An illuminated view of molecular biology

Por Barash, Yoseph, Wang, Xinchen
Publicado em 2010

Integrative deep models for alternative splicing

Por Jha, Anupama, Gazzara, Matthew R, Barash, Yoseph
Publicado no Bioinformatics (2017)

Model-based detection of alternative splicing signals

Por Barash, Yoseph, Blencowe, Benjamin J., Frey, Brendan J.
Publicado em 2010

Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations

Por Lee, David S. M., Ghanem, Louis R., Barash, Yoseph
Publicado no Nat Commun (2020)

MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data

Por Green, Christopher J, Gazzara, Matthew R, Barash, Yoseph
Publicado no Bioinformatics (2018)

In silico to in vivo splicing analysis using splicing code models

Por Gazzara, Matthew R., Vaquero-Garcia, Jorge, Lynch, Kristen W., Barash, Yoseph
Publicado no Methods (2013)

Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study

Por Jha, Anupama, K. Aicher, Joseph, R. Gazzara, Matthew, Singh, Deependra, Barash, Yoseph
Publicado no Genome Biol (2020)

Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing

Por Radens, Caleb M., Blake, Davia, Jewell, Paul, Barash, Yoseph, Lynch, Kristen W.
Publicado no RNA (2020)

Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates

Por Norton, Scott S, Vaquero-Garcia, Jorge, Lahens, Nicholas F, Grant, Gregory R, Barash, Yoseph
Publicado no Bioinformatics (2018)

Mapping RNA splicing variations in clinically-accessible and non-accessible tissues to facilitate Mendelian disease diagnosis using RNA-seq

Por Aicher, Joseph K, Jewell, Paul, Vaquero-Garcia, Jorge, Barash, Yoseph, Bhoj, Elizabeth J
Publicado no Genet Med (2020)

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression

Por Marion, Rosa M., Regev, Aviv, Segal, Eran, Barash, Yoseph, Koller, Daphne, Friedman, Nir, O'Shea, Erin K.
Publicado em 2004

Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes

Por Gazzara, Matthew R., Mallory, Michael J., Roytenberg, Renat, Lindberg, John P., Jha, Anupama, Lynch, Kristen W., Barash, Yoseph
Publicado no Genome Res (2017)

AVISPA: a web tool for the prediction and analysis of alternative splicing

Por Barash, Yoseph, Vaquero-Garcia, Jorge, González-Vallinas, Juan, Xiong, Hui Yuan, Gao, Weijun, Lee, Leo J, Frey, Brendan J
Publicado em 2013

Widespread JNK-dependent alternative splicing induces a positive feedback loop through CELF2-mediated regulation of MKK7 during T-cell activation

Por Martinez, Nicole M., Agosto, Laura, Qiu, Jinsong, Mallory, Michael J., Gazzara, Matthew R., Barash, Yoseph, Fu, Xiang-dong, Lynch, Kristen W.
Publicado no Genes Dev (2015)

A new view of transcriptome complexity and regulation through the lens of local splicing variations

Por Vaquero-Garcia, Jorge, Barrera, Alejandro, Gazzara, Matthew R, González-Vallinas, Juan, Lahens, Nicholas F, Hogenesch, John B, Lynch, Kristen W, Barash, Yoseph
Publicado no eLife (2016)

Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation

Por Brady, Lauren K., Wang, Hejia, Radens, Caleb M., Bi, Yue, Radovich, Milan, Maity, Amit, Ivan, Cristina, Ivan, Mircea, Barash, Yoseph, Koumenis, Constantinos
Publicado no PLoS Biol (2017)

Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript

Por Ghanem, Louis R., Kromer, Andrew, Silverman, Ian M., Ji, Xinjun, Gazzara, Matthew, Nguyen, Nhu, Aguilar, Gabrielle, Martinelli, Massimo, Barash, Yoseph, Liebhaber, Stephen A.
Publicado no Mol Cell Biol (2018)

A systematic analysis of intronic sequences downstream of 5′ splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation

Por Aznarez, Isabel, Barash, Yoseph, Shai, Ofer, He, David, Zielenski, Julian, Tsui, Lap-Chee, Parkinson, John, Frey, Brendan J., Rommens, Johanna M., Blencowe, Benjamin J.
Publicado em 2008

PRiMeUM: A Model for Predicting Risk of Metastasis in Uveal Melanoma

Por Vaquero-Garcia, Jorge, Lalonde, Emilie, Ewens, Kathryn G., Ebrahimzadeh, Jessica, Richard-Yutz, Jennifer, Shields, Carol L., Barrera, Alejandro, Green, Christopher J., Barash, Yoseph, Ganguly, Arupa
Publicado no Invest Ophthalmol Vis Sci (2017)

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing

Por Shinde, Mansi Y., Sidoli, Simone, Kulej, Katarzyna, Mallory, Michael J., Radens, Caleb M., Reicherter, Amanda L., Myers, Rebecca L., Barash, Yoseph, Lynch, Kristen W., Garcia, Benjamin A., Klein, Peter S.
Publicado no J Biol Chem (2017)