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Identification of causal genes and pathways is a critical step for understanding the genetic underpinnings of rare diseases.
Fast graph representation learning with pytorch geometric
Matthias Fey and Jan Eric Lenssen. 2019 · 1903
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Gnnexplainer: Generating explanations for graph neural networks
Rex Ying, Dylan Bourgeois, Jiaxuan You, Marinka Zitnik, and Jure Leskovec. 2019 · 1903
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Recurrent rhinovirus infections in a child with inherited mda5 deficiency
Ian T. Lamborn, Huie Jing, Yu Zhang, Scott B. Drutman, Jordan K. Abbott, Shirin Munir, Sangeeta Bade, Heardley M. Murdock, Celia P. Santos, Linda G. Brock, Evan Masutani, Emmanuel Y. Fordjour, Joshua J. McElwee, Jason D. Hughes, Dave P. Nichols, Aziz Belkadi, Andrew J. Oler, Corinne S. Happel, Helen F. Matthews, Laurent Abel, Peter L. Collins, Kanta Subbarao, Erwin W. Gelfand, Michael J. Ciancanelli, Jean-Laurent Casanova, and Helen C. Su. 2017 · 1972
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A density-based algorithm for discovering clusters in large spatial databases with noise
Martin Ester, Hans-Peter Kriegel, Jörg Sander, and Xiaowei Xu. 1996 · 1996
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Rnase l inhibitor (rli) antisense constructions block partially the down regulation of the 2-5a/rnase l pathway in encephalomyocarditis-virus-(emcv)-infected cells
Camille Martinand, Tamim Salehzada, Michelle Silhol, Bernard Lebleu, and Catherine Bisbal. 1998 · 1998
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The nucleotide-binding oligomerization domain-like receptor nlrc5 is involved in ifn-dependent antiviral immune responses
Sven Kuenzel, Andreas Till, Michael Winkler, Robert Häsler, Simone Lipinski, Sascha Jung, Joachim Grötzinger, Helmut Fickenscher, Stefan Schreiber, and Philip Rosenstiel. 2010 · 2000
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Interleukin-10 and the interleukin-10 receptor
Kevin W. Moore, Rene de Waal Malefyt, Robert L. Coffman, and Anne O’Garra. 2001 · 2001
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Fast and accurate short read alignment with burrows–wheeler transform
Heng Li and Richard Durbin. 2009 · 2009
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Sequencing technologies — the next generation
Michael L. Metzker. 2009 · 2009
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A framework for variation discovery and genotyping using next-generation dna sequencing data
Mark A DePristo, Eric Banks, Ryan Poplin, Kiran V Garimella, Jared R Maguire, Christopher Hartl, Anthony A Philippakis, Guillermo del Angel, Manuel A Rivas, Matt Hanna, Aaron McKenna, Tim J Fennell, Andrew M Kernytsky, Andrey Y Sivachenko, Kristian Cibulskis, Stacey B Gabriel, David Altshuler, and Mark J Daly. 2011 · 2011
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Ensembl biomarts: a hub for data retrieval across taxonomic space
R. J. Kinsella, A. Kahari, S. Haider, J. Zamora, G. Proctor, G. Spudich, J. Almeida-King, D. Staines, P. Derwent, A. Kerhornou, P. Kersey, and P. Flicek. 2011 · 2011
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Prioritizing candidate disease genes by network-based boosting of genome-wide association data
Insuk Lee, U. Martin Blom, Peggy I. Wang, Jung Eun Shim, and Edward M. Marcotte. 2011 · 2011
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Scikit-learn: Machine learning in Python
F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion, O. Grisel, M. Blondel, P. Prettenhofer, R. Weiss, V. Dubourg, J. Vanderplas, A. Passos, D. Cournapeau, M. Brucher, M. Perrot, and E. Duchesnay. 2011 · 2011
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A genetic algorithm for optimizing subnetwork markers for the study of breast cancer metastasis
Jiaxin Wu, Mingxin Gan, and Rui Jiang. 2011 · 2011
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“guilt by association” is the exception rather than the rule in gene networks
Jesse Gillis and Paul Pavlidis. 2012 · 2012
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Oas proteins and cgas: unifying concepts in sensing and responding to cytosolic nucleic acids
Veit Hornung, Rune Hartmann, Andrea Ablasser, and Karl-Peter Hopfner. 2014 · 2014
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Guidelines for investigating causality of sequence variants in human disease
D. G. MacArthur, T. A. Manolio, D. P. Dimmock, H. L. Rehm, J. Shendure, G. R. Abecasis, D. R. Adams, R. B. Altman, S. E. Antonarakis, E. A. Ashley, J. C. Barrett, L. G. Biesecker, D. F. Conrad, G. M. Cooper, N. J. Cox, M. J. Daly, M. B. Gerstein, D. B. Goldstein, J. N. Hirschhorn, S. M. Leal, L. A. Pennacchio, J. A. Stamatoyannopoulos, S. R. Sunyaev, D. Valle, B. F. Voight, W. Winckler, and C. Gunter. 2014 · 2014
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Rare variant association studies: considerations, challenges and opportunities
Paul L Auer and Guillaume Lettre. 2015 · 2015
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A global reference for human genetic variation
Adam Auton, 1000 Genomes Project Consortium, Shane McCarthy, Gil A. McVean, and Goncalo R. Abecasis. 2015 · 2015
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Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the american college of medical genetics and genomics and the association for molecular pathology
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W. Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector, Karl Voelkerding, and Heidi L. Rehm. 2015 · 2015
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, and Avi Ma’ayan. 2016 · 2016
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The ensembl variant effect predictor
William McLaren, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, and Fiona Cunningham. 2016 · 2016
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Severe viral respiratory infections in children with ifih1 loss-of-function mutations
Samira Asgari, Luregn J. Schlapbach, Stéphanie Anchisi, Christian Hammer, Istvan Bartha, Thomas Junier, Geneviève Mottet-Osman, Klara M. Posfay-Barbe, David Longchamp, Martin Stocker, Samuel Cordey, Laurent Kaiser, Thomas Riedel, Tony Kenna, Deborah Long, Andreas Schibler, Amalio Telenti, Caroline Tapparel, Paul J. McLaren, Dominique Garcin, and Jacques Fellay. 2017 · 2017
Cited alongside, same era.
A large-scale benchmark of gene prioritization methods
Dimitri Guala and Erik L. L. Sonnhammer. 2017 · 2017
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The e3 ubiquitin ligase trim40 attenuates antiviral immune responses by targeting mda5 and rig-i
Chunyuan Zhao, Mutian Jia, Hui Song, Zhongxia Yu, Wenwen Wang, Qi Li, Lining Zhang, Wei Zhao, and Xuetao Cao. 2017 · 2017
Cited alongside, same era.
Omim.org: leveraging knowledge across phenotype–gene relationships
Joanna S Amberger, Carol A Bocchini, Alan F Scott, and Ada Hamosh. 2018 · 2018
Cited alongside, same era.
fastp: an ultra-fast all-in-one fastq preprocessor
Shifu Chen, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018 · 2018
Cited alongside, same era.
A comprehensive survey on graph neural networks
Zonghan Wu, Shirui Pan, Fengwen Chen, Guodong Long, Chengqi Zhang, and Philip S. Yu. 2021 · 2021
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Interferon receptor trafficking and signaling: Journey to the cross roads
Natacha Zanin, Christine Viaris de Lesegno, Christophe Lamaze, and Cedric M. Blouin. 2021 · 2021
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Inherited IFNAR1 deficiency in a child with both critical COVID-19 pneumonia and multisystem inflammatory syndrome
Hassan Abolhassani, Nils Landegren, Paul Bastard, Marie Materna, Mohammadreza Modaresi, Likun Du, Maribel Aranda-Guillén, Fabian Sardh, Fanglei Zuo, Peng Zhang, Harold Marcotte, Nico Marr, Taushif Khan, Manar Ata, Fatima Al-Ali, Remi Pescarmona, Alexandre Belot, Vivien Béziat, Qian Zhang, Jean-Laurent Casanova, Olle Kämpe, Shen-Ying Zhang, Lennart Hammarström, and Qiang Pan-Hammarström. 2022 · 2022
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Nine quick tips for pathway enrichment analysis
Davide Chicco and Giuseppe Agapito. 2022 · 2022
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Gseapy: a comprehensive package for performing gene set enrichment analysis in python
Zhuoqing Fang, Xinyuan Liu, and Gary Peltz. 2022 · 2022
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Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2018 · 2018
Cited alongside, same era.
The post-gwas era: From association to function
Michael D. Gallagher and Alice S. Chen-Plotkin. 2018 · 2018
Cited alongside, same era.
Modeling the acmg/amp variant classification guidelines as a bayesian classification framework
Sean V. Tavtigian, Marc S. Greenblatt, Steven M. Harrison, Robert L. Nussbaum, Snehit A. Prabhu, Kenneth M. Boucher, and Leslie G. Biesecker. 2018 · 2018
Cited alongside, same era.
An end-to-end deep learning architecture for graph classification
Muhan Zhang, Zhicheng Cui, Marion Neumann, and Yixin Chen. 2018 · 2018
Cited alongside, same era.
Mx genes: host determinants controlling influenza virus infection and trans-species transmission
Otto Haller and Georg Kochs. 2019 · 2019
Cited alongside, same era.
Decoupled weight decay regularization
Ilya Loshchilov and Frank Hutter. 2019 · 2019
Cited alongside, same era.
Language models are unsupervised multitask learners
Alec Radford, Jeff Wu, Rewon Child, David Luan, Dario Amodei, and Ilya Sutskever. 2019 · 2019
Cited alongside, same era.
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Dna language models are powerful predictors of genome-wide variant effects
Gonzalo Benegas, Sanjit Singh Batra, and Yun S. Song. 2023 · 2023
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Genome-wide prediction of disease variant effects with a deep protein language model
Nadav Brandes, Grant Goldman, Charlotte H. Wang, Chun Jimmie Ye, and Vasilis Ntranos. 2023 · 2023
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A genomic mutational constraint map using variation in 76, 156 human genomes
Siwei Chen, Laurent C. Francioli, Genome Aggregation Database (gnomAD) Consortium, Grace Tiao, Benjamin M. Neale, Daniel G. MacArthur, and Konrad J. Karczewski. 2023 · 2023
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To transformers and beyond: Large language models for the genome
Micaela E. Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J. Theis, Alan Moses, and Bo Wang. 2023 · 2023
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The nucleotide transformer: Building and evaluating robust foundation models for human genomics
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza-Revilla, Nicolas Lopez Carranza, Adam Henryk Grzywaczewski, Francesco Oteri, Christian Dallago, Evan Trop, Bernardo P. de Almeida, Hassan Sirelkhatim, Guillaume Richard, Marcin Skwark, Karim Beguir, Marie Lopez, and Thomas Pierrot. 2023 · 2023
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Fulminant viral hepatitis in two siblings with inherited IL-10RB deficiency
Cecilia B Korol, Serkan Belkaya, Fahad Alsohime, Lazaro Lorenzo, Stéphanie Boisson-Dupuis, Joseph Brancale, Anna-Lena Neehus, Silvia Vilarinho, Alsum Zobaida, Rabih Halwani, Saleh Al-Muhsen, Jean-Laurent Casanova, and Emmanuelle Jouanguy. 2023 · 2023
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Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children
Danyel Lee, Jérémie Le Pen, Ahmad Yatim, Beihua Dong, Yann Aquino, Masato Ogishi, Rémi Pescarmona, Estelle Talouarn, Darawan Rinchai, Peng Zhang, Magali Perret, Zhiyong Liu, Iolanda Jordan, Sefika Elmas Bozdemir, Gulsum Iclal Bayhan, Camille Beaufils, Lucy Bizien, Aurelie Bisiaux, Weite Lei, Milena Hasan, Jie Chen, Christina Gaughan, Abhishek Asthana, Valentina Libri, Joseph M Luna, Fabrice Jaffré, H-Heinrich Hoffmann, Eleftherios Michailidis, Marion Moreews, Yoann Seeleuthner, Kaya Bilguvar, Shrikant Mane, Carlos Flores, Yu Zhang, Andrés A Arias, Rasheed Bailey, Agatha Schlüter, Baptiste Milisavljevic, Benedetta Bigio, Tom Le Voyer, Marie Materna, Adrian Gervais, Marcela Moncada-Velez, Francesca Pala, Tomi Lazarov, Romain Levy, Anna-Lena Neehus, Jérémie Rosain, Jessica Peel, Yi-Hao Chan, Marie-Paule Morin, Rosa Maria Pino-Ramirez, Serkan Belkaya, Lazaro Lorenzo, Jordi Anton, Selket Delafontaine, Julie Toubiana, Fanny Bajolle, Victoria Fumadó, Marta L DeDiego, Nadhira Fidouh, Flore Rozenberg, Jordi Pérez-Tur, Shuibing Chen, Todd Evans, Frédéric Geissmann, Pierre Lebon, Susan R Weiss, Damien Bonnet, Xavier Duval, CoV-Contact Cohort§, COVID Human Genetic Effort¶, Qiang Pan-Hammarström, Anna M Planas, Isabelle Meyts, Filomeen Haerynck, Aurora Pujol, Vanessa Sancho-Shimizu, Clifford L Dalgard, Jacinta Bustamante, Anne Puel, Stéphanie Boisson-Dupuis, Bertrand Boisson, Tom Maniatis, Qian Zhang, Paul Bastard, Luigi Notarangelo, Vivien Béziat, Rebeca Perez de Diego, Carlos Rodriguez-Gallego, Helen C Su, Richard P Lifton, Emmanuelle Jouanguy, Aurélie Cobat, Laia Alsina, Sevgi Keles, Elie Haddad, Laurent Abel, Alexandre Belot, Lluis Quintana-Murci, Charles M Rice, Robert H Silverman, Shen-Ying Zhang, and Jean-Laurent Casanova. 2023 · 2023
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Bend: Benchmarking dna language models on biologically meaningful tasks
Frederikke Isa Marin, Felix Teufel, Marc Horlacher, Dennis Madsen, Dennis Pultz, Ole Winther, and Wouter Boomsma. 2023 · 2023
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Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution
Eric Nguyen, Michael Poli, Marjan Faizi, Armin Thomas, Callum Birch-Sykes, Michael Wornow, Aman Patel, Clayton Rabideau, Stefano Massaroli, Yoshua Bengio, Stefano Ermon, Stephen A. Baccus, and Chris Ré. 2023 · 2023
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Inborn errors of type i interferon immunity in patients with symptomatic acute hepatitis e
Ali Saadat, Jérôme Gouttenoire, Paolo Ripellino, David Semela, Soraya Amar, Beat M. Frey, Stefano Fontana, Elise Mdawar-Bailly, Darius Moradpour, Jacques Fellay, and Montserrat Fraga. 2023 · 2023
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The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest
Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Katerina Nastou, Farrokh Mehryary, Radja Hachilif, Annika L Gable, Tao Fang, Nadezhda T Doncheva, Sampo Pyysalo, Peer Bork, Lars J Jensen, and Christian von Mering. 2023 · 2023
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A survey of large language models
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Dnabert-2: Efficient foundation model and benchmark for multi-species genome
Zhihan Zhou, Yanrong Ji, Weijian Li, Pratik Dutta, Ramana Davuluri, and Han Liu. 2023 · 2023
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The reactome pathway knowledgebase 2024
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