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An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression.
Published in:
eLife, 2024, p. 1, doi. 10.7554/eLife.89705
By:
- Siachisumo, Chileleko;
- Luzzi, Sara;
- Aldalaqan, Saad;
- Hysenaj, Gerald;
- Dalgliesh, Caroline;
- Cheung, Kathleen;
- Gazzara, Matthew R.;
- Yonchev, Ivaylo D.;
- James, Katherine;
- Chadegani, Mahsa Kheirollahi;
- Ehrmann, Ingrid E.;
- Smith, Graham R.;
- Cockell, Simon J.;
- Munkley, Jennifer;
- Wilson, Stuart A.;
- Barash, Yoseph;
- Elliott, David J.
Publication type:
Article
Trametinib Sensitivity is Defined by a Myeloid Differentiation Profile in Acute Myeloid Leukemia.
Published in:
Drugs in R&D, 2024, v. 24, n. 3, p. 489, doi. 10.1007/s40268-024-00491-5
By:
- Quesnel-Vallières, Mathieu;
- Schultz, David C.;
- Orlenko, Alena;
- Lo, Yancy;
- Moore, Jason;
- Ritchie, Marylyn;
- Roth, David;
- Carroll, Martin;
- Barash, Yoseph;
- Lynch, Kristen W.;
- Cherry, Sara
Publication type:
Article
Identifying common transcriptome signatures of cancer by interpreting deep learning models.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02681-3
By:
- Jha, Anupama;
- Quesnel-Vallières, Mathieu;
- Wang, David;
- Thomas-Tikhonenko, Andrei;
- Lynch, Kristen W;
- Barash, Yoseph
Publication type:
Article
Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02411-1
By:
- Schulz, Laura;
- Torres-Diz, Manuel;
- Cortés-López, Mariela;
- Hayer, Katharina E.;
- Asnani, Mukta;
- Tasian, Sarah K.;
- Barash, Yoseph;
- Sotillo, Elena;
- Zarnack, Kathi;
- König, Julian;
- Thomas-Tikhonenko, Andrei
Publication type:
Article
An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning.
Published in:
eLife, 2019, p. 1, doi. 10.7554/eLife.39304.001
By:
- Ehrmann, Ingrid;
- Crichton, James H.;
- Gazzara, Matthew R.;
- James, Katherine;
- Yilei Liu;
- Grellscheid, Sushma Nagaraja;
- Curk, Tomaž;
- de Rooij, Dirk;
- Steyn, Jannetta S.;
- Cockell, Simon;
- Adams, Ian R.;
- Barash, Yoseph;
- Elliott, David J.
Publication type:
Article
A new view of transcriptome complexity and regulation through the lens of local splicing variations.
Published in:
eLife, 2016, p. 1, doi. 10.7554/eLife.11752
By:
- Vaquero-Garcia, Jorge;
- Barrera, Alejandro;
- Gazzara, Matthew R.;
- González-Vallinas, Juan;
- Lahens, Nicholas F.;
- Hogenesch, John B.;
- Lynch, Kristen W.;
- Barash, Yoseph
Publication type:
Article
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer.
Published in:
Nucleic Acids Research, 2024, v. 52, n. D1, p. D213, doi. 10.1093/nar/gkad1043
By:
- Quesnel-Vallières, Mathieu;
- Jewell, San;
- Lynch, Kristen W;
- Thomas-Tikhonenko, Andrei;
- Barash, Yoseph
Publication type:
Article
Aberrant splicing in B-cell acute lymphoblastic leukemia.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 2, p. 1043, doi. 10.1093/nar/gky1231
By:
- Black, Kathryn L;
- Naqvi, Ammar S;
- Asnani, Mukta;
- Hayer, Katharina E;
- Yang, Scarlett Y;
- Gillespie, Elisabeth;
- Bagashev, Asen;
- Pillai, Vinodh;
- Tasian, Sarah K;
- Gazzara, Matthew R;
- Carroll, Martin;
- Taylor, Deanne;
- Lynch, Kristen W;
- Barash, Yoseph;
- Thomas-Tikhonenko, Andrei
Publication type:
Article
Aberrant splicing in B-cell acute lymphoblastic leukemia.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 21, p. 11357, doi. 10.1093/nar/gky946
By:
- Black, Kathryn L.;
- Naqvi, Ammar S.;
- Asnani, Mukta;
- Hayer, Katharina E.;
- Yang, Scarlett Y.;
- Gillespie, Elisabeth;
- Bagashev, Asen;
- Pillai, Vinodh;
- Tasian, Sarah K.;
- Gazzara, Matthew R.;
- Carroll, Martin;
- Taylor, Deanne;
- Lynch, Kristen W.;
- Barash, Yoseph;
- Thomas-Tikhonenko, Andrei
Publication type:
Article
Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations.
Published in:
Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-14404-y
By:
- Lee, David S. M.;
- Ghanem, Louis R.;
- Barash, Yoseph
Publication type:
Article
A Bayesian model for unsupervised detection of RNA splicing based subtypes in cancers.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-022-35369-0
By:
- Wang, David;
- Quesnel-Vallieres, Mathieu;
- Jewell, San;
- Elzubeir, Moein;
- Lynch, Kristen;
- Thomas-Tikhonenko, Andrei;
- Barash, Yoseph
Publication type:
Article
High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance.
Published in:
Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31818-y
By:
- Cortés-López, Mariela;
- Schulz, Laura;
- Enculescu, Mihaela;
- Paret, Claudia;
- Spiekermann, Bea;
- Quesnel-Vallières, Mathieu;
- Torres-Diz, Manuel;
- Unic, Sebastian;
- Busch, Anke;
- Orekhova, Anna;
- Kuban, Monika;
- Mesitov, Mikhail;
- Mulorz, Miriam M.;
- Shraim, Rawan;
- Kielisch, Fridolin;
- Faber, Jörg;
- Barash, Yoseph;
- Thomas-Tikhonenko, Andrei;
- Zarnack, Kathi;
- Legewie, Stefan
Publication type:
Article
AVISPA: a web tool for the prediction and analysis of alternative splicing
Published in:
Genome Biology, 2013, v. 14, n. 10, p. R114, doi. 10.1186/gb-2013-14-10-r114
By:
- Barash, Yoseph;
- Vaquero-Garcia, Jorge;
- González-Vallinas, Juan;
- Hui Yuan Xiong;
- Gao, Weijun;
- Lee, Leo J;
- Frey, Brendan J
Publication type:
Article
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates.
Published in:
Bioinformatics, 2018, v. 34, n. 9, p. 1488, doi. 10.1093/bioinformatics/btx790
By:
- Norton, Scott S;
- Vaquero-Garcia, Jorge;
- Lahens, Nicholas F;
- Grant, Gregory R;
- Barash, Yoseph
Publication type:
Article
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data.
Published in:
Bioinformatics, 2018, v. 34, n. 2, p. 300, doi. 10.1093/bioinformatics/btx565
By:
- Green, Christopher J;
- Gazzara, Matthew R;
- Barash, Yoseph
Publication type:
Article
Integrative deep models for alternative splicing.
Published in:
Bioinformatics, 2017, v. 33, n. 14, p. i274, doi. 10.1093/bioinformatics/btx268
By:
- Jha, Anupama;
- Gazzara, Matthew R.;
- Barash, Yoseph
Publication type:
Article
The Tumor Suppressor Adenomatous Polyposis Coli (apc) Is Required for Neural Crest-Dependent Craniofacial Development in Zebrafish.
Published in:
Journal of Developmental Biology, 2023, v. 11, n. 3, p. 29, doi. 10.3390/jdb11030029
By:
- Liu, Xiaolei;
- Jones, William D.;
- Quesnel-Vallières, Mathieu;
- Devadiga, Sudhish A.;
- Lorent, Kristin;
- Valvezan, Alexander J.;
- Myers, Rebecca L.;
- Li, Ning;
- Lengner, Christopher J.;
- Barash, Yoseph;
- Pack, Michael;
- Klein, Peter S.
Publication type:
Article
Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study.
Published in:
Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02055-7
By:
- Jha, Anupama;
- K. Aicher, Joseph;
- R. Gazzara, Matthew;
- Singh, Deependra;
- Barash, Yoseph
Publication type:
Article
Deciphering the splicing code.
Published in:
Nature, 2010, v. 465, n. 7294, p. 53, doi. 10.1038/nature09000
By:
- Barash, Yoseph;
- Calarco, John A.;
- Weijun Gao;
- Qun Pan;
- Xinchen Wang;
- Shai, Ofer;
- Blencowe, Benjamin J.;
- Frey, Brendan J.
Publication type:
Article
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.
Published in:
Bioinformatics, 2011, v. 27, n. 18, p. 2554, doi. 10.1093/bioinformatics/btr444
By:
- Xiong, Hui Yuan;
- Barash, Yoseph;
- Frey, Brendan J.
Publication type:
Article
Model-based detection of alternative splicing signals.
Published in:
Bioinformatics, 2010, v. 26, n. 12, p. i325, doi. 10.1093/bioinformatics/btq200
By:
- Barash, Yoseph;
- Blencowe, Benjamin J.;
- Frey, Brendan J.
Publication type:
Article
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays.
Published in:
Bioinformatics, 2004, v. 20, n. 6, p. 839, doi. 10.1093/bioinformatics/btg487
By:
- Yoseph Barash;
- Elinor Dehan;
- Meir Krupsky;
- Wilbur Franklin;
- Marc Geraci;
- Nir Friedman;
- Naftali Kaminski
Publication type:
Article
MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23608-9
By:
- Slaff, Barry;
- Radens, Caleb M.;
- Jewell, Paul;
- Jha, Anupama;
- Lahens, Nicholas F.;
- Grant, Gregory R.;
- Thomas-Tikhonenko, Andrei;
- Lynch, Kristen W.;
- Barash, Yoseph
Publication type:
Article
Disrupting upstream translation in mRNAs is associated with human disease.
Published in:
Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21812-1
By:
- Lee, David S. M.;
- Park, Joseph;
- Kromer, Andrew;
- Baras, Aris;
- Rader, Daniel J.;
- Ritchie, Marylyn D.;
- Ghanem, Louis R.;
- Barash, Yoseph
Publication type:
Article
The germ cell-specific RNA binding protein RBM46 is essential for spermatogonial differentiation in mice.
Published in:
PLoS Genetics, 2022, v. 18, n. 9, p. 1, doi. 10.1371/journal.pgen.1010416
By:
- Peart, Natoya J.;
- Johnson, Taylor A.;
- Lee, Sungkyoung;
- Sears, Matthew J.;
- Yang, Fang;
- Quesnel-Vallières, Mathieu;
- Feng, Huijuan;
- Recinos, Yocelyn;
- Barash, Yoseph;
- Zhang, Chaolin;
- Hermann, Brian P.;
- Wang, P. Jeremy;
- Geyer, Christopher B.;
- Carstens, Russ P.
Publication type:
Article
Transcriptome analysis of hypoxic cancer cells uncovers intron retention in EIF2B5 as a mechanism to inhibit translation.
Published in:
PLoS Biology, 2017, v. 15, n. 9, p. 1, doi. 10.1371/journal.pbio.2002623
By:
- Brady, Lauren K.;
- Wang, Hejia;
- Radens, Caleb M.;
- Bi, Yue;
- Radovich, Milan;
- Maity, Amit;
- Ivan, Cristina;
- Ivan, Mircea;
- Barash, Yoseph;
- Koumenis, Constantinos
Publication type:
Article
RNA splicing analysis using heterogeneous and large RNA-seq datasets.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-36585-y
By:
- Vaquero-Garcia, Jorge;
- Aicher, Joseph K.;
- Jewell, San;
- Gazzara, Matthew R.;
- Radens, Caleb M.;
- Jha, Anupama;
- Norton, Scott S.;
- Lahens, Nicholas F.;
- Grant, Gregory R.;
- Barash, Yoseph
Publication type:
Article
Genomic profiling of human vascular cells identifies TWIST1 as a causal gene for common vascular diseases.
Published in:
PLoS Genetics, 2020, v. 16, n. 1, p. 1, doi. 10.1371/journal.pgen.1008538
By:
- Nurnberg, Sylvia T.;
- Guerraty, Marie A.;
- Wirka, Robert C.;
- Rao, H. Shanker;
- Pjanic, Milos;
- Norton, Scott;
- Serrano, Felipe;
- Perisic, Ljubica;
- Elwyn, Susannah;
- Pluta, John;
- Zhao, Wei;
- Testa, Stephanie;
- Park, YoSon;
- Nguyen, Trieu;
- Ko, Yi-An;
- Wang, Ting;
- Hedin, Ulf;
- Sinha, Sanjay;
- Barash, Yoseph;
- Brown, Christopher D.
Publication type:
Article
CAMPAREE: a robust and configurable RNA expression simulator.
Published in:
BMC Genomics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12864-021-07934-2
By:
- Lahens, Nicholas F.;
- Brooks, Thomas G.;
- Sarantopoulou, Dimitra;
- Nayak, Soumyashant;
- Lawrence, Cris;
- Mrčela, Antonijo;
- Srinivasan, Anand;
- Schug, Jonathan;
- Hogenesch, John B.;
- Barash, Yoseph;
- Grant, Gregory R.
Publication type:
Article

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