron, Alban, Rufflé, Florence, Bai, Qiang, De Vos, John, Rivals, Eric, Commes, Thérèse
Publicado em 2014

Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation

Por De Cegli, Rossella, Iacobacci, Simona, Flore, Gemma, Gambardella, Gennaro, Mao, Lei, Cutillo, Luisa, Lauria, Mario, Klose, Joachim, Illingworth, Elizabeth, Banfi, Sandro, di Bernardo, Diego
Publicado em 2013

A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter assays

Por Liu, Ying, Irie, Takuma, Yada, Tetsushi, Suzuki, Yutaka
Publicado no Nucleic Acids Res (2017)

Designing gene libraries from protein profiles for combinatorial protein experiments

Por Wang, Wei, Saven, Jeffery G.
Publicado em 2002

Novel non-coding RNAs in Dictyostelium discoideum and their expression during development

Por Aspegren, Anders, Hinas, Andrea, Larsson, Pontus, Larsson, Anders, Söderbom, Fredrik
Publicado em 2004

Computing folding pathways between RNA secondary structures

Por Dotu, Ivan, Lorenz, William A., Van Hentenryck, Pascal, Clote, Peter
Publicado em 2010

Computational prediction of regulatory, premature transcription termination in bacteria

Por Millman, Adi, Dar, Daniel, Shamir, Maya, Sorek, Rotem
Publicado no Nucleic Acids Res (2017)

TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes

Por González, Aitor, Artufel, Marie, Rihet, Pascal
Publicado no Nucleic Acids Res (2019)

Realistic artificial DNA sequences as negative controls for computational genomics

Por Caballero, Juan, Smit, Arian F. A., Hood, Leroy, Glusman, Gustavo
Publicado em 2014

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

Por Zhou, Bailing, Zhao, Huiying, Yu, Jiafeng, Guo, Chengang, Dou, Xianghua, Song, Feng, Hu, Guodong, Cao, Zanxia, Qu, Yuanxu, Yang, Yuedong, Zhou, Yaoqi, Wang, Jihua
Publicado no Nucleic Acids Res (2018)

A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

Por Garton, Michael, Najafabadi, Hamed S., Schmitges, Frank W., Radovani, Ernest, Hughes, Timothy R., Kim, Philip M.
Publicado no Nucleic Acids Res (2015)

The complex evolutionary history of aminoacyl-tRNA synthetases

Por Chaliotis, Anargyros, Vlastaridis, Panayotis, Mossialos, Dimitris, Ibba, Michael, Becker, Hubert D., Stathopoulos, Constantinos, Amoutzias, Grigorios D.
Publicado no Nucleic Acids Res (2017)