From 81ccb6530051e8019056379224a78ed9776ee9ec Mon Sep 17 00:00:00 2001 From: Daniel Clarke Date: Mon, 9 Sep 2024 12:35:28 -0400 Subject: [PATCH] Run codegen:citations --- utils/citations/citations.ts | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/utils/citations/citations.ts b/utils/citations/citations.ts index e4a75079..2215cd7c 100644 --- a/utils/citations/citations.ts +++ b/utils/citations/citations.ts @@ -1,5 +1,6 @@ export default { "10.1002/cpz1.90": {"nature":"Xie, Z. et al. Gene Set Knowledge Discovery with Enrichr. Current Protocols vol. 1 (2021).","bibtex":{"type":"misc","record":" title={Gene Set Knowledge Discovery with Enrichr}, volume={1}, url={http://dx.doi.org/10.1002/cpz1.90}, DOI={10.1002/cpz1.90}, abstractNote={AbstractProfiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins that need to be further analyzed and integrated in the context of known biology. Enrichr (Chen et al., 2013; Kuleshov et al., 2016) is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets. Enrichr uniquely integrates knowledge from many high‐profile projects to provide synthesized information about mammalian genes and gene sets. The platform provides various methods to compute gene set enrichment, and the results are visualized in several interactive ways. This protocol provides a summary of the key features of Enrichr, which include using Enrichr programmatically and embedding an Enrichr button on any website. © 2021 Wiley Periodicals LLC.Basic Protocol 1: Analyzing lists of differentially expressed genes from transcriptomics, proteomics and phosphoproteomics, GWAS studies, or other experimental studiesBasic Protocol 2: Searching Enrichr by a single gene or key search termBasic Protocol 3: Preparing raw or processed RNA‐seq data through BioJupies in preparation for Enrichr analysisBasic Protocol 4: Analyzing gene sets for model organisms using modEnrichrBasic Protocol 5: Using Enrichr in GeneshotBasic Protocol 6: Using Enrichr in ARCHS4Basic Protocol 7: Using the enrichment analysis visualization Appyter to visualize Enrichr resultsBasic Protocol 8: Using the Enrichr APIBasic Protocol 9: Adding an Enrichr button to a website}, number={3}, journal={Current Protocols}, publisher={Wiley}, author={Xie, Zhuorui and Bailey, Allison and Kuleshov, Maxim V. and Clarke, Daniel J. B. and Evangelista, John E. and Jenkins, Sherry L. and Lachmann, Alexander and Wojciechowicz, Megan L. and Kropiwnicki, Eryk and Jagodnik, Kathleen M. and Jeon, Minji and Ma’ayan, Avi}, year={2021}, month=mar, language={en} "}}, + "10.1002/humu.23637": {"nature":"Pawliczek, P. et al. ClinGen Allele Registry links information about genetic variants. Human Mutation vol. 39 1690–1701 (2018).","bibtex":{"type":"misc","record":" title={ClinGen Allele Registry links information about genetic variants}, volume={39}, url={http://dx.doi.org/10.1002/humu.23637}, DOI={10.1002/humu.23637}, number={11}, journal={Human Mutation}, publisher={Wiley}, author={Pawliczek, Piotr and Patel, Ronak Y. and Ashmore, Lillian R. and Jackson, Andrew R. and Bizon, Chris and Nelson, Tristan and Powell, Bradford and Freimuth, Robert R. and Strande, Natasha and Shah, Neethu and Paithankar, Sameer and Wright, Matt W. and Dwight, Selina and Zhen, Jimmy and Landrum, Melissa and McGarvey, Peter and Babb, Larry and Plon, Sharon E. and Milosavljevic, Aleksandar}, year={2018}, month=oct, pages={1690–1701}, language={en} "}}, "10.1002/pro.3715": {"nature":"Kanehisa, M. Toward understanding the origin and evolution of cellular organisms. Protein Science vol. 28 1947–1951 (2019).","bibtex":{"type":"misc","record":" title={Toward understanding the origin and evolution of cellular organisms}, volume={28}, url={http://dx.doi.org/10.1002/pro.3715}, DOI={10.1002/pro.3715}, abstractNote={AbstractIn this era of high‐throughput biology, bioinformatics has become a major discipline for making sense out of large‐scale datasets. Bioinformatics is usually considered as a practical field developing databases and software tools for supporting other fields, rather than a fundamental scientific discipline for uncovering principles of biology. The KEGG resource that we have been developing is a reference knowledge base for biological interpretation of genome sequences and other high‐throughput data. It is now one of the most utilized biological databases because of its practical values. For me personally, KEGG is a step toward understanding the origin and evolution of cellular organisms.}, number={11}, journal={Protein Science}, publisher={Wiley}, author={Kanehisa, Minoru}, year={2019}, month=sep, pages={1947–1951}, language={en} "}}, "10.1016/j.cell.2017.10.049": {"nature":"Subramanian, A. et al. A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. Cell vol. 171 1437-1452.e17 (2017).","bibtex":{"type":"misc","record":" title={A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles}, volume={171}, url={http://dx.doi.org/10.1016/j.cell.2017.10.049}, DOI={10.1016/j.cell.2017.10.049}, number={6}, journal={Cell}, publisher={Elsevier BV}, author={Subramanian, Aravind and Narayan, Rajiv and Corsello, Steven M. and Peck, David D. and Natoli, Ted E. and Lu, Xiaodong and Gould, Joshua and Davis, John F. and Tubelli, Andrew A. and Asiedu, Jacob K. and Lahr, David L. and Hirschman, Jodi E. and Liu, Zihan and Donahue, Melanie and Julian, Bina and Khan, Mariya and Wadden, David and Smith, Ian C. and Lam, Daniel and Liberzon, Arthur and Toder, Courtney and Bagul, Mukta and Orzechowski, Marek and Enache, Oana M. and Piccioni, Federica and Johnson, Sarah A. and Lyons, Nicholas J. and Berger, Alice H. and Shamji, Alykhan F. and Brooks, Angela N. and Vrcic, Anita and Flynn, Corey and Rosains, Jacqueline and Takeda, David Y. and Hu, Roger and Davison, Desiree and Lamb, Justin and Ardlie, Kristin and Hogstrom, Larson and Greenside, Peyton and Gray, Nathanael S. and Clemons, Paul A. and Silver, Serena and Wu, Xiaoyun and Zhao, Wen-Ning and Read-Button, Willis and Wu, Xiaohua and Haggarty, Stephen J. and Ronco, Lucienne V. and Boehm, Jesse S. and Schreiber, Stuart L. and Doench, John G. and Bittker, Joshua A. and Root, David E. and Wong, Bang and Golub, Todd R.}, year={2017}, month=nov, pages={1437-1452.e17}, language={en} "}}, "10.1016/j.cell.2020.06.004": {"nature":"Sanford, J. A. et al. Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell vol. 181 1464–1474 (2020).","bibtex":{"type":"misc","record":" title={Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise}, volume={181}, url={http://dx.doi.org/10.1016/j.cell.2020.06.004}, DOI={10.1016/j.cell.2020.06.004}, number={7}, journal={Cell}, publisher={Elsevier BV}, author={Sanford, James A. and Nogiec, Christopher D. and Lindholm, Malene E. and Adkins, Joshua N. and Amar, David and Dasari, Surendra and Drugan, Jonelle K. and Fernández, Facundo M. and Radom-Aizik, Shlomit and Schenk, Simon and Snyder, Michael P. and Tracy, Russell P. and Vanderboom, Patrick and Trappe, Scott and Walsh, Martin J. and Adkins, Joshua N. and Amar, David and Dasari, Surendra and Drugan, Jonelle K. and Evans, Charles R. and Fernandez, Facundo M. and Li, Yafeng and Lindholm, Malene E. and Nogiec, Christopher D. and Radom-Aizik, Shlomit and Sanford, James A. and Schenk, Simon and Snyder, Michael P. and Tomlinson, Lyl and Tracy, Russell P. and Trappe, Scott and Vanderboom, Patrick and Walsh, Martin J. and Lee Alekel, D. and Bekirov, Iddil and Boyce, Amanda T. and Boyington, Josephine and Fleg, Jerome L. and Joseph, Lyndon J.O. and Laughlin, Maren R. and Maruvada, Padma and Morris, Stephanie A. and McGowan, Joan A. and Nierras, Concepcion and Pai, Vinay and Peterson, Charlotte and Ramos, Ed and Roary, Mary C. and Williams, John P. and Xia, Ashley and Cornell, Elaine and Rooney, Jessica and Miller, Michael E. and Ambrosius, Walter T. and Rushing, Scott and Stowe, Cynthia L. and Jack Rejeski, W. and Nicklas, Barbara J. and Pahor, Marco and Lu, Ching-ju and Trappe, Todd and Chambers, Toby and Raue, Ulrika and Lester, Bridget and Bergman, Bryan C. and Bessesen, David H. and Jankowski, Catherine M. and Kohrt, Wendy M. and Melanson, Edward L. and Moreau, Kerrie L. and Schauer, Irene E. and Schwartz, Robert S. and Kraus, William E. and Slentz, Cris A. and Huffman, Kim M. and Johnson, Johanna L. and Willis, Leslie H. and Kelly, Leslie and Houmard, Joseph A. and Dubis, Gabriel and Broskey, Nick and Goodpaster, Bret H. and Sparks, Lauren M. and Coen, Paul M. and Cooper, Dan M. and Haddad, Fadia and Rankinen, Tuomo and Ravussin, Eric and Johannsen, Neil and Harris, Melissa and Jakicic, John M. and Newman, Anne B. and Forman, Daniel D. and Kershaw, Erin and Rogers, Renee J. and Nindl, Bradley C. and Page, Lindsay C. and Stefanovic-Racic, Maja and Barr, Susan L. and Rasmussen, Blake B. and Moro, Tatiana and Paddon-Jones, Doug and Volpi, Elena and Spratt, Heidi and Musi, Nicolas and Espinoza, Sara and Patel, Darpan and Serra, Monica and Gelfond, Jonathan and Burns, Aisling and Bamman, Marcas M. and Buford, Thomas W. and Cutter, Gary R. and Bodine, Sue C. and Esser, Karyn and Farrar, Rodger P. and Goodyear, Laurie J. and Hirshman, Michael F. and Albertson, Brent G. and Qian, Wei-Jun and Piehowski, Paul and Gritsenko, Marina A. and Monore, Matthew E. and Petyuk, Vladislav A. and McDermott, Jason E. and Hansen, Joshua N. and Hutchison, Chelsea and Moore, Samuel and Gaul, David A. and Clish, Clary B. and Avila-Pacheco, Julian and Dennis, Courtney and Kellis, Manolis and Carr, Steve and Jean-Beltran, Pierre M. and Keshishian, Hasmik and Mani, D.R. and Clauser, Karl and Krug, Karsten and Mundorff, Charlie and Pearce, Cadence and Ivanova, Anna A. and Ortlund, Eric A. and Maner-Smith, Kristal and Uppal, Karan and Zhang, Tiantian and Sealfon, Stuart C. and Zaslavsky, Elena and Nair, Venugopalan and Li, SiDe and Jain, Nimisha and Ge, YongChao and Sun, Yifei and Nudelman, German and Ruf-zamojski, Frederique and Smith, Gregory and Pincas, Nhanna and Rubenstein, Aliza and Anne Amper, Mary and Seenarine, Nitish and Lappalainen, Tuuli and Lanza, Ian R. and Sreekumaran Nair, K. and Klaus, Katherine and Montgomery, Stephen B. and Smith, Kevin S. and Gay, Nicole R. and Zhao, Bingqing and Hung, Chia-Jiu and Zebarjadi, Navid and Balliu, Brunilda and Fresard, Laure and Burant, Charles F. and Li, Jun Z. and Kachman, Maureen and Soni, Tanu and Raskind, Alexander B. and Gerszten, Robert and Robbins, Jeremy and Ilkayeva, Olga and Muehlbauer, Michael J. and Newgard, Christopher B. and Ashley, Euan A. and Wheeler, Matthew T. and Jimenez-Morales, David and Raja, Archana and Dalton, Karen P. and Zhen, Jimmy and Suk Kim, Young and Christle, Jeffrey W. and Marwaha, Shruti and Chin, Elizabeth T. and Hershman, Steven G. and Hastie, Trevor and Tibshirani, Robert and Rivas, Manuel A.}, year={2020}, month=jun, pages={1464–1474}, language={en} "}}, @@ -8,9 +9,11 @@ export default { "10.1017/CBO9781139058452.002": {"nature":"Data Mining. Mining of Massive Datasets 1–17 (2011) doi:10.1017/cbo9781139058452.002.","bibtex":{"type":"misc","record":" url={http://dx.doi.org/10.1017/CBO9781139058452.002}, DOI={10.1017/cbo9781139058452.002}, journal={Mining of Massive Datasets}, publisher={Cambridge University Press}, year={2011}, month=oct, pages={1–17} "}}, "10.1038/75556": {"nature":"Ashburner, M. et al. Gene Ontology: tool for the unification of biology. Nature Genetics vol. 25 25–29 (2000).","bibtex":{"type":"misc","record":" title={Gene Ontology: tool for the unification of biology}, volume={25}, url={http://dx.doi.org/10.1038/75556}, DOI={10.1038/75556}, number={1}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Ashburner, Michael and Ball, Catherine A. and Blake, Judith A. and Botstein, David and Butler, Heather and Cherry, J. Michael and Davis, Allan P. and Dolinski, Kara and Dwight, Selina S. and Eppig, Janan T. and Harris, Midori A. and Hill, David P. and Issel-Tarver, Laurie and Kasarskis, Andrew and Lewis, Suzanna and Matese, John C. and Richardson, Joel E. and Ringwald, Martin and Rubin, Gerald M. and Sherlock, Gavin}, year={2000}, month=may, pages={25–29}, language={en} "}}, "10.1038/nature11247": {"nature":"An integrated encyclopedia of DNA elements in the human genome. Nature vol. 489 57–74 (2012).","bibtex":{"type":"misc","record":" title={An integrated encyclopedia of DNA elements in the human genome}, volume={489}, url={http://dx.doi.org/10.1038/nature11247}, DOI={10.1038/nature11247}, number={7414}, journal={Nature}, publisher={Springer Science and Business Media LLC}, year={2012}, month=sep, pages={57–74}, language={en} "}}, + "10.1038/nature14248": {"nature":"Integrative analysis of 111 reference human epigenomes. Nature vol. 518 317–330 (2015).","bibtex":{"type":"misc","record":" title={Integrative analysis of 111 reference human epigenomes}, volume={518}, url={http://dx.doi.org/10.1038/nature14248}, DOI={10.1038/nature14248}, number={7539}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Kundaje, Anshul and Meuleman, Wouter and Ernst, Jason and Bilenky, Misha and Yen, Angela and Heravi-Moussavi, Alireza and Kheradpour, Pouya and Zhang, Zhizhuo and Wang, Jianrong and Ziller, Michael J. and Amin, Viren and Whitaker, John W. and Schultz, Matthew D. and Ward, Lucas D. and Sarkar, Abhishek and Quon, Gerald and Sandstrom, Richard S. and Eaton, Matthew L. and Wu, Yi-Chieh and Pfenning, Andreas R. and Wang, Xinchen and Claussnitzer, Melina and Liu, Yaping and Coarfa, Cristian and Harris, R. Alan and Shoresh, Noam and Epstein, Charles B. and Gjoneska, Elizabeta and Leung, Danny and Xie, Wei and Hawkins, R. David and Lister, Ryan and Hong, Chibo and Gascard, Philippe and Mungall, Andrew J. and Moore, Richard and Chuah, Eric and Tam, Angela and Canfield, Theresa K. and Hansen, R. Scott and Kaul, Rajinder and Sabo, Peter J. and Bansal, Mukul S. and Carles, Annaick and Dixon, Jesse R. and Farh, Kai-How and Feizi, Soheil and Karlic, Rosa and Kim, Ah-Ram and Kulkarni, Ashwinikumar and Li, Daofeng and Lowdon, Rebecca and Elliott, GiNell and Mercer, Tim R. and Neph, Shane J. and Onuchic, Vitor and Polak, Paz and Rajagopal, Nisha and Ray, Pradipta and Sallari, Richard C. and Siebenthall, Kyle T. and Sinnott-Armstrong, Nicholas A. and Stevens, Michael and Thurman, Robert E. and Wu, Jie and Zhang, Bo and Zhou, Xin and Beaudet, Arthur E. and Boyer, Laurie A. and De Jager, Philip L. and Farnham, Peggy J. and Fisher, Susan J. and Haussler, David and Jones, Steven J. M. and Li, Wei and Marra, Marco A. and McManus, Michael T. and Sunyaev, Shamil and Thomson, James A. and Tlsty, Thea D. and Tsai, Li-Huei and Wang, Wei and Waterland, Robert A. and Zhang, Michael Q. and Chadwick, Lisa H. and Bernstein, Bradley E. and Costello, Joseph F. and Ecker, Joseph R. and Hirst, Martin and Meissner, Alexander and Milosavljevic, Aleksandar and Ren, Bing and Stamatoyannopoulos, John A. and Wang, Ting and Kellis, Manolis}, year={2015}, month=feb, pages={317–330}, language={en} "}}, "10.1038/ng.265": {"nature":"Pannicke, U. et al. Reticular dysgenesis (aleukocytosis) is caused by mutations in the gene encoding mitochondrial adenylate kinase 2. Nature Genetics vol. 41 101–105 (2008).","bibtex":{"type":"misc","record":" title={Reticular dysgenesis (aleukocytosis) is caused by mutations in the gene encoding mitochondrial adenylate kinase 2}, volume={41}, url={http://dx.doi.org/10.1038/ng.265}, DOI={10.1038/ng.265}, number={1}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Pannicke, Ulrich and Hönig, Manfred and Hess, Isabell and Friesen, Claudia and Holzmann, Karlheinz and Rump, Eva-Maria and Barth, Thomas F and Rojewski, Markus T and Schulz, Ansgar and Boehm, Thomas and Friedrich, Wilhelm and Schwarz, Klaus}, year={2008}, month=nov, pages={101–105}, language={en} "}}, "10.1038/ng.2653": {"nature":"Lonsdale, J. et al. The Genotype-Tissue Expression (GTEx) project. Nature Genetics vol. 45 580–585 (2013).","bibtex":{"type":"misc","record":" title={The Genotype-Tissue Expression (GTEx) project}, volume={45}, url={http://dx.doi.org/10.1038/ng.2653}, DOI={10.1038/ng.2653}, number={6}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Lonsdale, John and Thomas, Jeffrey and Salvatore, Mike and Phillips, Rebecca and Lo, Edmund and Shad, Saboor and Hasz, Richard and Walters, Gary and Garcia, Fernando and Young, Nancy and Foster, Barbara and Moser, Mike and Karasik, Ellen and Gillard, Bryan and Ramsey, Kimberley and Sullivan, Susan and Bridge, Jason and Magazine, Harold and Syron, John and Fleming, Johnelle and Siminoff, Laura and Traino, Heather and Mosavel, Maghboeba and Barker, Laura and Jewell, Scott and Rohrer, Dan and Maxim, Dan and Filkins, Dana and Harbach, Philip and Cortadillo, Eddie and Berghuis, Bree and Turner, Lisa and Hudson, Eric and Feenstra, Kristin and Sobin, Leslie and Robb, James and Branton, Phillip and Korzeniewski, Greg and Shive, Charles and Tabor, David and Qi, Liqun and Groch, Kevin and Nampally, Sreenath and Buia, Steve and Zimmerman, Angela and Smith, Anna and Burges, Robin and Robinson, Karna and Valentino, Kim and Bradbury, Deborah and Cosentino, Mark and Diaz-Mayoral, Norma and Kennedy, Mary and Engel, Theresa and Williams, Penelope and Erickson, Kenyon and Ardlie, Kristin and Winckler, Wendy and Getz, Gad and DeLuca, David and MacArthur, Daniel and Kellis, Manolis and Thomson, Alexander and Young, Taylor and Gelfand, Ellen and Donovan, Molly and Meng, Yan and Grant, George and Mash, Deborah and Marcus, Yvonne and Basile, Margaret and Liu, Jun and Zhu, Jun and Tu, Zhidong and Cox, Nancy J and Nicolae, Dan L and Gamazon, Eric R and Im, Hae Kyung and Konkashbaev, Anuar and Pritchard, Jonathan and Stevens, Matthew and Flutre, Timothèe and Wen, Xiaoquan and Dermitzakis, Emmanouil T and Lappalainen, Tuuli and Guigo, Roderic and Monlong, Jean and Sammeth, Michael and Koller, Daphne and Battle, Alexis and Mostafavi, Sara and McCarthy, Mark and Rivas, Manual and Maller, Julian and Rusyn, Ivan and Nobel, Andrew and Wright, Fred and Shabalin, Andrey and Feolo, Mike and Sharopova, Nataliya and Sturcke, Anne and Paschal, Justin and Anderson, James M and Wilder, Elizabeth L and Derr, Leslie K and Green, Eric D and Struewing, Jeffery P and Temple, Gary and Volpi, Simona and Boyer, Joy T and Thomson, Elizabeth J and Guyer, Mark S and Ng, Cathy and Abdallah, Assya and Colantuoni, Deborah and Insel, Thomas R and Koester, Susan E and Little, A Roger and Bender, Patrick K and Lehner, Thomas and Yao, Yin and Compton, Carolyn C and Vaught, Jimmie B and Sawyer, Sherilyn and Lockhart, Nicole C and Demchok, Joanne and Moore, Helen F}, year={2013}, month=may, pages={580–585}, language={en} "}}, "10.1038/s41467-018-03751-6": {"nature":"Lachmann, A. et al. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications vol. 9 (2018).","bibtex":{"type":"misc","record":" title={Massive mining of publicly available RNA-seq data from human and mouse}, volume={9}, url={http://dx.doi.org/10.1038/s41467-018-03751-6}, DOI={10.1038/s41467-018-03751-6}, abstractNote={AbstractRNA sequencing (RNA-seq) is the leading technology for genome-wide transcript quantification. However, publicly available RNA-seq data is currently provided mostly in raw form, a significant barrier for global and integrative retrospective analyses. ARCHS4 is a web resource that makes the majority of published RNA-seq data from human and mouse available at the gene and transcript levels. For developing ARCHS4, available FASTQ files from RNA-seq experiments from the Gene Expression Omnibus (GEO) were aligned using a cloud-based infrastructure. In total 187,946 samples are accessible through ARCHS4 with 103,083 mouse and 84,863 human. Additionally, the ARCHS4 web interface provides intuitive exploration of the processed data through querying tools, interactive visualization, and gene pages that provide average expression across cell lines and tissues, top co-expressed genes for each gene, and predicted biological functions and protein–protein interactions for each gene based on prior knowledge combined with co-expression.}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Lachmann, Alexander and Torre, Denis and Keenan, Alexandra B. and Jagodnik, Kathleen M. and Lee, Hoyjin J. and Wang, Lily and Silverstein, Moshe C. and Ma’ayan, Avi}, year={2018}, month=apr, language={en} "}}, + "10.1038/s41586-020-2493-4": {"nature":"Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature vol. 583 699–710 (2020).","bibtex":{"type":"misc","record":" title={Expanded encyclopaedias of DNA elements in the human and mouse genomes}, volume={583}, url={http://dx.doi.org/10.1038/s41586-020-2493-4}, DOI={10.1038/s41586-020-2493-4}, abstractNote={AbstractThe human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.}, number={7818}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Abascal, Federico and Acosta, Reyes and Addleman, Nicholas J. and Adrian, Jessika and Afzal, Veena and Ai, Rizi and Aken, Bronwen and Akiyama, Jennifer A. and Jammal, Omar Al and Amrhein, Henry and Anderson, Stacie M. and Andrews, Gregory R. and Antoshechkin, Igor and Ardlie, Kristin G. and Armstrong, Joel and Astley, Matthew and Banerjee, Budhaditya and Barkal, Amira A. and Barnes, If H. A. and Barozzi, Iros and Barrell, Daniel and Barson, Gemma and Bates, Daniel and Baymuradov, Ulugbek K. and Bazile, Cassandra and Beer, Michael A. and Beik, Samantha and Bender, M. A. and Bennett, Ruth and Bouvrette, Louis Philip Benoit and Bernstein, Bradley E. and Berry, Andrew and Bhaskar, Anand and Bignell, Alexandra and Blue, Steven M. and Bodine, David M. and Boix, Carles and Boley, Nathan and Borrman, Tyler and Borsari, Beatrice and Boyle, Alan P. and Brandsmeier, Laurel A. and Breschi, Alessandra and Bresnick, Emery H. and Brooks, Jason A. and Buckley, Michael and Burge, Christopher B. and Byron, Rachel and Cahill, Eileen and Cai, Lingling and Cao, Lulu and Carty, Mark and Castanon, Rosa G. and Castillo, Andres and Chaib, Hassan and Chan, Esther T. and Chee, Daniel R. and Chee, Sora and Chen, Hao and Chen, Huaming and Chen, Jia-Yu and Chen, Songjie and Cherry, J. Michael and Chhetri, Surya B. and Choudhary, Jyoti S. and Chrast, Jacqueline and Chung, Dongjun and Clarke, Declan and Cody, Neal A. L. and Coppola, Candice J. and Coursen, Julie and D’Ippolito, Anthony M. and Dalton, Stephen and Danyko, Cassidy and Davidson, Claire and Davila-Velderrain, Jose and Davis, Carrie A. and Dekker, Job and Deran, Alden and DeSalvo, Gilberto and Despacio-Reyes, Gloria and Dewey, Colin N. and Dickel, Diane E. and Diegel, Morgan and Diekhans, Mark and Dileep, Vishnu and Ding, Bo and Djebali, Sarah and Dobin, Alexander and Dominguez, Daniel and Donaldson, Sarah and Drenkow, Jorg and Dreszer, Timothy R. and Drier, Yotam and Duff, Michael O. and Dunn, Douglass and Eastman, Catharine and Ecker, Joseph R. and Edwards, Matthew D. and El-Ali, Nicole and Elhajjajy, Shaimae I. and Elkins, Keri and Emili, Andrew and Epstein, Charles B. and Evans, Rachel C. and Ezkurdia, Iakes and Fan, Kaili and Farnham, Peggy J. and Farrell, Nina P. and Feingold, Elise A. and Ferreira, Anne-Maud and Fisher-Aylor, Katherine and Fitzgerald, Stephen and Flicek, Paul and Foo, Chuan Sheng and Fortier, Kevin and Frankish, Adam and Freese, Peter and Fu, Shaliu and Fu, Xiang-Dong and Fu, Yu and Fukuda-Yuzawa, Yoko and Fulciniti, Mariateresa and Funnell, Alister P. W. and Gabdank, Idan and Galeev, Timur and Gao, Mingshi and Giron, Carlos Garcia and Garvin, Tyler H. and Gelboin-Burkhart, Chelsea Anne and Georgolopoulos, Grigorios and Gerstein, Mark B. and Giardine, Belinda M. and Gifford, David K. and Gilbert, David M. and Gilchrist, Daniel A. and Gillespie, Shawn and Gingeras, Thomas R. and Gong, Peng and Gonzalez, Alvaro and Gonzalez, Jose M. and Good, Peter and Goren, Alon and Gorkin, David U. and Graveley, Brenton R. and Gray, Michael and Greenblatt, Jack F. and Griffiths, Ed and Groudine, Mark T. and Grubert, Fabian and Gu, Mengting and Guigó, Roderic and Guo, Hongbo and Guo, Yu and Guo, Yuchun and Gursoy, Gamze and Gutierrez-Arcelus, Maria and Halow, Jessica and Hardison, Ross C. and Hardy, Matthew and Hariharan, Manoj and Harmanci, Arif and Harrington, Anne and Harrow, Jennifer L. and Hashimoto, Tatsunori B. and Hasz, Richard D. and Hatan, Meital and Haugen, Eric and Hayes, James E. and He, Peng and He, Yupeng and Heidari, Nastaran and Hendrickson, David and Heuston, Elisabeth F. and Hilton, Jason A. and Hitz, Benjamin C. and Hochman, Abigail and Holgren, Cory and Hou, Lei and Hou, Shuyu and Hsiao, Yun-Hua E. and Hsu, Shanna and Huang, Hui and Hubbard, Tim J. and Huey, Jack and Hughes, Timothy R. and Hunt, Toby and Ibarrientos, Sean and Issner, Robbyn and Iwata, Mineo and Izuogu, Osagie and Jaakkola, Tommi and Jameel, Nader and Jansen, Camden and Jiang, Lixia and Jiang, Peng and Johnson, Audra and Johnson, Rory and Jungreis, Irwin and Kadaba, Madhura and Kasowski, Maya and Kasparian, Mary and Kato, Momoe and Kaul, Rajinder and Kawli, Trupti and Kay, Michael and Keen, Judith C. and Keles, Sunduz and Keller, Cheryl A. and Kelley, David and Kellis, Manolis and Kheradpour, Pouya and Kim, Daniel Sunwook and Kirilusha, Anthony and Klein, Robert J. and Knoechel, Birgit and Kuan, Samantha and Kulik, Michael J. and Kumar, Sushant and Kundaje, Anshul and Kutyavin, Tanya and Lagarde, Julien and Lajoie, Bryan R. and Lambert, Nicole J. and Lazar, John and Lee, Ah Young and Lee, Donghoon and Lee, Elizabeth and Lee, Jin Wook and Lee, Kristen and Leslie, Christina S. and Levy, Shawn and Li, Bin and Li, Hairi and Li, Nan and Li, Shantao and Li, Xiangrui and Li, Yang I. and Li, Ying and Li, Yining and Li, Yue and Lian, Jin and Libbrecht, Maxwell W. and Lin, Shin and Lin, Yiing and Liu, Dianbo and Liu, Jason and Liu, Peng and Liu, Tingting and Liu, X. Shirley and Liu, Yan and Liu, Yaping and Long, Maria and Lou, Shaoke and Loveland, Jane and Lu, Aiping and Lu, Yuheng and Lécuyer, Eric and Ma, Lijia and Mackiewicz, Mark and Mannion, Brandon J. and Mannstadt, Michael and Manthravadi, Deepa and Marinov, Georgi K. and Martin, Fergal J. and Mattei, Eugenio and McCue, Kenneth and McEown, Megan and McVicker, Graham and Meadows, Sarah K. and Meissner, Alex and Mendenhall, Eric M. and Messer, Christopher L. and Meuleman, Wouter and Meyer, Clifford and Miller, Steve and Milton, Matthew G. and Mishra, Tejaswini and Moore, Dianna E. and Moore, Helen M. and Moore, Jill E. and Moore, Samuel H. and Moran, Jennifer and Mortazavi, Ali and Mudge, Jonathan M. and Munshi, Nikhil and Murad, Rabi and Myers, Richard M. and Nandakumar, Vivek and Nandi, Preetha and Narasimha, Anil M. and Narayanan, Aditi K. and Naughton, Hannah and Navarro, Fabio C. P. and Navas, Patrick and Nazarovs, Jurijs and Nelson, Jemma and Neph, Shane and Neri, Fidencio Jun and Nery, Joseph R. and Nesmith, Amy R. and Newberry, J. Scott and Newberry, Kimberly M. and Ngo, Vu and Nguyen, Rosy and Nguyen, Thai B. and Nguyen, Tung and Nishida, Andrew and Noble, William S. and Novak, Catherine S. and Novoa, Eva Maria and Nuñez, Briana and O’Donnell, Charles W. and Olson, Sara and Onate, Kathrina C. and Otterman, Ericka and Ozadam, Hakan and Pagan, Michael and Palden, Tsultrim and Pan, Xinghua and Park, Yongjin and Partridge, E. Christopher and Paten, Benedict and Pauli-Behn, Florencia and Pazin, Michael J. and Pei, Baikang and Pennacchio, Len A. and Perez, Alexander R. and Perry, Emily H. and Pervouchine, Dmitri D. and Phalke, Nishigandha N. and Pham, Quan and Phanstiel, Doug H. and Plajzer-Frick, Ingrid and Pratt, Gabriel A. and Pratt, Henry E. and Preissl, Sebastian and Pritchard, Jonathan K. and Pritykin, Yuri and Purcaro, Michael J. and Qin, Qian and Quinones-Valdez, Giovanni and Rabano, Ines and Radovani, Ernest and Raj, Anil and Rajagopal, Nisha and Ram, Oren and Ramirez, Lucia and Ramirez, Ricardo N. and Rausch, Dylan and Raychaudhuri, Soumya and Raymond, Joseph and Razavi, Rozita and Reddy, Timothy E. and Reimonn, Thomas M. and Ren, Bing and Reymond, Alexandre and Reynolds, Alex and Rhie, Suhn K. and Rinn, John and Rivera, Miguel and Rivera-Mulia, Juan Carlos and Roberts, Brian S. and Rodriguez, Jose Manuel and Rozowsky, Joel and Ryan, Russell and Rynes, Eric and Salins, Denis N. and Sandstrom, Richard and Sasaki, Takayo and Sathe, Shashank and Savic, Daniel and Scavelli, Alexandra and Scheiman, Jonathan and Schlaffner, Christoph and Schloss, Jeffery A. and Schmitges, Frank W. and See, Lei Hoon and Sethi, Anurag and Setty, Manu and Shafer, Anthony and Shan, Shuo and Sharon, Eilon and Shen, Quan and Shen, Yin and Sherwood, Richard I. and Shi, Minyi and Shin, Sunyoung and Shoresh, Noam and Siebenthall, Kyle and Sisu, Cristina and Slifer, Teri and Sloan, Cricket A. and Smith, Anna and Snetkova, Valentina and Snyder, Michael P. and Spacek, Damek V. and Srinivasan, Sharanya and Srivas, Rohith and Stamatoyannopoulos, George and Stamatoyannopoulos, John A. and Stanton, Rebecca and Steffan, Dave and Stehling-Sun, Sandra and Strattan, J. Seth and Su, Amanda and Sundararaman, Balaji and Suner, Marie-Marthe and Syed, Tahin and Szynkarek, Matt and Tanaka, Forrest Y. and Tenen, Danielle and Teng, Mingxiang and Thomas, Jeffrey A. and Toffey, Dave and Tress, Michael L. and Trout, Diane E. and Trynka, Gosia and Tsuji, Junko and Upchurch, Sean A. and Ursu, Oana and Uszczynska-Ratajczak, Barbara and Uziel, Mia C. and Valencia, Alfonso and Biber, Benjamin Van and van der Velde, Arjan G. and Van Nostrand, Eric L. and Vaydylevich, Yekaterina and Vazquez, Jesus and Victorsen, Alec and Vielmetter, Jost and Vierstra, Jeff and Visel, Axel and Vlasova, Anna and Vockley, Christopher M. and Volpi, Simona and Vong, Shinny and Wang, Hao and Wang, Mengchi and Wang, Qin and Wang, Ruth and Wang, Tao and Wang, Wei and Wang, Xiaofeng and Wang, Yanli and Watson, Nathaniel K. and Wei, Xintao and Wei, Zhijie and Weisser, Hendrik and Weissman, Sherman M. and Welch, Rene and Welikson, Robert E. and Weng, Zhiping and Westra, Harm-Jan and Whitaker, John W. and White, Collin and White, Kevin P. and Wildberg, Andre and Williams, Brian A. and Wine, David and Witt, Heather N. and Wold, Barbara and Wolf, Maxim and Wright, James and Xiao, Rui and Xiao, Xinshu and Xu, Jie and Xu, Jinrui and Yan, Koon-Kiu and Yan, Yongqi and Yang, Hongbo and Yang, Xinqiong and Yang, Yi-Wen and Yardımcı, Galip Gürkan and Yee, Brian A. and Yeo, Gene W. and Young, Taylor and Yu, Tianxiong and Yue, Feng and Zaleski, Chris and Zang, Chongzhi and Zeng, Haoyang and Zeng, Weihua and Zerbino, Daniel R. and Zhai, Jie and Zhan, Lijun and Zhan, Ye and Zhang, Bo and Zhang, Jialing and Zhang, Jing and Zhang, Kai and Zhang, Lijun and Zhang, Peng and Zhang, Qi and Zhang, Xiao-Ou and Zhang, Yanxiao and Zhang, Zhizhuo and Zhao, Yuan and Zheng, Ye and Zhong, Guoqing and Zhou, Xiao-Qiao and Zhu, Yun and Zimmerman, Jared and Moore, Jill E. and Purcaro, Michael J. and Pratt, Henry E. and Epstein, Charles B. and Shoresh, Noam and Adrian, Jessika and Kawli, Trupti and Davis, Carrie A. and Dobin, Alexander and Kaul, Rajinder and Halow, Jessica and Van Nostrand, Eric L. and Freese, Peter and Gorkin, David U. and Shen, Yin and He, Yupeng and Mackiewicz, Mark and Pauli-Behn, Florencia and Williams, Brian A. and Mortazavi, Ali and Keller, Cheryl A. and Zhang, Xiao-Ou and Elhajjajy, Shaimae I. and Huey, Jack and Dickel, Diane E. and Snetkova, Valentina and Wei, Xintao and Wang, Xiaofeng and Rivera-Mulia, Juan Carlos and Rozowsky, Joel and Zhang, Jing and Chhetri, Surya B. and Zhang, Jialing and Victorsen, Alec and White, Kevin P. and Visel, Axel and Yeo, Gene W. and Burge, Christopher B. and Lécuyer, Eric and Gilbert, David M. and Dekker, Job and Rinn, John and Mendenhall, Eric M. and Ecker, Joseph R. and Kellis, Manolis and Klein, Robert J. and Noble, William S. and Kundaje, Anshul and Guigó, Roderic and Farnham, Peggy J. and Cherry, J. Michael and Myers, Richard M. and Ren, Bing and Graveley, Brenton R. and Gerstein, Mark B. and Pennacchio, Len A. and Snyder, Michael P. and Bernstein, Bradley E. and Wold, Barbara and Hardison, Ross C. and Gingeras, Thomas R. and Stamatoyannopoulos, John A. and Weng, Zhiping}, year={2020}, month=jul, pages={699–710}, language={en} "}}, "10.1038/s41598-020-72664-6": {"nature":"Zhao, Y., Wong, L. & Goh, W. W. B. How to do quantile normalization correctly for gene expression data analyses. Scientific Reports vol. 10 (2020).","bibtex":{"type":"misc","record":" title={How to do quantile normalization correctly for gene expression data analyses}, volume={10}, url={http://dx.doi.org/10.1038/s41598-020-72664-6}, DOI={10.1038/s41598-020-72664-6}, abstractNote={AbstractQuantile normalization is an important normalization technique commonly used in high-dimensional data analysis. However, it is susceptible to class-effect proportion effects (the proportion of class-correlated variables in a dataset) and batch effects (the presence of potentially confounding technical variation) when applied blindly on whole data sets, resulting in higher false-positive and false-negative rates. We evaluate five strategies for performing quantile normalization, and demonstrate that good performance in terms of batch-effect correction and statistical feature selection can be readily achieved by first splitting data by sample class-labels before performing quantile normalization independently on each split (“Class-specific”). Via simulations with both real and simulated batch effects, we demonstrate that the “Class-specific” strategy (and others relying on similar principles) readily outperform whole-data quantile normalization, and is robust-preserving useful signals even during the combined analysis of separately-normalized datasets. Quantile normalization is a commonly used procedure. But when carelessly applied on whole datasets without first considering class-effect proportion and batch effects, can result in poor performance. If quantile normalization must be used, then we recommend using the “Class-specific” strategy.}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Zhao, Yaxing and Wong, Limsoon and Goh, Wilson Wen Bin}, year={2020}, month=sep, language={en} "}}, "10.1073/pnas.0506580102": {"nature":"Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences vol. 102 15545–15550 (2005).","bibtex":{"type":"misc","record":" title={Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles}, volume={102}, url={http://dx.doi.org/10.1073/pnas.0506580102}, DOI={10.1073/pnas.0506580102}, abstractNote={Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.}, number={43}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Subramanian, Aravind and Tamayo, Pablo and Mootha, Vamsi K. and Mukherjee, Sayan and Ebert, Benjamin L. and Gillette, Michael A. and Paulovich, Amanda and Pomeroy, Scott L. and Golub, Todd R. and Lander, Eric S. and Mesirov, Jill P.}, year={2005}, month=sep, pages={15545–15550}, language={en} "}}, "10.1093/bioinformatics/btac017": {"nature":"Lelong, S. et al. BioThings SDK: a toolkit for building high-performance data APIs in biomedical research. Bioinformatics vol. 38 2077–2079 (2022).","bibtex":{"type":"misc","record":" title={BioThings SDK: a toolkit for building high-performance data APIs in biomedical research}, volume={38}, url={http://dx.doi.org/10.1093/bioinformatics/btac017}, DOI={10.1093/bioinformatics/btac017}, abstractNote={Abstract\n \n Summary\n To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info and MyChem.info for integrating annotations on genes, variants and chemical compounds, respectively. These APIs are used by both individual researchers and application developers to simplify the process of annotation retrieval and identifier mapping. Here, we describe the BioThings Software Development Kit (SDK), a generalizable and reusable toolkit for integrating data from multiple disparate data sources and creating high-performance APIs. This toolkit allows users to easily create their own BioThings APIs for any data type of interest to them, as well as keep APIs up-to-date with their underlying data sources.\n \n \n Availability and implementation\n The BioThings SDK is built in Python and released via PyPI (https://pypi.org/project/biothings/). Its source code is hosted at its github repository (https://github.com/biothings/biothings.api).\n \n \n Supplementary information\n Supplementary data are available at Bioinformatics online.\n }, number={7}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Lelong, Sebastien and Zhou, Xinghua and Afrasiabi, Cyrus and Qian, Zhongchao and Cano, Marco Alvarado and Tsueng, Ginger and Xin, Jiwen and Mullen, Julia and Yao, Yao and Avila, Ricardo and Taylor, Greg and Su, Andrew I and Wu, Chunlei}, editor={Lu, Zhiyong}, year={2022}, month=jan, pages={2077–2079}, language={en} "}}, @@ -38,6 +41,8 @@ export default { "10.1093/nar/gkz446": {"nature":"Keenan, A. B. et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Research vol. 47 W212–W224 (2019).","bibtex":{"type":"misc","record":" title={ChEA3: transcription factor enrichment analysis by orthogonal omics integration}, volume={47}, url={http://dx.doi.org/10.1093/nar/gkz446}, DOI={10.1093/nar/gkz446}, abstractNote={AbstractIdentifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) is a transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene sets. The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF–gene co-expression from RNA-seq studies, TF–target associations from ChIP-seq experiments, and TF–gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate a composite rank that improves the prediction of the correct upstream TF compared to ranks produced by individual libraries. We compare ChEA3 with existing TF prediction tools and show that ChEA3 performs better. By integrating the ChEA3 libraries, we illuminate general transcription factor properties such as whether the TF behaves as an activator or a repressor. The ChEA3 web-server is available from https://amp.pharm.mssm.edu/ChEA3.}, number={W1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Keenan, Alexandra B and Torre, Denis and Lachmann, Alexander and Leong, Ariel K and Wojciechowicz, Megan L and Utti, Vivian and Jagodnik, Kathleen M and Kropiwnicki, Eryk and Wang, Zichen and Ma’ayan, Avi}, year={2019}, month=may, pages={W212–W224}, language={en} "}}, "10.1101/2021.12.16.473007": {"nature":"Virshup, I., Rybakov, S., Theis, F. J., Angerer, P. & Wolf, F. A. anndata: Annotated data. (2021) doi:10.1101/2021.12.16.473007.","bibtex":{"type":"misc","record":" title={anndata: Annotated data}, url={http://dx.doi.org/10.1101/2021.12.16.473007}, DOI={10.1101/2021.12.16.473007}, abstractNote={Summaryanndata is a Python package for handling annotated data matrices in memory and on disk (github.com/theislab/anndata), positioned between pandas and xarray. anndata offers a broad range of computationally efficient features including, among others, sparse data support, lazy operations, and a PyTorch interface.Statement of needGenerating insight from high-dimensional data matrices typically works through training models that annotate observations and variables via low-dimensional representations. In exploratory data analysis, this involvesiterativetraining and analysis using original and learned annotations and task-associated representations. anndata offers a canonical data structure for book-keeping these, which is neither addressed by pandas (McKinney, 2010), nor xarray (Hoyer & Hamman, 2017), nor commonly-used modeling packages like scikit-learn (Pedregosa et al., 2011).}, publisher={Cold Spring Harbor Laboratory}, author={Virshup, Isaac and Rybakov, Sergei and Theis, Fabian J. and Angerer, Philipp and Wolf, F. Alexander}, year={2021}, month=dec "}}, "10.1109/TVCG.2014.2346248": {"nature":"Lex, A., Gehlenborg, N., Strobelt, H., Vuillemot, R. & Pfister, H. UpSet: Visualization of Intersecting Sets. IEEE Transactions on Visualization and Computer Graphics vol. 20 1983–1992 (2014).","bibtex":{"type":"misc","record":" title={UpSet: Visualization of Intersecting Sets}, volume={20}, url={http://dx.doi.org/10.1109/TVCG.2014.2346248}, DOI={10.1109/tvcg.2014.2346248}, number={12}, journal={IEEE Transactions on Visualization and Computer Graphics}, publisher={Institute of Electrical and Electronics Engineers (IEEE)}, author={Lex, Alexander and Gehlenborg, Nils and Strobelt, Hendrik and Vuillemot, Romain and Pfister, Hanspeter}, year={2014}, month=dec, pages={1983–1992} "}}, + "10.1126/science.aar3146": {"nature":"Onuchic, V. et al. Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. Science vol. 361 (2018).","bibtex":{"type":"misc","record":" title={Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci}, volume={361}, url={http://dx.doi.org/10.1126/science.aar3146}, DOI={10.1126/science.aar3146}, abstractNote={Dissecting the epigenomic footprint\n \n Genome-wide epigenetic marks regulate gene expression, but the amount and function of variability in these marks are poorly understood. Working with human-derived samples, Onuchic\n et al.\n examined disease-associated genetic variation and sequence-dependent allele-specific methylation at gene regulatory loci. Regulatory sequences within individual chromosomal DNA molecules showed full or no methylation at specific sites corresponding to “on” and “off” switches. Interestingly, methylation did not occur on each DNA molecule, resulting in a variable fraction of methylated chromosomes. This stochastic type of gene regulation was more common for rare genetic variants, which may suggest a role in human disease.\n \n \n Science\n , this issue p.\n eaar3146\n }, number={6409}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Onuchic, Vitor and Lurie, Eugene and Carrero, Ivenise and Pawliczek, Piotr and Patel, Ronak Y. and Rozowsky, Joel and Galeev, Timur and Huang, Zhuoyi and Altshuler, Robert C. and Zhang, Zhizhuo and Harris, R. Alan and Coarfa, Cristian and Ashmore, Lillian and Bertol, Jessica W. and Fakhouri, Walid D. and Yu, Fuli and Kellis, Manolis and Gerstein, Mark and Milosavljevic, Aleksandar}, year={2018}, month=sep, language={en} "}}, + "10.1126/science.aaz1776": {"nature":"The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science vol. 369 1318–1330 (2020).","bibtex":{"type":"misc","record":" title={The GTEx Consortium atlas of genetic regulatory effects across human tissues}, volume={369}, url={http://dx.doi.org/10.1126/science.aaz1776}, DOI={10.1126/science.aaz1776}, abstractNote={The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.}, number={6509}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Aguet, François and Anand, Shankara and Ardlie, Kristin G. and Gabriel, Stacey and Getz, Gad A. and Graubert, Aaron and Hadley, Kane and Handsaker, Robert E. and Huang, Katherine H. and Kashin, Seva and Li, Xiao and MacArthur, Daniel G. and Meier, Samuel R. and Nedzel, Jared L. and Nguyen, Duyen T. and Segrè, Ayellet V. and Todres, Ellen and Balliu, Brunilda and Barbeira, Alvaro N. and Battle, Alexis and Bonazzola, Rodrigo and Brown, Andrew and Brown, Christopher D. and Castel, Stephane E. and Conrad, Donald F. and Cotter, Daniel J. and Cox, Nancy and Das, Sayantan and de Goede, Olivia M. and Dermitzakis, Emmanouil T. and Einson, Jonah and Engelhardt, Barbara E. and Eskin, Eleazar and Eulalio, Tiffany Y. and Ferraro, Nicole M. and Flynn, Elise D. and Fresard, Laure and Gamazon, Eric R. and Garrido-Martín, Diego and Gay, Nicole R. and Gloudemans, Michael J. and Guigó, Roderic and Hame, Andrew R. and He, Yuan and Hoffman, Paul J. and Hormozdiari, Farhad and Hou, Lei and Im, Hae Kyung and Jo, Brian and Kasela, Silva and Kellis, Manolis and Kim-Hellmuth, Sarah and Kwong, Alan and Lappalainen, Tuuli and Li, Xin and Liang, Yanyu and Mangul, Serghei and Mohammadi, Pejman and Montgomery, Stephen B. and Muñoz-Aguirre, Manuel and Nachun, Daniel C. and Nobel, Andrew B. and Oliva, Meritxell and Park, YoSon and Park, Yongjin and Parsana, Princy and Rao, Abhiram S. and Reverter, Ferran and Rouhana, John M. and Sabatti, Chiara and Saha, Ashis and Stephens, Matthew and Stranger, Barbara E. and Strober, Benjamin J. and Teran, Nicole A. and Viñuela, Ana and Wang, Gao and Wen, Xiaoquan and Wright, Fred and Wucher, Valentin and Zou, Yuxin and Ferreira, Pedro G. and Li, Gen and Melé, Marta and Yeger-Lotem, Esti and Barcus, Mary E. and Bradbury, Debra and Krubit, Tanya and McLean, Jeffrey A. and Qi, Liqun and Robinson, Karna and Roche, Nancy V. and Smith, Anna M. and Sobin, Leslie and Tabor, David E. and Undale, Anita and Bridge, Jason and Brigham, Lori E. and Foster, Barbara A. and Gillard, Bryan M. and Hasz, Richard and Hunter, Marcus and Johns, Christopher and Johnson, Mark and Karasik, Ellen and Kopen, Gene and Leinweber, William F. and McDonald, Alisa and Moser, Michael T. and Myer, Kevin and Ramsey, Kimberley D. and Roe, Brian and Shad, Saboor and Thomas, Jeffrey A. and Walters, Gary and Washington, Michael and Wheeler, Joseph and Jewell, Scott D. and Rohrer, Daniel C. and Valley, Dana R. and Davis, David A. and Mash, Deborah C. and Branton, Philip A. and Barker, Laura K. and Gardiner, Heather M. and Mosavel, Maghboeba and Siminoff, Laura A. and Flicek, Paul and Haeussler, Maximilian and Juettemann, Thomas and Kent, W. 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