Search Results - "Çelik, Muhammed Hasan"

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing by Cheng, Jun, Nguyen, Thi Yen Duong, Cygan, Kamil J, Çelik, Muhammed Hasan, Fairbrother, William G, Avsec, Žiga, Gagneur, Julien

“…Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing)…”
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MTSplice predicts effects of genetic variants on tissue-specific splicing by Cheng, Jun, Çelik, Muhammed Hasan, Kundaje, Anshul, Gagneur, Julien

“…We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human…”
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Identifying dysregulated regions in amyotrophic lateral sclerosis through chromatin accessibility outliers by Çelik, Muhammed Hasan, Gagneur, Julien, Lim, Ryan G., Wu, Jie, Thompson, Leslie M., Xie, Xiaohui

“…The high heritability of amyotrophic lateral sclerosis (ALS) contrasts with its low molecular diagnosis rate post-genetic testing, pointing to potential…”
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Publisher Correction: MTSplice predicts effects of genetic variants on tissue-specific splicing by Cheng, Jun, Çelik, Muhammed Hasan, Kundaje, Anshul, Gagneur, Julien

“…An amendment to this paper has been published and can be accessed via the original article…”
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Quantification of Proteins and Histone Marks in Drosophila Embryos Reveals Stoichiometric Relationships Impacting Chromatin Regulation by Bonnet, Jacques, Lindeboom, Rik G.H., Pokrovsky, Daniil, Stricker, Georg, Çelik, Muhammed Hasan, Rupp, Ralph A.W., Gagneur, Julien, Vermeulen, Michiel, Imhof, Axel, Müller, Jürg

“…Gene transcription in eukaryotes is regulated through dynamic interactions of a variety of different proteins with DNA in the context of chromatin. Here, we…”
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CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice by Cheng, Jun, Çelik, Muhammed Hasan, Nguyen, Thi Yen Duong, Avsec, Žiga, Gagneur, Julien

“…Pathogenic genetic variants often primarily affect splicing. However, it remains difficult to quantitatively predict whether and how genetic variants affect…”
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Assessing predictions of the impact of variants on splicing in CAGI5 by Mount, Stephen M., Avsec, Žiga, Carmel, Liran, Casadio, Rita, Çelik, Muhammed Hasan, Chen, Ken, Cheng, Jun, Cohen, Noa E., Fairbrother, William G., Fenesh, Tzila, Gagneur, Julien, Gotea, Valer, Holzer, Tamar, Lin, Chiao‐Feng, Martelli, Pier Luigi, Naito, Tatsuhiko, Nguyen, Thi Yen Duong, Savojardo, Castrense, Unger, Ron, Wang, Robert, Yang, Yuedong, Zhao, Huiying

“…Precision medicine and sequence‐based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical…”
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Exploring vaccine hesitancy in digital public discourse: From tribal polarization to socio-economic disparities by Ayaz, Huzeyfe, Celik, Muhammed Hasan, Koytak, Huseyin Zeyd, Yanik, Ibrahim Emre

“…This study analyzed online public discourse on Twitter (later rebranded as X) during the COVID-19 pandemic to understand key factors associated with vaccine…”
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CAGI5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice by Cheng, Jun, Çelik, Muhammed Hasan, Nguyen, Yen Duong, Avsec, Žiga, Gagneur, Julien

“…Pathogenic genetic variants are often primarily affecting splicing. However, it remains difficult to quantitatively predict whether and how genetic variants…”
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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification by Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., De María, Maite, Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., Gonzalez Martinez, Jose M., Hunt, Toby, Lagarde, Julien, Liang, Cindy E., Li, Haoran, Meade, Marcus Jerryd, Moraga Amador, David A., Prjibelski, Andrey D., Birol, Inanc, Bostan, Hamed, Brooks, Ashley M., Çelik, Muhammed Hasan, Chen, Ying, Du, Mei R. M., Felton, Colette, Göke, Jonathan, Hafezqorani, Saber, Herwig, Ralf, Kawaji, Hideya, Lee, Joseph, Li, Jian-Liang, Lienhard, Matthias, Mikheenko, Alla, Mulligan, Dennis, Nip, Ka Ming, Pertea, Mihaela, Ritchie, Matthew E., Sim, Andre D., Tang, Alison D., Wan, Yuk Kei, Wang, Changqing, Wong, Brandon Y., Yang, Chen, Barnes, If, Berry, Andrew E., Capella-Gutierrez, Salvador, Cousineau, Alyssa, Dhillon, Namrita, Fernandez-Gonzalez, Jose M., Ferrández-Peral, Luis, Garcia-Reyero, Natàlia, Götz, Stefan, Hernández-Ferrer, Carles, Kondratova, Liudmyla, Liu, Tianyuan, Martinez-Martin, Alessandra, Menor, Carlos, Mestre-Tomás, Jorge, Mudge, Jonathan M., Panayotova, Nedka G., Paniagua, Alejandro, Repchevsky, Dmitry, Ren, Xingjie, Rouchka, Eric, Saint-John, Brandon, Sapena, Enrique, Sheynkman, Leon, Smith, Melissa Laird, Suner, Marie-Marthe, Takahashi, Hazuki, Youngworth, Ingrid A., Carninci, Piero, Denslow, Nancy D., Guigó, Roderic, Hunter, Margaret E., Maehr, Rene, Shen, Yin, Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Au, Kin Fai, Sheynkman, Gloria M., Mortazavi, Ali, Conesa, Ana, Brooks, Angela N.

“…The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome…”
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A Text Mining Approach to Determinants of Attitude Towards Syrian Immigration in the Turkish Twittersphere by Koytak, Huseyin Zeyd, Celik, Muhammed Hasan

“…This study uses novel deep learning-based language models to extract meaningful information from vast chunks of textual data from Twitter on the competing…”
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