Measurement of average decoding rates of the 61 sense codons in vivo
Gardin, Justin, Yeasmin, Rukhsana, Yurovsky, Alisa, Cai, Ying, Skiena, Steve, Futcher, Bruce
Published in eLife (27.10.2014)
Published in eLife (27.10.2014)
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Passive and active DNA methylation and the interplay with genetic variation in gene regulation
Gutierrez-Arcelus, Maria, Lappalainen, Tuuli, Montgomery, Stephen B, Buil, Alfonso, Ongen, Halit, Yurovsky, Alisa, Bryois, Julien, Giger, Thomas, Romano, Luciana, Planchon, Alexandra, Falconnet, Emilie, Bielser, Deborah, Gagnebin, Maryline, Padioleau, Ismael, Borel, Christelle, Letourneau, Audrey, Makrythanasis, Periklis, Guipponi, Michel, Gehrig, Corinne, Antonarakis, Stylianos E, Dermitzakis, Emmanouil T
Published in eLife (04.06.2013)
Published in eLife (04.06.2013)
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Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription
Kilpinen, Helena, Waszak, Sebastian M., Gschwind, Andreas R., Raghav, Sunil K., Witwicki, Robert M., Orioli, Andrea, Migliavacca, Eugenia, Wiederkehr, Michaël, Gutierrez-Arcelus, Maria, Panousis, Nikolaos I., Yurovsky, Alisa, Lappalainen, Tuuli, Romano-Palumbo, Luciana, Planchon, Alexandra, Bielser, Deborah, Bryois, Julien, Padioleau, Ismael, Udin, Gilles, Thurnheer, Sarah, Hacker, David, Core, Leighton J., Lis, John T., Hernandez, Nouria, Reymond, Alexandre, Deplancke, Bart, Dermitzakis, Emmanouil T.
Published in Science (American Association for the Advancement of Science) (08.11.2013)
Published in Science (American Association for the Advancement of Science) (08.11.2013)
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Population Variation and Genetic Control of Modular Chromatin Architecture in Humans
Waszak, Sebastian M., Delaneau, Olivier, Gschwind, Andreas R., Kilpinen, Helena, Raghav, Sunil K., Witwicki, Robert M., Orioli, Andrea, Wiederkehr, Michael, Panousis, Nikolaos I., Yurovsky, Alisa, Romano-Palumbo, Luciana, Planchon, Alexandra, Bielser, Deborah, Padioleau, Ismael, Udin, Gilles, Thurnheer, Sarah, Hacker, David, Hernandez, Nouria, Reymond, Alexandre, Deplancke, Bart, Dermitzakis, Emmanouil T.
Published in Cell (27.08.2015)
Published in Cell (27.08.2015)
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Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing
Gutierrez-Arcelus, Maria, Ongen, Halit, Lappalainen, Tuuli, Montgomery, Stephen B, Buil, Alfonso, Yurovsky, Alisa, Bryois, Julien, Padioleau, Ismael, Romano, Luciana, Planchon, Alexandra, Falconnet, Emilie, Bielser, Deborah, Gagnebin, Maryline, Giger, Thomas, Borel, Christelle, Letourneau, Audrey, Makrythanasis, Periklis, Guipponi, Michel, Gehrig, Corinne, Antonarakis, Stylianos E, Dermitzakis, Emmanouil T
Published in PLoS genetics (01.01.2015)
Published in PLoS genetics (01.01.2015)
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Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference
Shen, Sam H., Stauft, Charles B., Gorbatsevych, Oleksandr, Song, Yutong, Ward, Charles B., Yurovsky, Alisa, Mueller, Steffen, Futcher, Bruce, Wimmer, Eckard
Published in Proceedings of the National Academy of Sciences - PNAS (14.04.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (14.04.2015)
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Journal Article
Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs
Yurovsky, Alisa, Amin, Mohammad Ruhul, Gardin, Justin, Chen, Yuping, Skiena, Steve, Futcher, Bruce
Published in PloS one (23.08.2018)
Published in PloS one (23.08.2018)
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Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria
Hegelmeyer, Nuri K, Parkin, Lia A, Previti, Mary L, Andrade, Joshua, Utama, Raditya, Sejour, Richard J, Gardin, Justin, Muller, Stephanie, Ketchum, Steven, Yurovsky, Alisa, Futcher, Bruce, Goodwin, Sara, Ueberheide, Beatrix, Seeliger, Jessica C
Published in mBio (31.10.2023)
Published in mBio (31.10.2023)
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Reply to Simmonds et al: Codon pair and dinucleotide bias have not been functionally distinguished
Futcher, Bruce, Gorbatsevych, Oleksandr, Shen, Sam H., Stauft, Charles B., Song, Yutong, Wang, Bingyin, Leatherwood, Janet, Gardin, Justin, Yurovsky, Alisa, Mueller, Steffen, Wimmer, Eckard
Published in Proceedings of the National Academy of Sciences - PNAS (14.07.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (14.07.2015)
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Correction: Passive and active DNA methylation and the interplay with genetic variation in gene regulation
Gutierrez-Arcelus, Maria, Lappalainen, Tuuli, Montgomery, Stephen B, Buil, Alfonso, Ongen, Halit, Yurovsky, Alisa, Bryois, Julien, Giger, Thomas, Romano, Luciana, Planchon, Alexandra, Falconnet, Emilie, Bielser, Deborah, Gagnebin, Maryline, Padioleau, Ismael, Borel, Christelle, Letourneau, Audrey, Makrythanasis, Periklis, Guipponi, Michel, Gehrig, Corinne, Antonarakis, Stylianos E, Dermitzakis, Emmanouil T
Published in eLife (14.06.2013)
Published in eLife (14.06.2013)
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FaStaNMF: a Fast and Stable Non-negative Matrix Factorization for Gene Expression
Sweeney, Michael D., Torre-Healy, Luke A., Ma, Virginia L., Hall, Margaret A., Chrastecka, Lucie, Yurovsky, Alisa, Moffitt, Richard A.
Published in IEEE/ACM transactions on computational biology and bioinformatics (19.07.2023)
Published in IEEE/ACM transactions on computational biology and bioinformatics (19.07.2023)
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Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data
Waszak, Sebastian M, Kilpinen, Helena, Gschwind, Andreas R, Orioli, Andrea, Raghav, Sunil K, Witwicki, Robert M, Migliavacca, Eugenia, Yurovsky, Alisa, Lappalainen, Tuuli, Hernandez, Nouria, Reymond, Alexandre, Dermitzakis, Emmanouil T, Deplancke, Bart
Published in Bioinformatics (15.01.2014)
Published in Bioinformatics (15.01.2014)
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Journal Article
Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing: e1004958
Gutierrez-Arcelus, Maria, Ongen, Halit, Lappalainen, Tuuli, Montgomery, Stephen B, Buil, Alfonso, Yurovsky, Alisa, Bryois, Julien, Padioleau, Ismael, Romano, Luciana, Planchon, Alexandra, Falconnet, Emilie, Bielser, Deborah, Gagnebin, Maryline, Giger, Thomas, Borel, Christelle, Letourneau, Audrey, Makrythanasis, Periklis, Guipponi, Michel, Gehrig, Corinne, Antonarakis, Stylianos E, Dermitzakis, Emmanouil T
Published in PLoS genetics (01.01.2015)
Published in PLoS genetics (01.01.2015)
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A graded neonatal mouse model of necrotizing enterocolitis demonstrates that mild enterocolitis is sufficient to activate microglia and increase cerebral cytokine expression
Sha, Cuilee, Van Brunt, Trevor, Kudria, Jacob, Schmidt, Donna, Yurovsky, Alisa, Bandovic, Jela, Giarrizzo, Michael, Lin, Joyce, Tsirka, Styliani-Anna, Bialkowska, Agnieszka B, Wollmuth, Lonnie, Speer, Esther, Hsieh, Helen
Published in bioRxiv : the preprint server for biology (01.05.2024)
Published in bioRxiv : the preprint server for biology (01.05.2024)
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