#+title: Main #+COLUMNS: %25ITEM %YEAR %TAGS %TODO #+filetags: biblio * Général ** TODO Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome :PROPERTIES: :TITLE: Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome :BTYPE: article :CUSTOM_ID: collins2017 :AUTHOR: Ryan L. Collins and Harrison Brand and Claire E. Redin and Carrie Hanscom and Caroline Antolik and Matthew R. Stone and Joseph T. Glessner and Tamara Mason and Giulia Pregno and Naghmeh Dorrani and Giorgia Mandrile and Daniela Giachino and Danielle Perrin and Cole Walsh and Michelle Cipicchio and Maura Costello and Alexei Stortchevoi and Joon-Yong An and Benjamin B. Currall and Catarina M. Seabra and Ashok Ragavendran and Lauren Margolin and Julian A. Martinez-Agosto and Diane Lucente and Brynn Levy and Stephan J. Sanders and Ronald J. Wapner and Fabiola Quintero-Rivera and Wigard Kloosterman and Michael E. Talkowski :JOURNAL: Genome Biology :YEAR: 2017 :VOLUME: 18 :NUMBER: 1 :PAGES: 36 :DOI: 10.1186/s13059-017-1158-6 :URL: http://dx.doi.org/10.1186/s13059-017-1158-6 :END: Défini des SV complexes avec illustrations ([[https://link.springer.com/article/10.1186/s13059-017-1158-6/figures/2][figure]] ) * Pseudogene :PROPERTIES: :CATEGORY: pseudogene :END: *** DONE Contexte CLOSED: [2024-06-24 lun. 11:52] **** DONE Overcoming challenges and dogmas to understand the functions of pseudogenes [cite:@cheetham2019] CLOSED: [2024-06-12 mer. 18:00] SCHEDULED: <2024-06-10 lun.> :PROPERTIES: :TITLE: Overcoming challenges and dogmas to understand the functions of pseudogenes :BTYPE: article :CUSTOM_ID: cheetham2019 :AUTHOR: Seth W. Cheetham and Geoffrey J. Faulkner and Marcel E. Dinger :JOURNAL: Nature Reviews Genetics :YEAR: 2019 :VOLUME: 21 :NUMBER: 3 :PAGES: 191-201 :DOI: 10.1038/s41576-019-0196-1 :URL: http://dx.doi.org/10.1038/s41576-019-0196-1 :END: **** DONE Blueprint Genetics’ approach to pseudogenes and other duplicated genomic regions CLOSED: [2024-06-14 ven. 17:17] :PROPERTIES: :TITLE: Blueprint Genetics’ approach to pseudogenes and other duplicated genomic regions :BTYPE: misc :CUSTOM_ID: blueprint2020 :AUTHOR: BluePrint Genetics :YEAR: 2020 :URL: https://blueprintgenetics.com/pseudogene/ :NOTE: Accessed 2024-06-14 :END: *** KILL Identification pseudogene: pas le scope CLOSED: [2024-07-22 Mon 17:07] **** DONE Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers CLOSED: [2024-06-10 lun. 16:55] :PROPERTIES: :TITLE: Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers :BTYPE: article :CUSTOM_ID: kalyana-sundaram2012 :AUTHOR: Shanker Kalyana-Sundaram and Chandan Kumar-Sinha and Sunita Shankar and Dan R. Robinson and Yi-Mi Wu and Xuhong Cao and Irfan A. Asangani and Vishal Kothari and John R. Prensner and Robert J. Lonigro and Matthew K. Iyer and Terrence Barrette and Achiraman Shanmugam and Saravana M. Dhanasekaran and Nallasivam Palanisamy and Arul M. Chinnaiyan :JOURNAL: Cell :YEAR: 2012 :VOLUME: 149 :NUMBER: 7 :PAGES: 1622-1634 :DOI: 10.1016/j.cell.2012.04.041 :URL: http://dx.doi.org/10.1016/j.cell.2012.04.041 :END: RNAseq seul 1 ou 2 read aligné sur région annotéte puis filtre puis utilisation d'ENCODE, YALE et base de donnée maison D'après[cite:@cheetham2019], ne prend en compte que les reads des régions divergentes des pseudogènes -> pseudogènes "anciens" en terme d'évolution **** DONE PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data :récent: :PROPERTIES: :TITLE: PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data :BTYPE: article :CUSTOM_ID: abrahamsson2022ppsifinder :AUTHOR: Sanna Abrahamsson and Frida Eiengård and Anna Rohlin and Marcela Dávila López :JOURNAL: BMC Bioinformatics :YEAR: 2022 :VOLUME: 23 :NUMBER: 1 :PAGES: 59 :DOI: 10.1186/s12859-022-04583-4 :URL: http://dx.doi.org/10.1186/s12859-022-04583-4 :END: Candidat intéressant, testé sur panel + validé sanger **** DONE Pseudofinder: detection of pseudogenes in prokaryotic genomes :récent: CLOSED: [2024-06-24 lun. 15:15] :PROPERTIES: :TITLE: Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes :BTYPE: article :CUSTOM_ID: syber2022pseudofinder :AUTHOR: Mitchell J Syberg-Olsen and Arkadiy I Garber and Patrick J Keeling and John P McCutcheon and Filip Husnik :JOURNAL: Molecular Biology and Evolution :YEAR: 2022 :VOLUME: 39 :NUMBER: 7 :PAGES: nil :DOI: 10.1093/molbev/msac153 :URL: http://dx.doi.org/10.1093/molbev/msac153 :END: **** DONE Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution CLOSED: [2024-07-17 Wed 16:39] SCHEDULED: <2024-07-15 lun.> :PROPERTIES: :TITLE: Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution :BTYPE: article :CUSTOM_ID: zheng2007pseudogenes :AUTHOR: Zheng, Deyou and Frankish, Adam and Baertsch, Robert and Kapranov, Philipp and Reymond, Alexandre and Choo, Siew Woh and Lu, Yontao and Denoeud, France and Antonarakis, Stylianos E and Snyder, Michael and others :JOURNAL: Genome research :VOLUME: 17 :NUMBER: 6 :PAGES: 839--851 :YEAR: 2007 :PUBLISHER: Cold Spring Harbor Lab :END: **** DONE PseudoPipe: an automated pseudogene identification pipeline CLOSED: [2024-06-26 mer. 14:03] :PROPERTIES: :TITLE: PseudoPipe: an automated pseudogene identification pipeline :BTYPE: article :CUSTOM_ID: zhang2006pseudopipe :AUTHOR: Zhaolei Zhang and Nicholas Carriero and Deyou Zheng and John Karro and Paul M. Harrison and Mark Gerstein :JOURNAL: Bioinformatics :YEAR: 2006 :VOLUME: 22 :NUMBER: 12 :PAGES: 1437-1439 :DOI: 10.1093/bioinformatics/btl116 :URL: http://dx.doi.org/10.1093/bioinformatics/btl116 :END: **** DONE Iterative gene prediction and pseudogene removal improves genome annotation :abandonné:ppfinder: CLOSED: [2024-06-26 mer. 14:38] SCHEDULED: <2024-06-26 mer.> :PROPERTIES: :TITLE: Iterative gene prediction and pseudogene removal improves genome annotation :BTYPE: article :CUSTOM_ID: van2006ppfinder :AUTHOR: Marijke J. van Baren and Michael R. Brent :JOURNAL: Genome Research :YEAR: 2006 :VOLUME: 16 :NUMBER: 5 :PAGES: 678-685 :DOI: 10.1101/gr.4766206 :URL: http://dx.doi.org/10.1101/gr.4766206 :END: **** DONE Retrocopy contributions to the evolution of the human genome :abandonné:retrofinder: CLOSED: [2024-06-27 jeu. 17:44] SCHEDULED: <2024-06-27 jeu.> :PROPERTIES: :TITLE: Retrocopy contributions to the evolution of the human genome :BTYPE: article :CUSTOM_ID: baertsch2008retrofinder :AUTHOR: Baertsch, Robert and Diekhans, Mark and Kent, W James and Haussler, David and Brosius, Jürgen :JOURNAL: BMC Genomics :YEAR: 2008 :VOLUME: 9 :NUMBER: 1 :PAGES: 466 :ISSN: 1471-2164 :DOI: 10.1186/1471-2164-9-466 :URL: http://dx.doi.org/10.1186/1471-2164-9-466 :PUBLISHER: Springer Science and Business Media LLC :END: **** DONE P-GRe: An efficient pipeline to maximised pseudogene prediction in plants/eucaryotes CLOSED: [2024-07-08 lun. 16:48] SCHEDULED: <2024-07-08 lun.> :PROPERTIES: :TITLE: P-GRe: An efficient pipeline to maximised pseudogene prediction in plants/eucaryotes :BTYPE: article :CUSTOM_ID: cabanac2023p :AUTHOR: Cabanac, S{\'e}bastien and Mathe, Catherine and Dunand, Christophe :JOURNAL: bioRxiv :PAGES: 2023--12 :YEAR: 2023 :URL: https://www.biorxiv.org/content/10.1101/2023.12.04.569967v1 :PUBLISHER: Cold Spring Harbor Laboratory :END: :LOGBOOK: CLOCK: [2024-07-08 lun. 16:22]--[2024-07-08 lun. 16:48] => 0:26 :END: **** DONE sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies :récent: CLOSED: [2024-07-09 mar. 10:05] SCHEDULED: <2024-07-09 mar.> :PROPERTIES: :TITLE: sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies :BTYPE: article :CUSTOM_ID: miller2021sideretro :AUTHOR: Miller, Thiago LA and Orpinelli Rego, Fernanda and Buzzo, Jos{\'e} Leonel L and Galante, Pedro AF :JOURNAL: Bioinformatics :VOLUME: 37 :NUMBER: 3 :PAGES: 419--421 :YEAR: 2021 :URL: https://academic.oup.com/bioinformatics/article/37/3/419/5876827?login=false :PUBLISHER: Oxford University Press :END: **** DONE Pseudogenes and Their Genome-Wide Prediction in Plants CLOSED: [2024-07-17 mer. 12:08] SCHEDULED: <2024-07-15 lun.> :PROPERTIES: :TITLE: Pseudogenes and Their Genome-Wide Prediction in Plants :BTYPE: article :CUSTOM_ID: ijms17121991 :AUTHOR: Xiao, Jin and Sekhwal, Manoj Kumar and Li, Pingchuan and Ragupathy, Raja and Cloutier, Sylvie and Wang, Xiue and You, Frank M. :JOURNAL: International Journal of Molecular Sciences :VOLUME: 17 :YEAR: 2016 :NUMBER: 12 :ARTICLE-NUMBER: 1991 :URL: https://www.mdpi.com/1422-0067/17/12/1991 :PUBMEDID: 27916797 :ISSN: 1422-0067 :ABSTRACT: Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu’s pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu’s pipeline identified 80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants. :DOI: 10.3390/ijms17121991 :END: **** DONE Automatic annotation of eukaryotic genes, pseudogenes and promoters CLOSED: [2024-07-17 Wed 15:00] SCHEDULED: <2024-07-17 mer.> :PROPERTIES: :TITLE: Automatic annotation of eukaryotic genes, pseudogenes and promoters :BTYPE: article :CUSTOM_ID: solovyev2006automatic :AUTHOR: Solovyev, Victor and Kosarev, Peter and Seledsov, Igor and Vorobyev, Denis :URL: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-s1-s10 :JOURNAL: Genome biology :VOLUME: 7 :PAGES: 1--12 :YEAR: 2006 :URL: https://link.springer.com/article/10.1186/Gb-2006-7-S1-S10 :PUBLISHER: Springer :END: **** DONE The GENCODE pseudogene resource CLOSED: [2024-07-17 Wed 15:15] SCHEDULED: <2024-07-17 Wed> :PROPERTIES: :TITLE: The GENCODE pseudogene resource :BTYPE: article :CUSTOM_ID: pei2012gencode :AUTHOR: Pei, Baikang and Sisu, Cristina and Frankish, Adam and Howald, C{\'e}dric and Habegger, Lukas and Mu, Xinmeng Jasmine and Harte, Rachel and Balasubramanian, Suganthi and Tanzer, Andrea and Diekhans, Mark and others :JOURNAL: Genome biology :VOLUME: 13 :PAGES: 1--26 :YEAR: 2012 :PUBLISHER: Springer :URL: https://link.springer.com/article/10.1186/gb-2012-13-9-r51 :END: **** DONE Discovery of non-reference processed pseudogenes in the Swedish population CLOSED: [2024-07-17 Wed 16:03] :PROPERTIES: :TITLE: Discovery of non-reference processed pseudogenes in the Swedish population :BTYPE: article :CUSTOM_ID: boer2023processen :AUTHOR: Esmee Ten Berk de Boer and Kristine Bilgrav Saether and Jesper Eisfeldt :JOURNAL: Frontiers in Genetics :YEAR: 2023 :VOLUME: 14 :NUMBER: nil :PAGES: nil :DOI: 10.3389/fgene.2023.1176626 :URL: http://dx.doi.org/10.3389/fgene.2023.1176626 :END: **** DONE Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance CLOSED: [2024-07-17 Wed 16:40] SCHEDULED: <2024-07-17 Wed> :PROPERTIES: :TITLE: Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance :BTYPE: article :CUSTOM_ID: yang24loss :AUTHOR: Yi Yang and Pengzhi Wang and Samir El Qaidi and Philip R. Hardwidge and Jinlin Huang and Guoqiang Zhu :JOURNAL: Applied Microbiology and Biotechnology :YEAR: 2024 :VOLUME: 108 :NUMBER: 1 :PAGES: 328 :DOI: 10.1007/s00253-023-12971-w :URL: http://dx.doi.org/10.1007/s00253-023-12971-w :END: **** DONE Re-recognition of pseudogenes: From molecular to clinical applications CLOSED: [2024-07-17 Wed 17:06] :PROPERTIES: :TITLE: Re-recognition of pseudogenes: From molecular to clinical applications :BTYPE: article :CUSTOM_ID: chen2020rerecognition :AUTHOR: Xu Chen and Lin Wan and Wei Wang and Wen-Jin Xi and An-Gang Yang and Tao Wang :JOURNAL: Theranostics :YEAR: 2020 :VOLUME: 10 :NUMBER: 4 :PAGES: 1479-1499 :DOI: 10.7150/thno.40659 :URL: http://dx.doi.org/10.7150/thno.40659 :END: **** DONE Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice CLOSED: [2024-07-17 Wed 17:18] SCHEDULED: <2024-07-17 mer.> :PROPERTIES: :TITLE: Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice :BTYPE: article :URL: https://academic.oup.com/plphys/article/151/1/3/6108462 :CUSTOM_ID: zou2009evolutionary :AUTHOR: Zou, Cheng and Lehti-Shiu, Melissa D and Thibaud-Nissen, Fran{\c{c}}oise and Prakash, Tanmay and Buell, C Robin and Shiu, Shin-Han :JOURNAL: Plant physiology :VOLUME: 151 :NUMBER: 1 :PAGES: 3--15 :YEAR: 2009 :PUBLISHER: American Society of Plant Biologists :END: **** DONE Identification of Pseudogenes in Brachypodium distachyon Chromosomes CLOSED: [2024-07-17 Wed 17:34] :PROPERTIES: :TITLE: Identification of Pseudogenes in Brachypodium distachyon Chromosomes :BTYPE: article :CUSTOM_ID: camiolo2018identification :AUTHOR: Camiolo, Salvatore and Porceddu, Andrea :JOURNAL: Brachypodium Genomics: Methods and Protocols :PAGES: 149--171 :YEAR: 2018 :PUBLISHER: Springer :END: **** DONE Structural characterization and duplication modes of pseudogenes in plants CLOSED: [2024-07-17 Wed 17:34] SCHEDULED: <2024-07-15 lun.> :PROPERTIES: :TITLE: Structural characterization and duplication modes of pseudogenes in plants :BTYPE: article :CUSTOM_ID: mascagni2021structural :AUTHOR: Mascagni, Flavia and Usai, Gabriele and Cavallini, Andrea and Porceddu, Andrea :JOURNAL: Scientific Reports :VOLUME: 11 :NUMBER: 1 :PAGES: 5292 :YEAR: 2021 :PUBLISHER: Nature Publishing Group UK London :URL: https://www.nature.com/articles/s41598-021-84778-6 :END: **** DONE Processed pseudogenes acquired somatically during cancer development CLOSED: [2024-07-17 Wed 17:36] SCHEDULED: <2024-07-15 lun.> :PROPERTIES: :TITLE: Processed pseudogenes acquired somatically during cancer development :BTYPE: article :CUSTOM_ID: cooke2014processed :AUTHOR: Cooke, Susanna L and Shlien, Adam and Marshall, John and Pipinikas, Christodoulos P and Martincorena, Inigo and Tubio, Jose MC and Li, Yilong and Menzies, Andrew and Mudie, Laura and Ramakrishna, Manasa and others :JOURNAL: Nature communications :VOLUME: 5 :NUMBER: 1 :PAGES: 3644 :YEAR: 2014 :PUBLISHER: Nature Publishing Group UK London :END: *** TODO Appel de variant sur pseudogène connu **** DONE [#A] Integrating gene annotation with orthology inference at scale CLOSED: [2024-08-06 mar. 10:19] SCHEDULED: <2024-07-30 Tue> :PROPERTIES: :TITLE: Integrating gene annotation with orthology inference at scale :BTYPE: article :CUSTOM_ID: Kirilenko_2023 :VOLUME: 380 :ISSN: 1095-9203 :URL: http://dx.doi.org/10.1126/science.abn3107 :DOI: 10.1126/science.abn3107 :NUMBER: 6643 :JOURNAL: Science :PUBLISHER: American Association for the Advancement of Science (AAAS) :AUTHOR: Kirilenko, Bogdan M. and Munegowda, Chetan and Osipova, Ekaterina and Jebb, David and Sharma, Virag and Blumer, Moritz and Morales, Ariadna E. and Ahmed, Alexis-Walid and Kontopoulos, Dimitrios-Georgios and Hilgers, Leon and Lindblad-Toh, Kerstin and Karlsson, Elinor K. and Hiller, Michael and Andrews, Gregory and Armstrong, Joel C. and Bianchi, Matteo and Birren, Bruce W. and Bredemeyer, Kevin R. and Breit, Ana M. and Christmas, Matthew J. and Clawson, Hiram and Damas, Joana and Di Palma, Federica and Diekhans, Mark and Dong, Michael X. and Eizirik, Eduardo and Fan, Kaili and Fanter, Cornelia and Foley, Nicole M. and Forsberg-Nilsson, Karin and Garcia, Carlos J. and Gatesy, John and Gazal, Steven and Genereux, Diane P. and Goodman, Linda and Grimshaw, Jenna and Halsey, Michaela K. and Harris, Andrew J. and Hickey, Glenn and Hiller, Michael and Hindle, Allyson G. and Hubley, Robert M. and Hughes, Graham M. and Johnson, Jeremy and Juan, David and Kaplow, Irene M. and Karlsson, Elinor K. and Keough, Kathleen C. and Kirilenko, Bogdan and Koepfli, Klaus-Peter and Korstian, Jennifer M. and Kowalczyk, Amanda and Kozyrev, Sergey V. and Lawler, Alyssa J. and Lawless, Colleen and Lehmann, Thomas and Levesque, Danielle L. and Lewin, Harris A. and Li, Xue and Lind, Abigail and Lindblad-Toh, Kerstin and Mackay-Smith, Ava and Marinescu, Voichita D. and Marques-Bonet, Tomas and Mason, Victor C. and Meadows, Jennifer R. S. and Meyer, Wynn K. and Moore, Jill E. and Moreira, Lucas R. and Moreno-Santillan, Diana D. and Morrill, Kathleen M. and Muntané, Gerard and Murphy, William J. and Navarro, Arcadi and Nweeia, Martin and Ortmann, Sylvia and Osmanski, Austin and Paten, Benedict and Paulat, Nicole S. and Pfenning, Andreas R. and Phan, BaDoi N.and Pollard, Katherine S. and Pratt, Henry E. and Ray, David A. and Reilly, Steven K. and Rosen, Jeb R. and Ruf, Irina and Ryan, Louise and Ryder, Oliver A. and Sabeti, Pardis C. and Schäffer, Daniel E. and Serres, Aitor and Shapiro, Beth and Smit, Arian F. A. and Springer, Mark and Srinivasan, Chaitanya and Steiner, Cynthia and Storer, Jessica M. and Sullivan, Kevin A. M. and Sullivan, Patrick F. and Sundström, Elisabeth and Supple, Megan A. and Swofford, Ross and Talbot, Joy-El and Teeling, Emma and Turner-Maier, Jason and Valenzuela, Alejandro and Wagner, Franziska and Wallerman, Ola and Wang, Chao and Wang, Juehan and Weng, Zhiping and Wilder, Aryn P. and Wirthlin, Morgan E. and Xue, James R. and Zhang, Xiaomeng :YEAR: 2023 :MONTH: apr :END: **** TODO Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation SCHEDULED: <2024-08-07 mer.> :PROPERTIES: :TITLE: Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation :BTYPE: article :CUSTOM_ID: steyaert2023systematic :AUTHOR: Wouter Steyaert and Lonneke Haer-Wigman and Rolph Pfundt and Debby Hellebrekers and Marloes Steehouwer and Juliet Hampstead and Elke de Boer and Alexander Stegmann and Helger Yntema and Erik-Jan Kamsteeg and Han Brunner and Alexander Hoischen and Christian Gilissen :JOURNAL: Nature Communications :YEAR: 2023 :VOLUME: 14 :NUMBER: 1 :PAGES: 6845 :DOI: 10.1038/s41467-023-42531-9 :URL: http://dx.doi.org/10.1038/s41467-023-42531-9 :END: **** DONE Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight CLOSED: [2024-07-26 Fri 12:12] SCHEDULED: <2024-07-26 Fri> :PROPERTIES: :TITLE: Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight :BTYPE: article :CUSTOM_ID: ebbert2019systematic :AUTHOR: Ebbert, Mark TW and Jensen, Tanner D and Jansen-West, Karen and Sens, Jonathon P and Reddy, Joseph S and Ridge, Perry G and Kauwe, John SK and Belzil, Veronique and Pregent, Luc and Carrasquillo, Minerva M and others :JOURNAL: Genome biology :VOLUME: 20 :PAGES: 1--23 :YEAR: 2019 :PUBLISHER: Springer :URL: https://link.springer.com/article/10.1186/s13059-019-1707-2 :DOI: 10.1186/s13059-019-1707-2 :END: **** KILL Errors in RNA-Seq quantification affect genes of relevance to human disease CLOSED: [2024-07-26 Fri 12:09] :PROPERTIES: :TITLE: Errors in RNA-Seq quantification affect genes of relevance to human disease :BTYPE: article :CUSTOM_ID: robert2015errors :AUTHOR: Robert, Christelle and Watson, Mick :JOURNAL: Genome biology :VOLUME: 16 :PAGES: 1--16 :YEAR: 2015 :PUBLISHER: Springer :END: * Facebook :PROPERTIES: :CATEGORY: facebook :END: Méthode - [X] article julien - [X] Recherche avec "attribute disclosure DNA" (erlich2014), "phenotypic prediction" "genetic triangulation" - [X] références du tableau 1 de [cite:@yakubu2019] - [X] identity tracing - [X] attribute disclore - [X] completion A replacer "Utilisation de données HapMap + généalogique + données génotype et phénotype -> retrouve lignage par rapport lignée fondatrice" ** Bibliographie générale *** DONE Actionable genotypes and their association with life span in Iceland CLOSED: [2024-07-12 ven. 15:01] :PROPERTIES: :TITLE: Actionable genotypes and their association with life span in Iceland :BTYPE: article :CUSTOM_ID: jensson2023actionable :AUTHOR: Jensson, Brynjar O and Arnadottir, Gudny A and Katrinardottir, Hildigunnur and Fridriksdottir, Run and Helgason, Hannes and Oddsson, Asmundur and Sveinbjornsson, Gardar and Eggertsson, Hannes P and Halldorsson, Gisli H and Atlason, Bjarni A and others :JOURNAL: New England Journal of Medicine :VOLUME: 389 :NUMBER: 19 :PAGES: 1741--1752 :YEAR: 2023 :PUBLISHER: Mass Medical Soc :END: *** DONE Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks :identity_tracing: CLOSED: [2024-07-10 mer. 14:56] :PROPERTIES: :TITLE: Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks :BTYPE: article :CUSTOM_ID: raisaro2017 :AUTHOR: Raisaro, Jean Louis and Tramer, Florian and Ji, Zhanglong and Bu, Diyue and Zhao, Yongan and Carey, Knox and Lloyd, David and Sofia, Heidi and Baker, Dixie and Flicek, Paul and others :JOURNAL: Journal of the American Medical Informatics Association :VOLUME: 24 :NUMBER: 4 :PAGES: 799--805 :YEAR: 2017 :PUBLISHER: Oxford University Press :END: *** DONE Addressing the concerns of the lacks family: quantification of kin genomic privacy CLOSED: [2024-07-11 Thu 19:49] :PROPERTIES: :TITLE: Addressing the concerns of the lacks family: quantification of kin genomic privacy :BTYPE: inproceedings :CUSTOM_ID: humbert2013addressing :AUTHOR: Humbert, Mathias and Ayday, Erman and Hubaux, Jean-Pierre and Telenti, Amalio :BOOKTITLE: Proceedings of the 2013 ACM SIGSAC conference on Computer \& communications security :PAGES: 1141--1152 :YEAR: 2013 :END: *** DONE An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information CLOSED: [2024-07-11 Thu 20:17] :PROPERTIES: :TITLE: An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information :BTYPE: article :CUSTOM_ID: deznabi2018inference :AUTHOR: Iman Deznabi and Mohammad Mobayen and Nazanin Jafari and Oznur Tastan and Erman Ayday :JOURNAL: IEEE/ACM Transactions on Computational Biology and Bioinformatics :YEAR: 2018 :VOLUME: 15 :NUMBER: 4 :PAGES: 1333-1343 :DOI: 10.1109/tcbb.2017.2709740 :URL: http://dx.doi.org/10.1109/TCBB.2017.2709740 :END: *** DONE Assessing transcriptomic reidentification risks using discriminative sequence models CLOSED: [2024-07-12 ven. 18:03] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Assessing transcriptomic reidentification risks using discriminative sequence models :BTYPE: article :CUSTOM_ID: sadhuka2023 :AUTHOR: Shuvom Sadhuka and Daniel Fridman and Bonnie Berger and Hyunghoon Cho :JOURNAL: Genome Research :YEAR: 2023 :VOLUME: nil :NUMBER: nil :PAGES: nil :DOI: 10.1101/gr.277699.123 :URL: http://dx.doi.org/10.1101/gr.277699.123 :END: Mise à jour des algorithme + coût *** DONE Bayesian method to predict individual SNP genotypes from gene expression data CLOSED: [2024-07-12 ven. 14:31] :PROPERTIES: :TITLE: Bayesian method to predict individual SNP genotypes from gene expression data :BTYPE: article :CUSTOM_ID: schadt2012bayesian :AUTHOR: Schadt, Eric E and Woo, Sangsoon and Hao, Ke :JOURNAL: Nature genetics :VOLUME: 44 :NUMBER: 5 :PAGES: 603--608 :YEAR: 2012 :PUBLISHER: Nature Publishing Group US New York :URL: https://www.nature.com/articles/ng.2248 :END: *** KILL Data Sharing Under the General Data Protection Regulation CLOSED: [2024-07-12 ven. 15:17] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Data Sharing Under the General Data Protection Regulation :BTYPE: article :CUSTOM_ID: vlahou21:_data_sharin_under_gener_data_protec_regul :AUTHOR: Antonia Vlahou and Dara Hallinan and Rolf Apweiler and Angel Argiles and Joachim Beige and Ariela Benigni and Rainer Bischoff and Peter C. Black and Franziska Boehm and Jocelyn Céraline and George P. Chrousos and Christian Delles and Pieter Evenepoel and Ivo Fridolin and Griet Glorieux and Alain J. van Gool and Isabel Heidegger and John P.A. Ioannidis and Joachim Jankowski and Vera Jankowski and Carmen Jeronimo and Ashish M. Kamat and Rosalinde Masereeuw and Gert Mayer and Harald Mischak and Alberto Ortiz and Giuseppe Remuzzi and Peter Rossing and Joost P. Schanstra and Bernd J. Schmitz-Dräger and Goce Spasovski and Jan A. Staessen and Dimitrios Stamatialis and Peter Stenvinkel and Christoph Wanner and Stephen B. Williams and Faiez Zannad and Carmine Zoccali and Raymond Vanholder :JOURNAL: Hypertension :YEAR: 2021 :VOLUME: 77 :NUMBER: 4 :PAGES: 1029-1035 :DOI: 10.1161/hypertensionaha.120.16340 :URL: http://dx.doi.org/10.1161/HYPERTENSIONAHA.120.16340 :END: Trop général, pas d'apport ("il faut harmoziser") Mais 2 liens intéressants *** DONE De-anonymizing genomic databases using phenotypic traits CLOSED: [2024-07-11 jeu. 11:38] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: De-anonymizing genomic databases using phenotypic traits :BTYPE: inproceedings :CUSTOM_ID: humbert2015anonymizing :AUTHOR: Humbert, Mathias and Huguenin, K{\'e}vin and Hugonot, Joachim and Ayday, Erman and Hubaux, Jean-Pierre :BOOKTITLE: 15th Privacy Enhancing Technologies Symposium (PETS) :VOLUME: 2015 :NUMBER: 2 :PAGES: 99--114 :YEAR: 2015 :URL: https://hal.science/hal-01151960/file/Humbert2015PETS.pdf :END: *** DONE Detection of sharing by descent, long-range phasing and haplotype imputation CLOSED: [2024-07-11 Thu 21:17] :PROPERTIES: :TITLE: Detection of sharing by descent, long-range phasing and haplotype imputation :BTYPE: article :CUSTOM_ID: kong2008detection :AUTHOR: Augustine Kong and Gisli Masson and Michael L Frigge and Arnaldur Gylfason and Pasha Zusmanovich and Gudmar Thorleifsson and Pall I Olason and Andres Ingason and Stacy Steinberg and Thorunn Rafnar and Patrick Sulem and Magali Mouy and Frosti Jonsson and Unnur Thorsteinsdottir and Daniel F Gudbjartsson and Hreinn Stefansson and Kari Stefansson :JOURNAL: Nature Genetics :YEAR: 2008 :VOLUME: 40 :NUMBER: 9 :PAGES: 1068-1075 :DOI: 10.1038/ng.216 :URL: http://dx.doi.org/10.1038/ng.216 :END: *** DONE Deterministic identification of specific individuals from GWAS results :attribute_disclosure: CLOSED: [2024-07-11 Thu 21:18] :PROPERTIES: :TITLE: Deterministic identification of specific individuals from GWAS results :BTYPE: article :CUSTOM_ID: cai2015 :AUTHOR: Ruichu Cai and Zhifeng Hao and Marianne Winslett and Xiaokui Xiao and Yin Yang and Zhenjie Zhang and Shuigeng Zhou :JOURNAL: Bioinformatics :YEAR: 2015 :VOLUME: 31 :NUMBER: 11 :PAGES: 1701-1707 :DOI: 10.1093/bioinformatics/btv018 :URL: http://dx.doi.org/10.1093/bioinformatics/btv018 :END: *** DONE [#A] Ensuring privacy and security of genomic data and functionalities CLOSED: [2024-07-11 Thu 21:17] :PROPERTIES: :TITLE: Ensuring privacy and security of genomic data and functionalities :BTYPE: article :CUSTOM_ID: yakubu2019 :VOLUME: 21 :ISSN: 1477-4054 :URL: http://dx.doi.org/10.1093/bib/bbz013 :DOI: 10.1093/bib/bbz013 :NUMBER: 2 :JOURNAL: Briefings in Bioinformatics :PUBLISHER: Oxford University Press (OUP) :AUTHOR: Mohammed Yakubu, Abukari and Chen, Yi-Ping Phoebe :YEAR: 2019 :MONTH: feb :PAGES: 511–526 :END: Suite d'erlich2014 ? *** DONE Epigenome data release: a participant-centered approach to privacy protection CLOSED: [2024-07-09 mar. 14:57] SCHEDULED: <2024-07-09 mar.> :PROPERTIES: :TITLE: Epigenome data release: a participant-centered approach to privacy protection :BTYPE: article :URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0723-0#citeas :CUSTOM_ID: dyke2015epigenome :AUTHOR: Dyke, Stephanie OM and Cheung, Warren A and Joly, Yann and Ammerpohl, Ole and Lutsik, Pavlo and Rothstein, Mark A and Caron, Maxime and Busche, Stephan and Bourque, Guillaume and R{\"o}nnblom, Lars and others :JOURNAL: Genome biology :VOLUME: 16 :PAGES: 1--12 :YEAR: 2015 :PUBLISHER: Springer :END: :LOGBOOK: CLOCK: [2024-07-09 mar. 14:33]--[2024-07-09 mar. 14:57] => 0:24 :END: - [cite:@erlich2014] on peut retrouver l'identité d'un individé mais il faut dans la majorité des cas données génétique d'une autre source - Cas spéciaux: exemple du chromosome Y [cite:@Gitschier_2009] - RNA: complexe pour retrouver - SNPs visible dans épigénétique mais on peut en masquer une bonne partie *** DONE Estimating the success of re-identifications in incomplete datasets using generative models CLOSED: [2024-07-12 ven. 15:36] :PROPERTIES: :TITLE: Estimating the success of re-identifications in incomplete datasets using generative models :BTYPE: article :CUSTOM_ID: rocher2019estimating :AUTHOR: Rocher, Luc and Hendrickx, Julien M and De Montjoye, Yves-Alexandre :JOURNAL: Nature communications :VOLUME: 10 :NUMBER: 1 :PAGES: 1--9 :YEAR: 2019 :PUBLISHER: Nature Publishing Group :URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650473/ :END: *** DONE Ethical implications of epigenetics in the era of personalized medicine CLOSED: <2024-07-09 mar. 13:46> :PROPERTIES: :TITLE: Ethical implications of epigenetics in the era of personalized medicine :BTYPE: article :CUSTOM_ID: santalo2022ethic :AUTHOR: Josep Santaló and María Berdasco :JOURNAL: Clinical Epigenetics :YEAR: 2022 :VOLUME: 14 :NUMBER: 1 :PAGES: 44 :DOI: 10.1186/s13148-022-01263-1 :URL: http://dx.doi.org/10.1186/s13148-022-01263-1 :END: :LOGBOOK: CLOCK: [2024-07-09 mar. 13:32]--[2024-07-09 mar. 13:46] => 0:14 CLOCK: [2024-07-09 mar. 11:41]--[2024-07-09 mar. 12:00] => 0:19 CLOCK: [2024-07-09 mar. 11:20]--[2024-07-09 mar. 11:26] => 0:06 :END: Seule partie intéressante : filtrer site SNP et renvoie vers [cite:@dyke2015epigenome] *** DONE Investigative genetic genealogy: Current methods, knowledge and practice CLOSED: [2024-08-01 jeu. 15:24] :PROPERTIES: :TITLE: Investigative genetic genealogy: Current methods, knowledge and practice :BTYPE: article :CUSTOM_ID: kling2021investigative :AUTHOR: Kling, Daniel and Phillips, Christopher and Kennett, Debbie and Tillmar, Andreas :JOURNAL: Forensic Science International: Genetics :VOLUME: 52 :PAGES: 102474 :YEAR: 2021 :PUBLISHER: Elsevier :DOI: 10.1016/j.fsigen.2021.102474 :END: *** DONE Privacy challenges and research opportunities for genomic data sharing CLOSED: [2024-07-12 ven. 18:16] :PROPERTIES: :TITLE: Privacy challenges and research opportunities for genomic data sharing :BTYPE: article :CUSTOM_ID: bonomi2020privacy :AUTHOR: Bonomi, Luca and Huang, Yingxiang and Ohno-Machado, Lucila :JOURNAL: Nature genetics :VOLUME: 52 :NUMBER: 7 :PAGES: 646--654 :YEAR: 2020 :URL: https://www.nature.com/articles/s41588-020-0651-0 :DOI: 10.1038/s41588-020-0651-0 :PUBLISHER: Nature Publishing Group US New York :END: *** KILL Genetic data are not always personal—disaggregating the identifiability and sensitivity of genetic data CLOSED: [2024-07-12 ven. 18:15] :PROPERTIES: :TITLE: Genetic data are not always personal—disaggregating the identifiability and sensitivity of genetic data :BTYPE: article :CUSTOM_ID: rahnasto2023genetic :AUTHOR: Rahnasto, Johanna :JOURNAL: Journal of Law and the Biosciences :VOLUME: 10 :NUMBER: 2 :PAGES: lsad029 :YEAR: 2023 :PUBLISHER: Oxford University Press :END: *** KILL Identification of anonymous DNA using genealogical triangulation CLOSED: [2024-07-12 ven. 18:13] :PROPERTIES: :TITLE: Identification of anonymous DNA using genealogical triangulation :BTYPE: article :CUSTOM_ID: ellenbogen2019identification :AUTHOR: Ellenbogen, Paul and Narayanan, Arvind :JOURNAL: bioRxiv :PAGES: 531269 :YEAR: 2019 :PUBLISHER: Cold Spring Harbor Laboratory :END: Pas eu le temps de lire mais juste un algo de plus *** KILL [#B] https://www.cell.com/ajhg/fulltext/S0002-9297(15)00200-1 CLOSED: [2024-07-12 ven. 18:12] impact méthylation prédiction IMC *** KILL [#B] https://www.sciencedirect.com/science/article/pii/S1872497321000132 CLOSED: [2024-07-12 ven. 18:17] *** DONE Identification of individuals by trait prediction using whole-genome sequencing data CLOSED: [2024-07-11 Thu 21:18] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Identification of individuals by trait prediction using whole-genome sequencing data :BTYPE: article :CUSTOM_ID: lippert2017 :AUTHOR: Lippert, Christoph and Sabatini, Riccardo and Maher, M Cyrus and Kang, Eun Yong and Lee, Seunghak and Arikan, Okan and Harley, Alena and Bernal, Axel and Garst, Peter and Lavrenko, Victor and others :JOURNAL: Proceedings of the National Academy of Sciences :VOLUME: 114 :NUMBER: 38 :PAGES: 10166--10171 :YEAR: 2017 :PUBLISHER: National Acad Sciences :URL: https://www.pnas.org/doi/full/10.1073/pnas.1711125114 :END: *** KILL Identifying disease-causing mutations with privacy protection CLOSED: [2024-07-12 ven. 18:18] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Identifying disease-causing mutations with privacy protection :BTYPE: article :CUSTOM_ID: akgün2020identying :AUTHOR: Mete Akgün and Ali Burak Ünal and Bekir Ergüner and Nico Pfeifer and Oliver Kohlbacher :JOURNAL: Bioinformatics :YEAR: 2020 :VOLUME: 36 :NUMBER: 21 :PAGES: 5205-5213 :DOI: 10.1093/bioinformatics/btaa641 :URL: http://dx.doi.org/10.1093/bioinformatics/btaa641 :END: Mitigation, pas le scope *** DONE Identifying Participants in the Personal Genome Project by Name (A Re-identification Experiment) :identity_tracing:identity_tracing: CLOSED: [2024-07-10 mer. 11:16] :PROPERTIES: :TITLE: Identifying Participants in the Personal Genome Project by Name (A Re-identification Experiment) :BTYPE: misc :CUSTOM_ID: sweeney2013 :AUTHOR: Latanya Sweeney and Akua Abu and Julia Winn :YEAR: 2013 :EPRINT: 1304.7605 :ARCHIVEPREFIX: arXiv :PRIMARYCLASS: cs.CY :URL: https://arxiv.org/abs/1304.7605 :END: *** DONE Identifying Personal Genomes by Surname Inference :identity_tracing: CLOSED: [2024-07-09 mar. 17:00] SCHEDULED: <2024-07-09 mar.> :PROPERTIES: :TITLE: Identifying Personal Genomes by Surname Inference :BTYPE: article :CUSTOM_ID: gymrek2013 :AUTHOR: Melissa Gymrek and Amy L. McGuire and David Golan and Eran Halperin and Yaniv Erlich :JOURNAL: Science :YEAR: 2013 :VOLUME: 339 :NUMBER: 6117 :PAGES: 321-324 :DOI: 10.1126/science.1229566 :URL: http://dx.doi.org/10.1126/science.1229566 :END: *** DONE Identity inference of genomic data using long-range familial searches :identity_tracing: CLOSED: [2024-07-10 mer. 17:50] SCHEDULED: <2024-07-09 mar.> :PROPERTIES: :TITLE: Identity inference of genomic data using long-range familial searches :BTYPE: article :CUSTOM_ID: erlich2018 :AUTHOR: Yaniv Erlich and Tal Shor and Itsik Pe’er and Shai Carmi :JOURNAL: Science :YEAR: 2018 :VOLUME: 362 :NUMBER: 6415 :PAGES: 690-694 :DOI: 10.1126/science.aau4832 :URL: http://dx.doi.org/10.1126/science.aau4832 :END: *** DONE Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data CLOSED: [2024-07-11 Thu 20:29] :PROPERTIES: :TITLE: Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data :BTYPE: article :CUSTOM_ID: he2020inference :AUTHOR: Zaobo He and Jiguo Yu and Ji Li and Qilong Han and Guangchun Luo and Yingshu Li :JOURNAL: IEEE/ACM Transactions on Computational Biology and Bioinformatics :YEAR: 2020 :VOLUME: 17 :NUMBER: 3 :PAGES: 930-937 :DOI: 10.1109/tcbb.2018.2810180 :URL: http://dx.doi.org/10.1109/TCBB.2018.2810180 :END: *** DONE Inferential Genotyping of Y Chromosomes in Latter-Day Saints Founders and Comparison to Utah Samples in the HapMap Project :surname_inference: CLOSED: [2024-07-09 mar. 15:33] SCHEDULED: <2024-07-09 mar.> :PROPERTIES: :TITLE: Inferential Genotyping of Y Chromosomes in Latter-Day Saints Founders and Comparison to Utah Samples in the HapMap Project :BTYPE: article :CUSTOM_ID: Gitschier_2009 :VOLUME: 84 :ISSN: 0002-9297 :URL: http://dx.doi.org/10.1016/j.ajhg.2009.01.018 :DOI: 10.1016/j.ajhg.2009.01.018 :NUMBER: 2 :JOURNAL: The American Journal of Human Genetics :PUBLISHER: Elsevier BV :AUTHOR: Gitschier, Jane :YEAR: 2009 :MONTH: feb :PAGES: 251–258 :END: Nom de familles à partir de 30 STR du chrY, voir[cite:@gymrek2013] pour suite *** DONE Major flaws in “Identification of individuals by trait prediction using whole-genome sequencing data” CLOSED: [2024-07-11 jeu. 13:54] :PROPERTIES: :TITLE: Major flaws in “Identification of individuals by trait prediction using whole-genome sequencing data” :BTYPE: article :CUSTOM_ID: erlich2017major :AUTHOR: Erlich, Yaniv :JOURNAL: BioRxiv :PAGES: 185330 :YEAR: 2017 :PUBLISHER: Cold Spring Harbor Laboratory :URL: https://www.biorxiv.org/content/biorxiv/early/2017/09/07/185330.1.full.pdf :END: *** KILL On inferring presence of an individual in a mixture: a Bayesian approach CLOSED: [2024-07-15 lun. 11:14] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: On inferring presence of an individual in a mixture: a Bayesian approach :BTYPE: article :CUSTOM_ID: clayton10 :AUTHOR: David Clayton :JOURNAL: Biostatistics :YEAR: 2010 :VOLUME: 11 :NUMBER: 4 :PAGES: 661-673 :DOI: 10.1093/biostatistics/kxq035 :URL: http://dx.doi.org/10.1093/biostatistics/kxq035 :END: *** KILL Assessing and managing risk when sharing aggregate genetic variant data CLOSED: [2024-07-12 ven. 17:59] :PROPERTIES: :TITLE: Assessing and managing risk when sharing aggregate genetic variant data :BTYPE: article :CUSTOM_ID: craig2011assessing :AUTHOR: Craig, David W and Goor, Robert M and Wang, Zhenyuan and Paschall, Justin and Ostell, Jim and Feolo, Michael and Sherry, Stephen T and Manolio, Teri A :JOURNAL: Nature Reviews Genetics :VOLUME: 12 :NUMBER: 10 :PAGES: 730--736 :YEAR: 2011 :PUBLISHER: Nature Publishing Group UK London :END: Rien de plus *** DONE On Jim Watson's APOE status: genetic information is hard to hide CLOSED: [2024-07-12 ven. 15:04] :PROPERTIES: :TITLE: On Jim Watson's APOE status: genetic information is hard to hide :BTYPE: article :CUSTOM_ID: nyholt2009jim :AUTHOR: Nyholt, Dale R and Yu, Chang-En and Visscher, Peter M :JOURNAL: European Journal of Human Genetics :VOLUME: 17 :NUMBER: 2 :PAGES: 147--149 :YEAR: 2009 :PUBLISHER: Nature Publishing Group :END: *** DONE Privacy in pharmacogenetics: An $\{$End-to-End$\}$ case study of personalized warfarin dosing CLOSED: [2024-07-11 jeu. 15:37] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Privacy in pharmacogenetics: An $\{$End-to-End$\}$ case study of personalized warfarin dosing :BTYPE: inproceedings :CUSTOM_ID: fredrikson2014privacy :AUTHOR: Fredrikson, Matthew and Lantz, Eric and Jha, Somesh and Lin, Simon and Page, David and Ristenpart, Thomas :BOOKTITLE: 23rd USENIX security symposium (USENIX Security 14) :PAGES: 17--32 :YEAR: 2014 :URL: https://www.usenix.org/system/files/conference/usenixsecurity14/sec14-paper-fredrikson-privacy.pdf :END: *** DONE [#B] Privacy in the Genomic Era CLOSED: [2024-07-12 ven. 17:37] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Privacy in the Genomic Era :BTYPE: article :CUSTOM_ID: naveed2015privacy :VOLUME: 48 :ISSN: 1557-7341 :URL: http://dx.doi.org/10.1145/2767007 :DOI: 10.1145/2767007 :NUMBER: 1 :JOURNAL: ACM Computing Surveys :PUBLISHER: Association for Computing Machinery (ACM) :AUTHOR: Naveed, Muhammad and Ayday, Erman and Clayton, Ellen W. and Fellay, Jacques and Gunter, Carl A. and Hubaux, Jean-Pierre and Malin, Bradley A. and Wang, Xiaofeng :YEAR: 2015 :MONTH: aug :PAGES: 1–44 :END: 2-3 citations en plus des autres *** DONE Privacy risks from genomic data-sharing beacons :identity_tracing: CLOSED: [2024-07-10 mer. 11:50] :PROPERTIES: :TITLE: Privacy risks from genomic data-sharing beacons :BTYPE: article :CUSTOM_ID: shringarpure2015 :AUTHOR: Shringarpure, Suyash S and Bustamante, Carlos D :JOURNAL: The American Journal of Human Genetics :VOLUME: 97 :NUMBER: 5 :PAGES: 631--646 :YEAR: 2015 :PUBLISHER: Elsevier :END: *** DONE Quantifying Interdependent Risks in Genomic Privacy CLOSED: [2024-07-11 Thu 20:04] :PROPERTIES: :TITLE: Quantifying Interdependent Risks in Genomic Privacy :BTYPE: article :CUSTOM_ID: humbert2017quantifying :AUTHOR: Mathias Humbert and Erman Ayday and Jean-Pierre Hubaux and Amalio Telenti :JOURNAL: ACM Transactions on Privacy and Security :YEAR: 2017 :VOLUME: 20 :NUMBER: 1 :PAGES: 1-31 :DOI: 10.1145/3035538 :URL: http://dx.doi.org/10.1145/3035538 :END: *** DONE Re-identification of individuals in genomic data-sharing beacons via allele inference :identity_tracing: CLOSED: [2024-07-10 mer. 16:37] :PROPERTIES: :TITLE: Re-identification of individuals in genomic data-sharing beacons via allele inference :BTYPE: article :CUSTOM_ID: vonthenen2019 :AUTHOR: Von Thenen, Nora and Ayday, Erman and Cicek, A Ercument :JOURNAL: Bioinformatics :VOLUME: 35 :NUMBER: 3 :PAGES: 365--371 :YEAR: 2019 :PUBLISHER: Oxford University Press :END: *** KILL Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays CLOSED: [2024-07-11 Thu 21:19] SCHEDULED: <2024-07-11 jeu.> :PROPERTIES: :TITLE: Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays :BTYPE: article :CUSTOM_ID: homer2008resolving :AUTHOR: Nils Homer and Szabolcs Szelinger and Margot Redman and David Duggan and Waibhav Tembe and Jill Muehling and John V. Pearson and Dietrich A. Stephan and Stanley F. Nelson and David W. Craig :JOURNAL: PLoS Genetics :YEAR: 2008 :VOLUME: 4 :NUMBER: 8 :PAGES: e1000167 :DOI: 10.1371/journal.pgen.1000167 :URL: http://dx.doi.org/10.1371/journal.pgen.1000167 :END: Superseded by *** DONE Simple demographics often identify people uniquely CLOSED: [2024-07-12 ven. 17:25] :PROPERTIES: :TITLE: Simple demographics often identify people uniquely :BTYPE: article :CUSTOM_ID: sweeney2000simple :AUTHOR: Sweeney, Latanya :JOURNAL: Health (San Francisco) :VOLUME: 671 :NUMBER: 2000 :PAGES: 1--34 :YEAR: 2000 :END: *** DONE [#A] Routes for breaching and protecting genetic privacy :review: CLOSED: [2024-07-09 mar. 16:35] SCHEDULED: <2024-07-09 mar.> :PROPERTIES: :TITLE: Routes for breaching and protecting genetic privacy :BTYPE: article :CUSTOM_ID: erlich2014 :AUTHOR: Erlich, Yaniv and Narayanan, Arvind :JOURNAL: Nature Reviews Genetics :VOLUME: 15 :NUMBER: 6 :PAGES: 409--421 :YEAR: 2014 :PUBLISHER: Nature Publishing Group UK London :URL: https://www.nature.com/articles/nrg3723 :END: Revue des différentes stratégie + algorithme *** DONE SNPs for a universal individual identification panel CLOSED: [2024-07-12 ven. 09:44] :PROPERTIES: :TITLE: SNPs for a universal individual identification panel :BTYPE: article :CUSTOM_ID: pakstis2010snps :AUTHOR: Pakstis, Andrew J and Speed, William C and Fang, Rixun and Hyland, Fiona CL and Furtado, Manohar R and Kidd, Judith R and Kidd, Kenneth K :JOURNAL: Human genetics :VOLUME: 127 :PAGES: 315--324 :YEAR: 2010 :PUBLISHER: Springer :END: ** Décipher *** DONE Framework ethique : inutile https://www.deciphergenomics.org/files/pdfs/decipher_ethical_framework.pdf CLOSED: [2024-07-15 lun. 16:13] *** DONE DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources CLOSED: [2024-07-15 lun. 16:03] :PROPERTIES: :TITLE: DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources :BTYPE: article :CUSTOM_ID: firth2009decipher :AUTHOR: Firth, Helen V and Richards, Shola M and Bevan, A Paul and Clayton, Stephen and Corpas, Manuel and Rajan, Diana and Van Vooren, Steven and Moreau, Yves and Pettett, Roger M and Carter, Nigel P :JOURNAL: The American Journal of Human Genetics :VOLUME: 84 :NUMBER: 4 :PAGES: 524--533 :YEAR: 2009 :PUBLISHER: Elsevier :END: inutile sur l'aspec réglèmentaire *** DONE The GDPR and genomic data CLOSED: [2024-07-15 lun. 16:43] :PROPERTIES: :TITLE: The GDPR and genomic data :CUSTOM_ID: mitchell2018gpdr :BTYPE: article :AUTHOR: Mitchell, Colin and Ordish, Johan and Johnson, Emma and Brigden, Tanya and Hall, Alison :YEAR: 2009 :END: ** Maladies rares *** DONE The risk of re-identification versus the need to identify individuals in rare disease research CLOSED: [2024-07-24 Wed 18:16] SCHEDULED: <2024-07-23 Tue> :PROPERTIES: :TITLE: The risk of re-identification versus the need to identify individuals in rare disease research :BTYPE: article :CUSTOM_ID: hansson2016risk :AUTHOR: Hansson, Mats G and Lochm{\"u}ller, Hanns and Riess, Olaf and Schaefer, Franz and Orth, Michael and Rubinstein, Yaffa and Molster, Caron and Dawkins, Hugh and Taruscio, Domenica and Posada, Manuel and others :JOURNAL: European Journal of Human Genetics :VOLUME: 24 :NUMBER: 11 :PAGES: 1553--1558 :YEAR: 2016 :PUBLISHER: Nature Publishing Group :URL: https://www.nature.com/articles/ejhg201652 :END: *** Prévalence maladies rare **** KILL https://www.nature.com/articles/nrg.2017.116 CLOSED: [2024-07-18 Thu 14:55] Généralité sur processus génétique **** Stats ****** DONE Prevalence and practice for rare diseases in primary care: a national cross-sectional study in the USA CLOSED: [2024-07-18 Thu 17:27] SCHEDULED: <2024-07-18 Thu> :PROPERTIES: :TITLE: Prevalence and practice for rare diseases in primary care: a national cross-sectional study in the USA :BTYPE: article :CUSTOM_ID: Jo_2019 :VOLUME: 9 :ISSN: 2044-6055 :URL: http://dx.doi.org/10.1136/bmjopen-2018-027248 :DOI: 10.1136/bmjopen-2018-027248 :NUMBER: 4 :JOURNAL: BMJ Open :PUBLISHER: BMJ :AUTHOR: Jo, Ara and Larson, Samantha and Carek, Peter and Peabody, Michael R and Peterson, Lars E and Mainous, Arch G :YEAR: 2019 :MONTH: apr :PAGES: e027248 :END: ****** DONE A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes CLOSED: [2024-07-19 Fri 17:27] SCHEDULED: <2024-07-19 Fri> :PROPERTIES: :TITLE: A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes :BTYPE: article :CUSTOM_ID: macarthur2012systematic :AUTHOR: Daniel G. MacArthur and Suganthi Balasubramanian and Adam Frankish and Ni Huang and James Morris and Klaudia Walter and Luke Jostins and Lukas Habegger and Joseph K. Pickrell and Stephen B. Montgomery and Cornelis A. Albers and Zhengdong D. Zhang and Donald F. Conrad and Gerton Lunter and Hancheng Zheng and Qasim Ayub and Mark A. DePristo and Eric Banks and Min Hu and Robert E. Handsaker and Jeffrey A. Rosenfeld and Menachem Fromer and Mike Jin and Xinmeng Jasmine Mu and Ekta Khurana and Kai Ye and Mike Kay and Gary Ian Saunders and Marie-Marthe Suner and Toby Hunt and If H. A. Barnes and Clara Amid and Denise R. Carvalho-Silva and Alexandra H. Bignell and Catherine Snow and Bryndis Yngvadottir and Suzannah Bumpstead and David N. Cooper and Yali Xue and Irene Gallego Romero and Jun Wang and Yingrui Li and Richard A. Gibbs and Steven A. McCarroll and Emmanouil T. Dermitzakis and Jonathan K. Pritchard and Jeffrey C. Barrett and Jennifer Harrow and Matthew E. Hurles and Mark B. Gerstein and Chris Tyler-Smith and 1000 Genomes Project Consortium :JOURNAL: Science :YEAR: 2012 :VOLUME: 335 :NUMBER: 6070 :PAGES: 823-828 :DOI: 10.1126/science.1215040 :URL: http://dx.doi.org/10.1126/science.1215040 :END: ****** DONE Estimating the number of diseases – the concept of rare, ultra-rare, and hyper-rare CLOSED: [2024-07-19 Fri 17:28] SCHEDULED: <2024-07-18 Thu> :PROPERTIES: :TITLE: Estimating the number of diseases – the concept of rare, ultra-rare, and hyper-rare :BTYPE: article :CUSTOM_ID: smith2022estimating :VOLUME: 25 :ISSN: 2589-0042 :URL: http://dx.doi.org/10.1016/j.isci.2022.104698 :DOI: 10.1016/j.isci.2022.104698 :NUMBER: 8 :JOURNAL: iScience :PUBLISHER: Elsevier BV :AUTHOR: Smith, C. I. Edvard and Bergman, Peter and Hagey, Daniel W. :YEAR: 2022 :MONTH: aug :PAGES: 104698 :END: ****** DONE How many rare diseases are there? CLOSED: [2024-07-19 Fri 17:24] SCHEDULED: <2024-07-19 Fri> :PROPERTIES: :TITLE: How many rare diseases are there? :BTYPE: article :CUSTOM_ID: haendel2019how :AUTHOR: Melissa Haendel and Nicole Vasilevsky and Deepak Unni and Cristian Bologa and Nomi Harris and Heidi Rehm and Ada Hamosh and Gareth Baynam and Tudor Groza and Julie McMurry and Hugh Dawkins and Ana Rath and Courtney Thaxton and Giovanni Bocci and Marcin P. Joachimiak and Sebastian Köhler and Peter N. Robinson and Chris Mungall and Tudor I. Oprea :JOURNAL: Nature Reviews Drug Discovery :YEAR: 2019 :VOLUME: 19 :NUMBER: 2 :PAGES: 77-78 :DOI: 10.1038/d41573-019-00180-y :URL: http://dx.doi.org/10.1038/d41573-019-00180-y :END: ****** KILL Prévalence française revoir avec Julien CLOSED: [2024-07-22 Mon 17:05] SCHEDULED: <2024-07-22 Mon> ****** DONE BNDMR CLOSED: [2024-07-19 Fri 15:46] BNDMR https://www.bndmr.fr/publications/nombre-de-cas-par-mr/ ****** DONE Orphadata: épidémiologie (XML) CLOSED: [2024-07-19 Fri 09:38] :PROPERTIES: :TITLE: Epidemiology of Rare Disease :BTYPE: misc :CUSTOM_ID: orphadata2024epidemio :URL: https://www.orphadata.com/epidemiology/ :AUTHOR: Orphanet :YEAR: 2024 :MONTH: jul :END: ****** DONE The HPO - ORDO ontological module CLOSED: [2024-07-19 Fri 14:59] :PROPERTIES: :TITLE: The HPO - ORDO ontological module :BTYPE: misc :CUSTOM_ID: hoomm2024ordo :URL: https://www.orphadata.com/hoom/ :AUTHOR: Orphanet :YEAR: 2024 :MONTH: jul :END: ****** DONE Orphadata : fréquence phénotypes associé CLOSED: [2024-07-19 Fri 12:19] :PROPERTIES: :TITLE: Phenotypes Associated with Rare Disorders :BTYPE: misc :CUSTOM_ID: orphadata2024phenotype :URL: https://www.orphadata.com/phenotypes/ :AUTHOR: Orphanet :YEAR: 2024 :MONTH: jul :END: ****** DONE Orphadata : zygosite, age de début CLOSED: [2024-07-19 Fri 12:25] :PROPERTIES: :TITLE: Natural History of Rare Diseases :BTYPE: misc :CUSTOM_ID: orphadata2024natural :URL: https://www.orphadata.com/phenotypes/ :AUTHOR: Orphanet :YEAR: 2024 :MONTH: jul :END: https://www.orphadata.com/natural-history/ ****** DONE Orphanet: prevalence et incidence : biblio CLOSED: [2024-07-19 Fri 09:42] :PROPERTIES: :TITLE: Prevalence and incidence of rare diseases: Bibliographic data :BTYPE: misc :CUSTOM_ID: orphanet2023prevalence :URL: https://www.orpha.net/pdfs/orphacom/cahiers/docs/GB/Prevalence_of_rare_diseases_by_alphabetical_list.pdf :AUTHOR: Orphanet :YEAR: 2023 :MONTH: nov :END: ****** DONE The burden of rare diseases CLOSED: [2024-07-18 Thu 17:34] SCHEDULED: <2024-07-18 Thu> :PROPERTIES: :TITLE: The burden of rare diseases :BTYPE: article :CUSTOM_ID: ferreira2019burden :VOLUME: 179 :ISSN: 1552-4833 :URL: http://dx.doi.org/10.1002/ajmg.a.61124 :DOI: 10.1002/ajmg.a.61124 :NUMBER: 6 :JOURNAL: American Journal of Medical Genetics Part A :PUBLISHER: Wiley :AUTHOR: Ferreira, Carlos R. :YEAR: 2019 :MONTH: mar :PAGES: 885–892 :END: ****** KILL Frequency-based rare diagnoses as a novel and accessible approach for studying rare diseases in large datasets: a cross-sectional study CLOSED: [2024-07-18 Thu 14:45] :PROPERTIES: :TITLE: Frequency-based rare diagnoses as a novel and accessible approach for studying rare diseases in large datasets: a cross-sectional study :BTYPE: article :CUSTOM_ID: troster2023frequence :VOLUME: 23 :ISSN: 1471-2288 :URL: http://dx.doi.org/10.1186/s12874-023-01972-y :DOI: 10.1186/s12874-023-01972-y :NUMBER: 1 :JOURNAL: BMC Medical Research Methodology :PUBLISHER: Springer Science and Business Media LLC :AUTHOR: Tröster, Thomas S. and von Wyl, Viktor and Beeler, Patrick E. and Dressel, Holger :YEAR: 2023 :MONTH: jun :END: ****** DONE Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database CLOSED: [2024-07-19 Fri 15:05] SCHEDULED: <2024-07-18 Thu> :PROPERTIES: :TITLE: Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database :BTYPE: article :CUSTOM_ID: nguengang2019estimating :VOLUME: 28 :ISSN: 1476-5438 :URL: http://dx.doi.org/10.1038/s41431-019-0508-0 :DOI: 10.1038/s41431-019-0508-0 :NUMBER: 2 :JOURNAL: European Journal of Human Genetics :PUBLISHER: Springer Science and Business Media LLC :AUTHOR: Nguengang Wakap, Stéphanie and Lambert, Deborah M. and Olry, Annie and Rodwell, Charlotte and Gueydan, Charlotte and Lanneau, Valérie and Murphy, Daniel and Le Cam, Yann and Rath, Ana :YEAR: 2019 :MONTH: sep :PAGES: 165–173 :END: ****** DONE Determining the incidence of rare diseases CLOSED: [2024-07-18 Thu 17:09] SCHEDULED: <2024-07-18 Thu> 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Andrea and He, Max and Ye, Zhan and Peissig, Peggy and Van Wormer, Jeffrey J. and Haws, Robert and Brilliant, Murray H. and Steiner, Robert D. :YEAR: 2015 :MONTH: apr :PAGES: 659–669 :END: ****** TODO [#A] Statistical methods for assessing the effects of de novo variants on birth defects :PROPERTIES: :TITLE: Statistical methods for assessing the effects of de novo variants on birth defects :BTYPE: article :CUSTOM_ID: xie2024statistical :VOLUME: 18 :ISSN: 1479-7364 :URL: http://dx.doi.org/10.1186/s40246-024-00590-z :DOI: 10.1186/s40246-024-00590-z :NUMBER: 1 :JOURNAL: Human Genomics :PUBLISHER: Springer Science and Business Media LLC :AUTHOR: Xie, Yuhan and Wu, Ruoxuan and Li, Hongyu and Dong, Weilai and Zhou, Geyu and Zhao, Hongyu :YEAR: 2024 :MONTH: mar :END: ****** TODO https://en.wikipedia.org/wiki/Substitution_matrix ***** Selon nucléotide adjacents ****** DONE Patterns and rates of exonic de novo mutations in autism spectrum disorders CLOSED: [2024-07-25 Thu 16:20] :PROPERTIES: 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