Suchergebnisse - Dmitry Penzar

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  1. 1
    GENA-LM: A Family of Open-Source Foundational DNA Language Models for Long Sequences

    GENA-LM: A Family of Open-Source Foundational DNA Language Models for Long Sequences von Veniamin Fishman, Yuri Kuratov, Aleksei Shmelev, Maxim Petrov, Dmitry Penzar, Denis Shepelin, Nikolay Chekanov, Olga Kardymon, Mikhail Burtsev

    Veröffentlicht 2023
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  2. 2
    GENA-LM: a family of open-source foundational DNA language models for long sequences

    GENA-LM: a family of open-source foundational DNA language models for long sequences von Veniamin Fishman, Yuri Kuratov, Aleksei Shmelev, Maxim Petrov, Dmitry Penzar, Denis Shepelin, Nikolay Chekanov, Olga Kardymon, Mikhail Burtsev

    Veröffentlicht 2025
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  3. 3
    LegNet: a best-in-class deep learning model for short DNA regulatory regions

    LegNet: a best-in-class deep learning model for short DNA regulatory regions von Dmitry Penzar, Daria Nogina, Elizaveta Noskova, Arsenii Zinkevich, G. A. Meshcheryakov, Andrey Lando, Abdul Muntakim Rafi, Carl G. de Boer, Ivan V. Kulakovskiy

    Veröffentlicht 2023
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  4. 4
    Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

    Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study von Giovanna Ambrosini, Ilya E. Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornés, Daria D. Nikolaeva, Benoît Ballester, Jan Grau, Ivo Große, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Philipp Bücher

    Veröffentlicht 2020
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  5. 5
    Landscape of allele-specific transcription factor binding in the human genome

    Landscape of allele-specific transcription factor binding in the human genome von Sergey Abramov, Alexandr Boytsov, Daria Bykova, Dmitry Penzar, Ivan Yevshin, Semyon Kolmykov, М. В. Фридман, Alexander V. Favorov, Ilya E. Vorontsov, Eugene F. Baulin, Fedor Kolpakov, Vsevolod J. Makeev, Ivan V. Kulakovskiy

    Veröffentlicht 2021
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  6. 6
    Massively parallel characterization of transcriptional regulatory elements

    Massively parallel characterization of transcriptional regulatory elements von Vikram Agarwal, Fumitaka Inoue, Max Schubach, Dmitry Penzar, Beth Martin, Pyaree Mohan Dash, Pia Keukeleire, Zicong Zhang, Ajuni Sohota, Jingjing Zhao, Ilias Georgakopoulos-Soares, William Stafford Noble, Galip Gürkan Yardımcı, Ivan V. Kulakovskiy, Martin Kircher, Jay Shendure, Nadav Ahituv

    Veröffentlicht 2025
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  7. 7
    <i>Severe acute respiratory syndrome-related coronavirus</i>: The species and its viruses – a statement of the Coronavirus Study Group

    <i>Severe acute respiratory syndrome-related coronavirus</i>: The species and its viruses – a statement of the Coronavirus Study Group von Alexander E. Gorbalenya, Susan C. Baker, Ralph S. Baric, Raoul J. de Groot, Christian Drosten, Anastasia Gulyaeva, Bart L. Haagmans, Chris Lauber, A. M. Leontovich, Benjamin W. Neuman, Dmitry Penzar, Stanley Perlman, Leo L. M. Poon, Dmitry V. Samborskiy, Igor A. Sidorov, Isabel Sola, John Ziebuhr

    Veröffentlicht 2020
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  8. 8
    The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

    The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 von Alexander E. Gorbalenya, Susan C. Baker, Ralph S. Baric, Raoul J. de Groot, Christian Drosten, Anastasia Gulyaeva, Bart L. Haagmans, Chris Lauber, A. M. Leontovich, Benjamin W. Neuman, Dmitry Penzar, Stanley Perlman, Leo L. M. Poon, Dmitry V. Samborskiy, Igor A. Sidorov, Isabel Sola, John Ziebuhr

    Veröffentlicht 2020
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  9. 9
    Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

    Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay von Dustin Shigaki, Orit Adato, Aashish N. Adhikari, Shengcheng Dong, Alex Hawkins‐Hooker, Fumitaka Inoue, Tamar Juven‐Gershon, Henry Kenlay, Beth Martin, Ayoti Patra, Dmitry Penzar, Max Schubach, Chenling Xiong, Zhongxia Yan, Alan P. Boyle, Anat Kreimer, Ivan V. Kulakovskiy, John E. Reid, Ron Unger, Nir Yosef, Jay Shendure, Nadav Ahituv, Martin Kircher, M Beer

    Veröffentlicht 2019
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  10. 10
    Ribonanza: deep learning of RNA structure through dual crowdsourcing

    Ribonanza: deep learning of RNA structure through dual crowdsourcing von Shujun He, Rui Huang, Jill Townley, Rachael C. Kretsch, Thomas G. Karagianes, David Cox, H. Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, A. E. Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, E.S. Martynov, Maxim V. Shugaev, Habib S.T. Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Shlomo Ron, Jonathan Romano, John J. Nicol, Nye G, Yuan Wu, Christian A. Choe, Walter Reade, Rhiju Das

    Veröffentlicht 2024
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  11. 11
    A community effort to optimize sequence-based deep learning models of gene regulation

    A community effort to optimize sequence-based deep learning models of gene regulation von Abdul Muntakim Rafi, Daria Nogina, Dmitry Penzar, Dohoon Lee, Danyeong Lee, N. S. KIM, Sangyeup Kim, Dohyeon Kim, Yeojin Shin, Il‐Youp Kwak, G. A. Meshcheryakov, Andrey Lando, Arsenii Zinkevich, Byeongchan Kim, Juhyun Lee, Taein Kang, Eeshit Dhaval Vaishnav, Payman Yadollahpour, Susanne Bornelöv, Fredrik Svensson, Maria‐Anna Trapotsi, Duc Tran, Tin Nguyen, Xinming Tu, Wuwei Zhang, Wei Qiu, Rohan Ghotra, Yiyang Yu, Ethan Labelson, Aayush Prakash, Ashwin Narayanan, Peter K. Koo, Xiaoting Chen, David T. Jones, Michele Tinti, Yuanfang Guan, Maolin Ding, Ken Chen, Yuedong Yang, Ke Ding, Gunjan Dixit, Jiayu Wen, Zhihan Zhou, Pratik Dutta, Rekha Sathian, Pallavi Surana, Yanrong Ji, Han Liu, Ramana V. Davuluri, Yu Hiratsuka, Mao Takatsu, Tsai‐Min Chen, Chih-Han Huang, Hsuan-Kai Wang, Edward S.C. Shih, Sz-Hau Chen, Chih‐Hsun Wu, Jhih-Yu Chen, Kuei-Lin Huang, Ibrahim Alsaggaf, P W Greaves, Carl Barton, Cen Wan, Nicholas Allen Baclig Abad, Cindy Körner, Lars Feuerbach, Benedikt Brors, Yichao Li, Sebastian Röner, Pyaree Mohan Dash, Max Schubach, Onuralp Söylemez, Andreas Møller, Gabija Kavaliauskaite, Jesper Grud Skat Madsen, Zhixiu Lu, Owen Queen, Ashley Babjac, Scott Emrich, Konstantinos Kardamiliotis, Konstantinos Kyriakidis, Andigoni Malousi, Ashok Palaniappan, Krishna Kant Gupta, Prasanna Kumar Saravanam, Jacob Bradford, Dimitri Perrin, Robert Salomone, Carl Schmitz, Jiaxing Chen, Jingzhe Wang, Yang AiWei, Sun Kim, Jake Albrecht, Aviv Regev, Wuming Gong, Ivan V. Kulakovskiy, Pablo Meyer, Carl G. de Boer

    Veröffentlicht 2024
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  12. 12
    CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

    CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods von Shantanu Jain, Constantina Bakolitsa, Steven E. Brenner, Predrag Radivojac, John Moult, Susanna Repo, Roger A. Hoskins, Gaia Andreoletti, Daniel Barsky, Ajithavalli Chellapan, Hoyin Chu, Navya Dabbiru, Naveen K. Kollipara, Melissa Ly, Andrew J. Neumann, Lipika R. Pal, Eric Odell, Gaurav Pandey, Robin C. Peters-Petrulewicz, Rajgopal Srinivasan, Stephen F. Yee, Sri Jyothsna Yeleswarapu, Maya Zuhl, Ogün Adebalı, Ayoti Patra, M Beer, Raghavendra Hosur, Jian Peng, Brady Bernard, M. Victoria Berry, Shengcheng Dong, Alan P. Boyle, Aashish N. Adhikari, Jingqi Chen, Zhiqiang Hu, Robert Wang, Yaqiong Wang, Max J. Miller, Yanran Wang, Yana Bromberg, Paola Turina, Emidio Capriotti, James J. Han, Kıvılcım Öztürk, Hannah Carter, Giulia Babbi, Samuele Bovo, Pietro Di Lena, Pier Luigi Martelli, Castrense Savojardo, Rita Casadio, Melissa Cline, Greet De Baets, Sandra Bonache, Orland Dı́ez, Sara Gutiérrez‐Enríquez, Alejandro Fernández, Gemma Montalban, Lars Ootes, Selen Özkan, Natàlia Padilla, Casandra Riera, Xavier de la Cruz, Mark Diekhans, Peter J. Huwe, Qiong Wei, Qifang Xu, Roland L. Dunbrack, Valer Gotea, Laura Elnitski, Gennady Margolin, Piero Fariselli, Ivan V. Kulakovskiy, Vsevolod J. Makeev, Dmitry Penzar, Ilya E. Vorontsov, Alexander V. Favorov, Julia Forman, Marcia A. Hasenahuer, Marı́a Silvina Fornasari, Gustavo Parisi, Žiga Avsec, Muhammed Hasan Çelik, Thi Yen Duong Nguyen, Julien Gagneur, Fangyuan Shi, Matthew D. Edwards, Yuchun Guo, Kevin Tian, Haoyang Zeng, David K. Gifford, Jonathan Göke, Jan Zaucha, Julian Gough, Graham R. S. Ritchie, Adam Frankish, Jonathan M. Mudge, Jennifer Harrow, Erin L. Young, Yao Yu

    Veröffentlicht 2024
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