☆ 4.7 Article

Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles

GENOME MEDICINE (2012)

期刊

GENOME MEDICINE

卷 4, 期 -, 页码 -

出版社

BMC

DOI: 10.1186/gm376

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Genetics & Heredity

资金

Canadian Institutes for Health Research
Ontario Institute for Cancer Research by government of Ontario
National Sciences and Engineering Research Council of Canada
Michael Smith Foundation for Health Research (MSFHR)
National Institute of General Medical Sciences [R01GM084875]
Canadian Institutes of Health Research/MSFHR Strategic Training Program in Bioinformatics

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Reagent

摘要

Background: MEDLINE (R)/PubMed (R) currently indexes over 18 million biomedical articles, providing unprecedented opportunities and challenges for text analysis. Using Medical Subject Heading Over-representation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and predicting novel indirect associations. Methods: A procedure is introduced for quantitative comparison of MeSHOPs derived from a group of MEDLINE (R) articles for a biomedical topic (for example, articles for a specific gene or disease). Similarity scores are computed to compare MeSHOPs of genes and diseases. Results: Similarity scores successfully infer novel associations between diseases and genes. The number of papers addressing a gene or disease has a strong influence on predicted associations, revealing an important bias for gene-disease relationship prediction. Predictions derived from comparisons of MeSHOPs achieves a mean 8% AUC improvement in the identification of gene-disease relationships compared to gene-independent baseline properties. Conclusions: MeSHOP comparisons are demonstrated to provide predictive capacity for novel relationships between genes and human diseases. We demonstrate the impact of literature bias on the performance of gene-disease prediction methods. MeSHOPs provide a rich source of annotation to facilitate relationship discovery in biomedical informatics.

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Lau, Georgina Long, Hilda A. Pickett, Antonia L. Pritchard, Gulietta M. Pupo, Robyn P. M. Saw, Sarah-Jane Schramm, Catherine A. Shang, Ping Shang, Andrew J. Spillane, Jonathan R. Stretch, Varsha Tembe, John F. Thompson, Ricardo E. Vilain, James S. Wilmott, Jean Y. Yang, Nicholas K. Hayward, Graham J. Mann, Richard A. Scolyer, John Bartlett, Prashant Bavi, Dianne E. Chadwick, Michelle Chan-Seng-Yue, Sean Cleary, Ashton A. Connor, Karolina Czajka, Robert E. Denroche, Neesha C. Dhani, Jenna Eagles, Steven Gallinger, Robert C. Grant, David Hedley, Michael A. Hollingsworth, Gun Ho Jang, Jeremy Johns, Sangeetha Kalimuthu, Sheng-Ben Liang, Ilinca Lungu, Xuemei Luo, Faridah Mbabaali, Treasa A. McPherson, Jessica K. Miller, Malcolm J. Moore, Faiyaz Notta, Danielle Pasternack, Gloria M. Petersen, Michael H. A. Roehrl, Michelle Sam, Iris Selander, Stefano Serra, Sagedeh Shahabi, Sarah P. Thayer, Lee E. Timms, Gavin W. Wilson, Julie M. Wilson, Bradly G. Wouters, John D. McPherson, Timothy A. Beck, Vinayak Bhandari, Colin C. Collins, Neil E. Fleshner, Natalie S. Fox, Michael Fraser, Lawrence E. Heisler, Emilie Lalonde, Julie Livingstone, Alice Meng, Veronica Y. Sabelnykova, Yu-Jia Shiah, Theodorus Van Der Kwast, Robert G. Bristow, Shuai Ding, Daiming Fan, Lin Li, Yongzhan Nie, Xiao Xiao, Rui Xing, Shanlin Yang, Yingyan Yu, Yong Zhou, Rosamonde E. Banks, Guillaume Bourque, Paul Brennan, Louis Letourneau, Yasser Riazalhosseini, Ghislaine Scelo, Naveen Vasudev, Juris Viksna, Mark Lathrop, Jorg Tost, Sung-Min Ahn, Samuel Aparicio, Laurent Arnould, M. R. Aure, Shriram G. Bhosle, Ewan Birney, Ake Borg, Sandrine Boyault, Arie B. Brinkman, Jane E. Brock, Annegien Broeks, Anne-Lise Borresen-Dale, Carlos Caldas, Suet-Feung Chin, Helen Davies, Christine Desmedt, Luc Dirix, Serge Dronov, Anna Ehinger, Jorunn E. Eyfjord, Aquila Fatima, John A. Foekens, P. Andrew Futreal, Oystein Garred, Dilip D. Giri, Dominik Glodzik, Dorthe Grabau, Holmfridur Hilmarsdottir, Gerrit K. Hooijer, Jocelyne Jacquemier, Se Jin Jang, Jon G. Jonasson, Jos Jonkers, Hyung-Yong Kim, Tari A. King, Stian Knappskog, Gu Kong, Savitri Krishnamurthy, Sunil R. Lakhani, Anita Langerod, Denis Larsimont, Hee Jin Lee, Jeong-Yeon Lee, Ming Ta Michael Lee, Ole Christian Lingjaerde, Gaetan MacGrogan, John W. M. Martens, Sarah O'Meara, Iris Pauporte, Sarah Pinder, Xavier Pivot, Elena Provenzano, Colin A. Purdie, Manasa Ramakrishna, Kamna Ramakrishnan, Jorge Reis-Filho, Andrea L. Richardson, Markus Ringner, Javier Bartolome Rodriguez, F. German Rodriguez-Gonzalez, Gilles Romieu, Roberto Salgado, Torill Sauer, Rebecca Shepherd, Anieta M. Sieuwerts, Peter T. Simpson, Marcel Smid, Christos Sotiriou, Paul N. Span, Olafur Andri Stefansson, Alasdair Stenhouse, Henk G. Stunnenberg, Fred Sweep, Benita Kiat Tee Tan, Gilles Thomas, Alastair M. Thompson, Stefania Tommasi, Isabelle Treilleux, Andrew Tutt, Naoto T. Ueno, Steven Van Laere, Gert G. Van den Eynden, Peter Vermeulen, Alain Viari, Anne Vincent-Salomon, Bernice H. Wong, Lucy Yates, Xueqing Zou, Carolien H. M. van Deurzen, Marc J. van de Vijver, Laura van't Veer, Ole Ammerpohl, Sietse Aukema, Anke K. Bergmann, Stephan H. Bernhart, Arndt Borkhardt, Christoph Borst, Birgit Burkhardt, Alexander Claviez, Maria Elisabeth Goebler, Andrea Haake, Siegfried Haas, Martin Hansmann, Jessica Hoell, Michael Hummel, Dennis Karsch, Wolfram Klapper, Michael Kneba, Markus Kreuz, Dieter Kube, Ralf Kueppers, Dido Lenze, Markus Loeffler, Cristina Lopez, Luisa Mantovani-Loeffler, Peter Moeller, German Ott, Bernhard Radlwimmer, Julia Richter, Marius Rohde, Philip C. Rosenstiel, Andreas Rosenwald, Markus B. Schilhabel, Stefan Schreiber, Peter F. Stadler, Peter Staib, Stephan Stilgenbauer, Stephanie Sungalee, Monika Szczepanowski, Umut H. Toprak, Lorenz H. P. Truemper, Rabea Wagener, Thorsten Zenz, Volker Hovestadt, Christof von Kalle, Marcel Kool, Andrey Korshunov, Pablo Landgraf, Hans Lehrach, Paul A. Northcott, Stefan M. Pfister, Guido Reifenberger, Hans-Joerg Warnatz, Stephan Wolf, Marie-Laure Yaspo, Yassen Assenov, Clarissa Gerhauser, Sarah Minner, Thorsten Schlomm, Ronald Simon, Guido Sauter, Holger Sueltmann, Nidhan K. Biswas, Arindam Maitra, Partha P. Majumder, Rajiv Sarin, Stefano Barbi, Giada Bonizzato, Cinzia Cantu, Angelo P. Dei Tos, Matteo Fassan, Sonia Grimaldi, Claudio Luchini, Giuseppe Malleo, Giovanni Marchegiani, Michele Milella, Salvatore Paiella, Antonio Pea, Paolo Pederzoli, Andrea Ruzzenente, Roberto Salvia, Nicola Sperandio, Yasuhito Arai, Natsuko Hama, Nobuyoshi Hiraoka, Fumie Hosoda, Hiromi Nakamura, Hidenori Ojima, Takuji Okusaka, Yasushi Totoki, Tomoko Urushidate, Masashi Fukayama, Shumpei Ishikawa, Hitoshi Katai, Hiroto Katoh, Daisuke Komura, Hirofumi Rokutan, Mihoko Saito-Adachi, Akihiro Suzuki, Hirokazu Taniguchi, Kenji Tatsuno, Tetsuo Ushiku, Shinichi Yachida, Shogo Yamamoto, Hiroshi Aikata, Koji Arihiro, Shun-ichi Ariizumi, Kazuaki Chayama, Mayuko Furuta, Kunihito Gotoh, Shinya Hayami, Satoshi Hirano, Yoshiiku Kawakami, Kazuhiro Maejima, Toru Nakamura, Kaoru Nakano, Hideki Ohdan, Aya Sasaki-Oku, Hiroko Tanaka, Masaki Ueno, Masakazu Yamamoto, Hiroki Yamaue, Su Pin Choo, Ioana Cutcutache, Narong Khuntikeo, Choon Kiat Ong, Chawalit Pairojkul, Irinel Popescu, Keun Soo Ahn, Marta Aymerich, Armando Lopez-Guillermo, Carlos Lopez-Otin, Xose S. Puente, Elias Campo, Fernanda Amary, Daniel Baumhoer, Sam Behjati, Bodil Bjerkehagen, P. A. Futreal, Ola Myklebost, Nischalan Pillay, Patrick Tarpey, Roberto Tirabosco, Olga Zaikova, Adrienne M. Flanagan, Jacqueline Boultwood, David T. Bowen, Mario Cazzola, Anthony R. Green, Eva Hellstrom-Lindberg, Luca Malcovati, Jyoti Nangalia, Elli Papaemmanuil, Paresh Vyas, Yeng Ang, Hugh Barr, Duncan Beardsmore, Matthew Eldridge, James Gossage, Nicola Grehan, George B. Hanna, Stephen J. Hayes, Ted R. Hupp, David Khoo, Jesper Lagergren, Laurence B. Lovat, Shona MacRae, Maria O'Donovan, J. Robert O'Neill, Simon L. Parsons, Shaun R. Preston, Sonia Puig, Tom Roques, Grant Sanders, Sharmila Sothi, Simon Tavare, Olga Tucker, Richard Turkington, Timothy J. Underwood, Ian Welch, Rebecca C. Fitzgerald, Daniel M. Berney, Johann S. De Bono, Declan Cahill, Niedzica Camacho, Nening M. Dennis, Tim Dudderidge, Sandra E. Edwards, Cyril Fisher, Christopher S. Foster, Mohammed Ghori, Pelvender Gill, Vincent J. Gnanapragasam, Gunes Gundem, Freddie C. Hamdy, Steve Hawkins, Steven Hazell, William Howat, William B. Isaacs, Katalin Karaszi, Jonathan D. Kay, Vincent Khoo, Zsofia Kote-Jarai, Barbara Kremeyer, Pardeep Kumar, Adam Lambert, Daniel A. Leongamornlert, Naomi Livni, Yong-Jie Lu, Hayley J. Luxton, Luke Marsden, Charlie E. Massie, Lucy Matthews, Erik Mayer, Ultan McDermott, Sue Merson, David E. Neal, Anthony Ng, David Nicol, Christopher Ogden, Edward W. Rowe, Nimish C. Shah, Sarah Thomas, Alan Thompson, Clare Verrill, Tapio Visakorpi, Anne Y. Warren, Hayley C. Whitaker, Hongwei Zhang, Nicholas van As, Rosalind A. Eeles, Adam Abeshouse, Nishant Agrawal, Rehan Akbani, Hikmat Al Ahmadie, Monique Albert, Kenneth Aldape, Adrian Ally, Elizabeth L. Appelbaum, Joshua Armenia, Sylvia Asa, J. Todd Auman, Miruna Balasundaram, Saianand Balu, Jill Barnholtz-Sloan, Oliver F. Bathe, Stephen B. Baylin, Christopher Benz, Andrew Berchuck, Mario Berrios, Darell Bigner, Michael Birrer, Tom Bodenheimer, Lori Boice, Moiz S. Bootwalla, Marcus Bosenberg, Reanne Bowlby, Jeffrey Boyd, Russell R. Broaddus, Malcolm Brock, Denise Brooks, Susan Bullman, Samantha J. Caesar-Johnson, Thomas E. Carey, Rebecca Carlsen, Robert Cerfolio, Vishal S. Chandan, Hsiao-Wei Chen, Andrew D. Cherniack, Jeremy Chien, Juok Cho, Eric Chuah, Carrie Cibulskis, Leslie Cope, Matthew G. Cordes, Erin Curley, Bogdan Czerniak, Ludmila Danilova, Ian J. Davis, Timothy Defreitas, John A. Demchok, Noreen Dhalla, Rajiv Dhir, HarshaVardhan Doddapaneni, Adel El-Naggar, Ina Felau, Martin L. Ferguson, Gaetano Finocchiaro, Kwun M. Fong, Scott Frazer, William Friedman, Catrina C. Fronick, Lucinda A. Fulton, Stacey B. Gabriel, Jianjiong Gao, Nils Gehlenborg, Jeffrey E. Gershenwald, Ronald Ghossein, Nasra H. Giama, Richard A. Gibbs, Carmen Gomez, Ramaswamy Govindan, D. Neil Hayes, Apurva M. Hegde, David Heiman, Zachary Heins, Austin J. Hepperla, Andrea Holbrook, Robert A. Holt, Alan P. Hoyle, Ralph H. Hruban, Jianhong Hu, Mei Huang, David Huntsman, Jason Huse, Christine A. Iacobuzio Donahue, Michael Ittmann, Joy C. Jayaseelan, Stuart R. Jefferys, Corbin D. Jones, Steven J. M. Jones, Hartmut Juhl, Koo Jeong Kang, Beth Karlan, Katayoon Kasaian, Electron Kebebew, Hark Kyun Kim, Viktoriya Korchina, Ritika Kundra, Phillip H. Lai, Eric Lander, Xuan Le, Darlene Lee, Douglas A. Levine, Lora Lewis, Tim Ley, Haiyan Irene Li, Pei Lin, W. M. Linehan, Fei Fei Liu, Yiling Lu, Lisa Lype, Yussanne Ma, Dennis T. Maglinte, Elaine R. Mardis, Jeffrey Marks, Marco A. Marra, Thomas J. Matthew, Michael Mayo, Karen McCune, Samuel R. Meier, Shaowu Meng, Piotr A. Mieczkowski, Tom Mikkelsen, Christopher A. Miller, Gordon B. Mills, Richard A. Moore, Carl Morrison, Lisle E. Mose, Catherine D. Moser, Andrew J. Mungall, Karen Mungall, David Mutch, Donna M. Muzny, Jerome Myers, Yulia Newton, Michael S. Noble, Peter O'Donnell, Brian Patrick O'Neill, Angelica Ochoa, Joong-Won Park, Joel S. Parker, Harvey Pass, Alessandro Pastore, Nathan A. Pennell, Charles M. Perou, Nicholas Petrelli, Olga Potapova, Janet S. Rader, Suresh Ramalingam, W. Kimryn Rathmell, Victor Reuter, Sheila M. Reynolds, Matthew Ringel, Jeffrey Roach, Lewis R. Roberts, A. Gordon Robertson, Sara Sadeghi, Charles Saller, Francisco Sanchez-Vega, Dirk Schadendorf, Jacqueline E. Schein, Heather K. Schmidt, Nikolaus Schultz, Raja Seethala, Yasin Senbabaoglu, Troy Shelton, Yan Shi, Juliann Shih, Ilya Shmulevich, Craig Shriver, Sabina Signoretti, Janae Simons, Samuel Singer, Payal Sipahimalani, Tara J. Skelly, Karen Smith McCune, Nicholas D. Socci, Matthew G. Soloway, Anil K. Sood, Angela Tam, Donghui Tan, Roy Tarnuzzer, Nina Thiessen, R. Houston Thompson, Leigh B. Thorne, Ming Tsao, Christopher Umbricht, David J. Van Den Berg, Erwin G. Van Meir, Umadevi Veluvolu, Douglas Voet, Linghua Wang, Paul Weinberger, Daniel J. Weisenberger, Dennis Wigle, Matthew D. Wilkerson, Richard K. Wilson, Boris Winterhoff, Maciej Wiznerowicz, Tina Wong, Winghing Wong, Liu Xi, Christina Yau, Hailei Zhang, Hongxin Zhang, Jiashan Zhang

NATURE (2020)

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Article Biotechnology & Applied Microbiology

Butler enables rapid cloud-based analysis of thousands of human genomes

Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel, Brice Aminou, Javier Bartolome, Keith A. Boroevich, Rich Boyce, Angela N. Brooks, Alex Buchanan, Ivo Buchhalter, Adam P. Butler, Niall J. Byrne, Andy Cafferkey, Peter J. Campbell, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Brandi N. Davis-Dusenbery, Francisco M. De La Vega, Jonas Demeulemeester, Michelle T. Dow, Lewis Jonathan Dursi, Juergen Eils, Roland Eils, Kyle Ellrott, Claudiu Farcas, Francesco Favero, Nodirjon Fayzullaev, Vincent Ferretti, Paul Flicek, Nuno A. Fonseca, Josep Ll Gelpi, Gad Getz, Bob Gibson, Robert L. Grossman, Olivier Harismendy, Allison P. Heath, Michael C. Heinold, Julian M. Hess, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Barbara Hutter, Carolyn M. Hutter, Daniel Huebschmann, Seiya Imoto, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Jongsun Jung, Rolf Kabbe, Andre Kahles, Jules N. A. Kerssemakers, Hyung-Lae Kim, Hyunghwan Kim, Jihoon Kim, Youngwook Kim, Kortine Kleinheinz, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Ignaty Leshchiner, Jia Liu, Dimitri Livitz, George L. Mihaiescu, Sanja Mijalkovic, Ana Mijalkovic Lazic, Satoru Miyano, Naoki Miyoshi, Hardeep K. Nahal-Bose, Hidewaki Nakagawa, Mia Nastic, Steven J. Newhouse, Jonathan Nicholson, Brian D. O'Connor, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Larsson Omberg, B. F. Francis Ouellette, Nagarajan Paramasivam, Marc D. Perry, Todd D. Pihl, Manuel Prinz, Montserrat Puiggros, Petar Radovic, Keiran M. Raine, Esther Rheinbay, Mara Rosenberg, Romina Royo, Gunnar Raetsch, Gordon Saksena, Matthias Schlesner, Solomon Shorser, Charles Short, Heidi J. Sofia, Jonathan Spring, Lincoln D. Stein, Adam J. Struck, Grace Tiao, Nebojsa Tijanic, David Torrents, Peter Van Loo, Miguel Vazquez, David Vicente, Jeremiah A. Wala, Zhining Wang, Joachim Weischenfeldt, Johannes Werner, Ashley Williams, Youngchoon Woo, Adam J. Wright, Qian Xiang, Liming Yang, Denis Yuen, Christina K. Yung, Junjun Zhang

NATURE BIOTECHNOLOGY (2020)

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Letter Biochemistry & Molecular Biology

Asthma-associated polymorphisms in 17q12-21 locus modulate methylation and gene expression of GSDMA in naive CD4+ T cells

Anne-Marie Madore, Lucile Pain, Anne-Marie Boucher-Lafleur, Andreanne Morin, Jolyane Meloche, Marie-Michelle Simon, Bing Ge, Tony Kwan, Warren A. Cheung, Tomi Pastinen, Catherine Laprise

JOURNAL OF GENETICS AND GENOMICS (2020)

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Article Genetics & Heredity

metPropagate: network-guided propagation of metabolomic information for prioritization of metabolic disease genes

Emma J. Graham Linck, Phillip A. Richmond, Maja Tarailo-Graovac, Udo Engelke, Leo A. J. Kluijtmans, Karlien L. M. Coene, Ron A. Wevers, Wyeth Wasserman, Clara D. M. van Karnebeek, Sara Mostafavi

NPJ GENOMIC MEDICINE (2020)

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Article Genetics & Heredity

GeneBreaker: Variant simulation to improve the diagnosis of Mendelian rare genetic diseases

Phillip A. Richmond, Tamar V. Av-Shalom, Oriol Fornes, Bhavi Modi, Alison M. Elliott, Wyeth W. Wasserman

Summary: This article discusses Mendelian rare genetic diseases, the challenges they present for diagnosis, the impact of whole-genome sequencing on diagnosis rates, and the necessity for improvements in genomic variant calling and prioritization. It also introduces GeneBreaker as a tool for creating synthetic rare disease cases for benchmarking variant calling approaches and testing the efficacy of variant prioritization.

HUMAN MUTATION (2021)

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Article Oncology

High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations

Mingju Cao, Xiaojian Shao, Peter Chan, Warren Cheung, Tony Kwan, Tomi Pastinen, Bernard Robaire

CLINICAL EPIGENETICS (2020)

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Article Biochemical Research Methods

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper

Phillip Andrew Richmond, Alice Mary Kaye, Godfrain Jacques Kounkou, Tamar Vered Av-Shalom, Wyeth W. Wasserman

Summary: FlexTyper is a reverse mapping method that uses high-throughput sequence queries to quickly extract useful information and enable rapid counting of target sequences. The method can be used for recovering depth of coverage, accurate genotyping, and sensitive detection of pathogen sequences within RNA-seq data.

PLOS COMPUTATIONAL BIOLOGY (2021)

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Article Biochemical Research Methods

RevUP: an online scoring system for regulatory variants implicated in rare diseases

Solenne Correard, Brittany Hewitson, Robin van der Lee, Wyeth W. Wasserman

Summary: In order to evaluate the impact of regulatory variants on diseases, a scoring system has been developed to calculate the Regulatory Variant Evidence score (RVE-score). This scoring system combines information from public databases and user input to assess the causative role of regulatory variants in diseases.

BIOINFORMATICS (2022)

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Review Genetics & Heredity

Obtaining genetics insights from deep learning via explainable artificial intelligence

Gherman Novakovsky, Nick Dexter, Maxwell W. Libbrecht, Wyeth W. Wasserman, Sara Mostafavi

Summary: This Review describes the advances in explainable artificial intelligence (xAI) in genomics, where researchers are using deep learning approaches to gain biological insights behind the models, moving beyond the traditional 'black box' nature.

NATURE REVIEWS GENETICS (2023)

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Article Biochemistry & Molecular Biology

OnTarget: in silico design of MiniPromoters for targeted delivery of expression

Oriol Fornes, Tamar Av-Shalom, Andrea J. Korecki, Rachelle A. Farkas, David J. Arenillas, Anthony Mathelier, Elizabeth M. Simpson, Wyeth W. Wasserman

Summary: MiniPromoters are short DNA sequences that can drive gene expression in specific cells and tissues. OnTarget is a webserver that simplifies the process of designing MiniPromoters by combining user-provided data with internal data to identify candidate promoters and enhancers.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biotechnology & Applied Microbiology

ExplaiNN: interpretable and transparent neural networks for genomics

Gherman Novakovsky, Oriol Fornes, Manu Saraswat, Sara Mostafavi, Wyeth W. W. Wasserman

Summary: ExplaiNN combines the expressiveness of CNNs with the interpretability of linear models, achieving comparable performance to state-of-the-art methods in predicting TF binding, chromatin accessibility, and de novo motifs. Its transparent predictions provide both global and local biological insights into the data. ExplaiNN serves as a plug-and-play platform for pretrained models and annotated position weight matrices, aiming to accelerate the adoption of deep learning in genomic sequence analysis by domain experts.

GENOME BIOLOGY (2023)

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Article Genetics & Heredity

Refining the genomic determinants underlying escape from X-chromosome inactivation

Samantha Peeters, Tiffany Leung, Oriol Fornes, Rachelle A. Farkas, Wyeth W. Wasserman, Carolyn J. Brown

Summary: X-chromosome inactivation (XCI) silences one X chromosome in female mammals, but some genes can escape inactivation and continue to be expressed. Through enrichment analysis of transcription factor binding, we identified factors at the transcription start sites of escape genes. Further experiments demonstrated that gene-proximal elements are sufficient to drive escape from XCI, and multiple elements can work together in a context-specific manner.

NAR GENOMICS AND BIOINFORMATICS (2023)

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Article Biotechnology & Applied Microbiology

Biologically relevant transfer learning improves transcription factor binding prediction

Gherman Novakovsky, Manu Saraswat, Oriol Fornes, Sara Mostafavi, Wyeth W. Wasserman

Summary: The study assesses a transfer learning strategy for TF binding prediction, showing that transfer learning can improve model performance by pre-training a multi-task model and fine-tuning single-task models, especially when using biologically relevant TFs in the pre-training step.

GENOME BIOLOGY (2021)

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