From 1714fac0e26cac9630ed9e514c7f4907ad6eb558 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 14 Aug 2024 08:43:30 -0700 Subject: [PATCH] [create-pull-request] automated change (#134) Co-authored-by: vincerubinetti <8326331+vincerubinetti@users.noreply.github.com> --- _cite/.cache/cache.db | Bin 327680 -> 356352 bytes _data/citations.yaml | 17743 ++++++++++++++++++++-------------------- 2 files changed, 9046 insertions(+), 8697 deletions(-) diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 74a72484d668e24988f95778278d1167951add73..c7f96d4acf1b626cdb252d850525c452a9f6ad99 100644 GIT binary patch delta 10398 zcmbta3v?URnbw^dNq#D_oj8f}@We^T%aSGeol>y;j^D312_!gUX>3g_%_t)&j$K-3 z6+#L%U2+t-<)rpqw&Zb=ZF|mg z4!-$k?w$X?-~HcLhYl@1^yZT5SC}(RCew~%;-w_>%-)M~68GCzC%WwBhmPg!ustZ= zW3!}9U6m8}C(bx4D?4Cn8vJj{j!XQSv`AEnDv_w-i!6%=`Eue{A|nG~#Wxa^2g14* z)qGmeyevMFC@d)`-N(DrBm09&R33Y_1~P)r&)*W+w}f{jpW~Lq+3CtMzBKuGpBB?qDL4?){4xn7p13r>eAw_cDHhcR z4oJROEJTJ-&iNe@*$m)R+rEp(up^OGwgwiHpgGOm}rvS(UrvsFMuLJ}C24 zR#jKwgDdEvQc{%fahFz?L?XKCEG@09EUl=-cbC)a%SaKmml3nQp>11ZgA+beUXHKo zaoO6bky3I~7OA1;8WJktZ%C8U)>+@R-plW_hOK3mk1gM|9OC}UeeakzpRVEkWjI{HErNw<5PZjZCNth}PkgB*6zV>R4b`gk+RNv|q(l;N|T z^hNy2C0=5i`lODee@ZR^)?6uP{WYzs;Wn?c7F)k*RWiSm`IoG+^ncAboV7orG5y($ zbjye4(X0=$PV*1*AJLpz&OyVSoRB#C*NmwrYq<3m&Xi6kYq$+7aDT26Nk6C@aC$th zQYYY2R)M_RP@baHgq^b!%0TGyStMI8G{Nn1x+*k8?T~*aCHlYD0tfOx> z5=&m0(*@tIc9vJWJY}UQKplOeo^vGjK46==yqR+Yf@XR>K$H@R$?SG{oGy>2+=WYe z7IK`O04RgZk9%%oU|fs*Vdz0MXs06^unYPFP24IyftJ{gJoR zPg*!HXF3F@e|gU371`9 zg4isspptr1w+hDT1WJy@Ib0;lJ&99no z;cw@LxDDpr=GENW{956xa6*uTHT+wPp0MUvkEP}CgHy$~@gEX;^~b_mI&qS>ECVgwB{tAhVS7#D&akxvwIfP{@M2`NAj&Mwqko~MMk3QHv+Y_ z@fl`3;oj7Xw8Yuh%y#7D@l;m8AAG%y=G?`XW`i07cNf!%rqst5)6-d9ieoq4CW zk4P!%bM|SnH$@enSwses)C0f%^Y_RVDeB}akCQzqYR|S6WOs_n{&hXMJW1Vu#|K{` zm(5WVefRf;zD9PXUgla~B0H1R>9cQrh3rUCCraKW{VD2--GyX(lDhB4_fL_&6m`k( z?k2rS>fTT8EFwKA>Y?#^(w(Fx?!7eoKS)=SyyuSxc9G5$_0Z){k&YC#=OvZ2rzqQ1 zZ;`enb?V_CUQ1e2RLHZQw4|tfdnMVHr0)LlwKtLG6!qC~+mA?7iY#gOk;Wu-*T4UK zGigXsS03vl^(o4^@ltR%A2bT5EvNhLymN8e)NM^dAjfk0ZYvVDUBaI&{145|Q`WtL zmo!`cX8GX%qczsotj}5>vpxWt^T?d$OwZ^B&6%FrZ_pf|44MO!L35^O!UoL&%Ah$w z88indgXT=nXa>!ho|w@LngcHlnlnA48Z-wegXREb(46U+kU?{RGHA~9Owgb?Kp8Y= zdS)VM(46U+5rgIcWzZa;44MO!L35^O_8Bw>D1+tzWzd}I8O5MEKp8a$NQ34~&jbvb z1C&8?fMS|6l{PGVdT?cysm)~jLiV1lhD=9BR@$GeKeIe&KE}N%yliR%?_ZpI#2&A+ znGU8|t=2SC8ZmuQr%yDJ^(E)UKJ*=T!Kb~i&az0-!Xfhw8##L7R&IHs=3~pm!iC2t z%~2&9l#fq-zAqq)y^1;FLk#`Rf(|p98WgwmZc}Ef^g?KAG1dtEw^tKy?1<&`s@9FqqhTHb3$4 zzljO^b6c!s4p*7OQ%29cEv&RwL@ENuW6r5JeINLk&rE9siA@$2Ys&XV-a9z&|Y z*gyzjY}p86z=&)=&(Rn2xTW;*r}><;t1GJ zVx6YzGOHuEic?1_`Nz4$*pY1dowtSDEPbSESOsYgYw?D}HP3E22XaF$j-p_QWFCi& zvowlw^a7A4mnQDG;gxyFm%;A$0l)Y_yxwLCrgnc-;{KznSzUF}!n%sF1&_+uvJu$A zNZ%UgmeA{uk!&+tkl6en_{yINft9*GT2%@xP}wZxZd0b5zTetwew4qR+zsk>1Iaxc zi+3zgw~H65+g#Z&pVOld_dtw6Au!e?Y25pDxcB~~x-DEfe-`ClRqRC9*%ccMDv<#A zOR-0egf%sSepHNtJFe^O-&XH%SBu-!A*iuKijNYN7dP2@p-rGl=$vXbAGo!pZ86`N zSiiwLtU)J3)x>sRlQt@;R0@%T#G9u#*?Pt#RqU68()j+EJWkI}357IL!sStYKUqc9 zem;-5Y2oWa5t={*z`ANlynO*App8ZgoZHuY6~iEaK+7OuBR~WrLUP{%by&DG@!NOX z7TLY3DvJ#eYIMLPn(#igc;#evmm=#LK2sH+0v@Q^nrI*n6usXZJ=WpFAcu zDr!(3gBZ}NgdAQqAhrQ?l6HJDt3}rJF|oHf@r(DCcV_p-#wBC}QO*yavo%VC3ZT*= zLg-T<5@a{&@~{RAy2Kq4d=Hkx>s`$dEYx9`-w>1l^cJyE)}zWW9q8wa44~;~G>hYH zM$oPrzW`{)l9_=9`3M7zjQ|>q2wL&^prw}5?{x4_;j!hX{MLRvw1Rl6k^fQ4LjF6? 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Davidson + - Richard J. Abdill + - Samantha P. Graham + - Vincent Rubinetti + - Frank W. Albert - Casey S. Greene - publisher: eLife Sciences Publications, Ltd - date: '2023-02-09' - link: https://doi.org/10.7554/elife.84855 + - Sean Davis + - Ran Blekhman + publisher: Zenodo + date: '2023-10-11' + link: https://doi.org/gsvhxn orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.7554/eLife.84855.3 - title: Analysis of science journalism reveals gender and regional disparities in - coverage +- id: doi:10.1016/j.ajhg.2023.12.001 + title: 'Building a vertically integrated genomic learning health system: The biobank + at the Colorado Center for Personalized Medicine' authors: - - Natalie R Davidson - - Casey S Greene - publisher: eLife - date: '2024-05-28' - link: https://doi.org/gtw9dx + - Laura K. Wiley + - Jonathan A. Shortt + - Emily R. Roberts + - Jan Lowery + - Elizabeth Kudron + - Meng Lin + - David Mayer + - Melissa Wilson + - Tonya M. Brunetti + - Sameer Chavan + - Tzu L. Phang + - Nikita Pozdeyev + - Joseph Lesny + - Stephen J. Wicks + - Ethan T. Moore + - Joshua L. Morgenstern + - Alanna N. Roff + - Elise L. Shalowitz + - Adrian Stewart + - Cole Williams + - Michelle N. Edelmann + - Madelyne Hull + - J. Tacker Patton + - Lisen Axell + - Lisa Ku + - Yee Ming Lee + - Jean Jirikowic + - Anna Tanaka + - Emily Todd + - Sarah White + - Brett Peterson + - Emily Hearst + - Richard Zane + - Casey S. Greene + - Rasika Mathias + - Marilyn Coors + - Matthew Taylor + - Debashis Ghosh + - Michael G. Kahn + - Ian M. Brooks + - Christina L. Aquilante + - David Kao + - Nicholas Rafaels + - Kristy R. Crooks + - Steve Hess + - Kathleen C. Barnes + - Christopher R. Gignoux + publisher: The American Journal of Human Genetics + date: '2024-01-01' + link: https://doi.org/gtcwqq orcid: 0000-0001-8713-9213 member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.7554/eLife.84855.2 - title: Analysis of science journalism reveals gender and regional disparities in - coverage + plugin: sources.py + file: sources.yaml + image: https://private-user-images.githubusercontent.com/542643/294239653-924e038d-77d7-4bf0-aa80-7d532faa66fc.png +- id: doi:10.1101/2023.06.28.546898 + title: Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry + Estimates from Direct-to-Consumer Canine Genetic Tests authors: - - Natalie R. Davidson + - Halie M. Rando + - Kiley Graim + - Greg Hampikian - Casey S. Greene - publisher: eLife Sciences Publications, Ltd - date: '2024-05-17' - link: https://doi.org/gtvsrt + publisher: Cold Spring Harbor Laboratory + date: '2023-06-29' + link: https://doi.org/10.1101/2023.06.28.546898 orcid: 0000-0001-8713-9213 member: casey-greene - plugin: orcid.py - file: orcid.yaml + plugin: sources.py + file: sources.yaml + image: https://user-images.githubusercontent.com/8975841/250271905-4eed44ba-528a-4a61-a4ec-fa90d51e61f9.jpg - id: doi:10.1101/2024.04.25.590992 title: Missing cell types in single-cell references impact deconvolution of bulk data but are detectable @@ -70,6 +123,37 @@ member: casey-greene plugin: orcid.py file: orcid.yaml +- id: doi:10.1101/2023.07.31.551386 + title: 'MousiPLIER: A Mouse Pathway-Level Information Extractor Model' + authors: + - Shuo Zhang + - Benjamin J. Heil + - Weiguang Mao + - Maria Chikina + - Casey S. Greene + - Elizabeth A. Heller + publisher: Cold Spring Harbor Laboratory + date: '2023-08-02' + link: https://doi.org/10.1101/2023.07.31.551386 + orcid: 0000-0001-8713-9213 + member: casey-greene + plugin: sources.py + file: sources.yaml + image: https://user-images.githubusercontent.com/542643/262141715-23a165d3-0156-4ba0-afc6-0ef260c46d7c.png +- id: doi:10.1093/bioadv/vbae004 + title: "Optimizer\u2019s dilemma: optimization strongly influences model selection\ + \ in transcriptomic prediction" + authors: + - Jake Crawford + - Maria Chikina + - Casey S Greene + publisher: Bioinformatics Advances + date: '2024-01-01' + link: https://doi.org/gtdh5z + orcid: 0000-0001-8713-9213 + member: casey-greene + plugin: orcid.py + file: orcid.yaml - id: doi:10.1128/spectrum.03157-23 title: "Pseudomonas aeruginosa\n transcriptome analysis of metal\ \ restriction in\n ex vivo\n cystic fibrosis sputum" @@ -87,33 +171,26 @@ member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.5281/zenodo.8186993 - title: Human Microbiome Compendium dataset +- id: doi:10.1101/2024.04.19.590243 + title: 'The Single-cell Pediatric Cancer Atlas: Data portal and open-source tools + for single-cell transcriptomics of pediatric tumors' authors: - - Richard J. Abdill - - Samantha P. Graham - - Vincent Rubinetti - - Frank W. Albert + - Allegra G. Hawkins + - Joshua A. Shapiro + - Stephanie J. Spielman + - David S. Mejia + - Deepashree Venkatesh Prasad + - Nozomi Ichihara + - Arkadii Yakovets + - Kurt G. Wheeler + - Chante J. Bethell + - Steven M. Foltz + - "Jennifer O\u2019Malley" - Casey S. Greene - - Sean Davis - - Ran Blekhman - publisher: Zenodo - date: '2023-10-11' - link: https://doi.org/gsvhxn - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1093/bioadv/vbae004 - title: "Optimizer\u2019s dilemma: optimization strongly influences model selection\ - \ in transcriptomic prediction" - authors: - - Jake Crawford - - Maria Chikina - - Casey S Greene - publisher: Bioinformatics Advances - date: '2024-01-01' - link: https://doi.org/gtdh5z + - Jaclyn N. Taroni + publisher: Cold Spring Harbor Laboratory + date: '2024-04-24' + link: https://doi.org/gt6s6h orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py @@ -128,255 +205,127 @@ member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.1186/s13059-023-03077-7 - title: Performance of computational algorithms to deconvolve heterogeneous bulk - ovarian tumor tissue depends on experimental factors - authors: - - Ariel A. Hippen - - Dalia K. Omran - - Lukas M. Weber - - Euihye Jung - - Ronny Drapkin - - Jennifer A. Doherty - - Stephanie C. Hicks - - Casey S. 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Greene - - Sean Davis - - Ran Blekhman - publisher: Cold Spring Harbor Laboratory - date: '2023-10-11' - link: https://doi.org/gsvf5z - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: sources.py - file: sources.yaml - image: https://user-images.githubusercontent.com/542643/274611735-0b4d7372-d935-4a0d-b3a3-909012346b35.png -- id: doi:10.1101/2023.08.21.554169 - title: Analysis ofPseudomonas aeruginosatranscription in anex vivocystic - fibrosis sputum model identifies metal restriction as a gene expression stimulus - authors: - - Samuel L. Neff - - Georgia Doing - - Taylor Reiter - - Thomas H. Hampton - - Casey S. Greene - - Deborah A. 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Heller - publisher: Cold Spring Harbor Laboratory - date: '2023-08-02' - link: https://doi.org/10.1101/2023.07.31.551386 + - Milton Pividori + - Casey Greene + publisher: Zenodo + date: '2023-06-22' + link: https://doi.org/10.5281/zenodo.8044955 orcid: 0000-0001-8713-9213 member: casey-greene - plugin: sources.py - file: sources.yaml - image: https://user-images.githubusercontent.com/542643/262141715-23a165d3-0156-4ba0-afc6-0ef260c46d7c.png -- id: doi:10.1101/2023.07.20.549951 - title: BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific - perturbations from bulk + plugin: orcid.py + file: orcid.yaml +- id: doi:10.5281/zenodo.7805407 + title: Data underlying OpenPBTA Manuscript Figures and Molecular Alterations authors: - - Natalie R. Davidson - - Casey S. Greene - publisher: Cold Spring Harbor Laboratory - date: '2023-07-22' - link: https://doi.org/10.1101/2023.07.20.549951 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: sources.py - file: sources.yaml - image: https://user-images.githubusercontent.com/542643/262144782-78a11c8e-1b10-44e0-85ec-1b709cfd94e4.png -- id: doi:10.1093/nar/gkad289 - title: 'MyGeneset.info: an interactive and programmatic platform for community-curated - and user-created collections of genes' - authors: - - Ricardo Avila - - Vincent Rubinetti - - Xinghua Zhou - - Dongbo Hu - - Zhongchao Qian - - Marco Alvarado Cano - - Everaldo Rodolpho - - Ginger Tsueng - - Casey Greene - - Chunlei Wu - publisher: Nucleic Acids Research - date: '2023-04-18' - link: https://doi.org/10.1093/nar/gkad289 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: sources.py - file: sources.yaml - image: https://user-images.githubusercontent.com/542643/232873400-6146a32d-b11b-4514-8b26-14c6e4d6bcac.jpeg -- id: doi:10.1101/2023.06.28.546898 - title: Is a Picture Worth 1,000 SNPs? Effects of User-Submitted Photographs on Ancestry - Estimates from Direct-to-Consumer Canine Genetic Tests - authors: - - Halie M. Rando - - Kiley Graim - - Greg Hampikian + - Joshua A. Shapiro + - Krutika S. Gaonkar + - Stephanie J. Spielman + - Candace L. Savonen + - Chante J. Bethell + - Run Jin + - Komal S. Rathi + - Yuankun Zhu + - Laura E. Egolf + - Bailey K. Farrow + - Daniel P. Miller + - Yang Yang + - Tejaswi Koganti + - Nighat Noureen + - Mateusz P. Koptyra + - Nhat Duong + - Mariarita Santi + - Jung Kim + - Shannon Robins + - Phillip B. Storm + - Stephen C. Mack + - Jena V. Lilly + - Hongbo M. Xie + - Payal Jain + - Pichai Raman + - Brian R. Rood + - Rishi R. Lulla + - Javad Nazarian + - Adam A. Kraya + - Zalman Vaksman + - Allison P. Heath + - Cassie Kline + - Laura Scolaro + - Angela N. Viaene + - Xiaoyan Huang + - Gregory P. Way + - Steven M. Foltz + - Bo Zhang + - Anna R. Poetsch + - Sabine Mueller + - Brian M. Ennis + - Michael Prados + - Sharon J. 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Hogan publisher: Cold Spring Harbor Laboratory - date: '2023-06-26' - link: https://doi.org/10.1101/2023.06.26.546586 + date: '2023-08-21' + link: https://doi.org/10.1101/2023.08.21.554169 orcid: 0000-0001-8713-9213 member: casey-greene plugin: sources.py file: sources.yaml - image: https://user-images.githubusercontent.com/542643/252371308-1ae174fe-1eb6-47c4-882b-5a3b982bc533.png -- id: doi:10.5281/zenodo.8044955 - title: 'greenelab/phenoplier: a computational framework to integrate genetic studies - with gene co-expression patterns' - authors: - - Milton Pividori - - Casey Greene - publisher: Zenodo - date: '2023-06-22' - link: https://doi.org/10.5281/zenodo.8044955 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.5281/zenodo.8071382 - title: 'greenelab/phenoplier: a computational framework to integrate genetic studies - with gene co-expression patterns' + image: https://user-images.githubusercontent.com/542643/274611350-b55a8531-8fee-4125-8054-4db365ab8009.png +- id: doi:10.7554/ELIFE.84855 + title: Analysis of science journalism reveals gender and regional disparities in + coverage authors: - - ' Milton Pividori' - - ' Casey Greene' - publisher: Zenodo - date: '2023-06-22' - link: https://doi.org/gsdcgn + - Natalie R Davidson + - Casey S Greene + publisher: eLife + date: '2024-05-28' + link: https://doi.org/grrw83 orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.1101/2023.06.14.544991 - title: Deconvolution reveals compositional differences in high-grade serous ovarian - cancer subtypes - authors: - - Ariel A. 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Taroni - publisher: Zenodo - date: '2023-04-06' - link: https://doi.org/10.5281/zenodo.7805407 + publisher: arXiv + date: '2022-01-01' + link: https://doi.org/gt6s6j orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.1371/journal.pcbi.1010984 - title: The effect of non-linear signal in classification problems using gene expression +- id: doi:10.1038/s43018-022-00507-6 + title: 'Author Correction: A phase I/Ib trial and biological correlate analysis + of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced + HNSCC' authors: - - Benjamin J. Heil - - Jake Crawford - - Casey S. Greene - publisher: PLOS Computational Biology - date: '2023-03-27' - link: https://doi.org/10.1371/journal.pcbi.1010984 + - Laurel B. Darragh + - Michael M. Knitz + - Junxiao Hu + - Eric T. 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A. Hastings + - Seung-min Park + - Graham Mackintosh + - Robert J. Reynolds + - Adrienne L. Hoarfrost + - Aenor Sawyer + - Casey S. Greene + - Benjamin S. Glicksberg + - Corey A. Theriot + - Daniel C. Berrios + - Jack Miller + - Joel Babdor + - Richard Barker - Sergio E. Baranzini - Afshin Beheshti - Stuart Chalk @@ -698,26 +533,39 @@ link: https://arxiv.org/abs/2112.12554 - type: editorial link: https://www.nature.com/articles/s42256-023-00643-3 -- id: doi:10.1038/s42003-023-04588-6 - title: Cross-platform normalization enables machine learning model training on microarray - and RNA-seq data simultaneously +- id: doi:10.1101/2023.07.20.549951 + title: BuDDI:Bulk Deconvolution with Domain Invarianceto predict cell-type-specific + perturbations from bulk authors: - - Steven M. Foltz + - Natalie R. Davidson - Casey S. Greene - - Jaclyn N. Taroni - publisher: Communications Biology - date: '2023-02-25' - link: https://doi.org/10.1038/s42003-023-04588-6 + publisher: Cold Spring Harbor Laboratory + date: '2023-07-22' + link: https://doi.org/10.1101/2023.07.20.549951 orcid: 0000-0001-8713-9213 member: casey-greene plugin: sources.py file: sources.yaml - image: https://www.biorxiv.org/content/biorxiv/early/2017/03/21/118349/F1.medium.gif + image: https://user-images.githubusercontent.com/542643/262144782-78a11c8e-1b10-44e0-85ec-1b709cfd94e4.png +- id: doi:10.1186/s13040-023-00332-2 + title: Changing word meanings in biomedical literature reveal pandemics and new + technologies + authors: + - David N. Nicholson + - Faisal Alquaddoomi + - Vincent Rubinetti + - Casey S. Greene + publisher: BioData Mining + date: '2023-05-05' + link: https://doi.org/10.1186/s13040-023-00332-2 + orcid: 0000-0001-8713-9213 + member: casey-greene + plugin: sources.py + file: sources.yaml + image: https://user-images.githubusercontent.com/542643/179368710-0f832059-fc60-410c-b9bf-43d1cf381f18.png buttons: - type: preprint - link: http://doi.org/10.1101/118349 - - type: source - link: https://github.com/greenelab/RNAseq_titration_results + link: https://doi.org/10.1101/2022.06.27.497742 - id: doi:10.1128/msystems.00342-22 title: Compendium-Wide Analysis of Pseudomonas aeruginosa Core and Accessory Genes Reveals Transcriptional Patterns across Strains PAO1 and PA14 @@ -764,70 +612,269 @@ buttons: - type: preprint link: https://doi.org/10.1101/2022.01.24.477642 -- id: doi:10.7554/eLife.84855.1 - title: Analysis of science journalism reveals gender and regional disparities in - coverage +- id: doi:10.1101/2023.06.14.544991 + title: Deconvolution reveals compositional differences in high-grade serous ovarian + cancer subtypes authors: + - Ariel A. 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Mundo + - Dimitri Perrin + - David Mai + - Nils Wellhausen + - COVID-19 Review Consortium + - Anthony Gitter + - Casey S. Greene + publisher: arXiv + date: '2022-01-01' + link: https://doi.org/gp4ftc orcid: 0000-0001-8713-9213 member: casey-greene - plugin: sources.py - file: sources.yaml - image: https://www.biorxiv.org/content/biorxiv/early/2020/11/07/2020.11.06.371963/F4.medium.gif - tags: - - cancer - - single cell - - ovarian cancer - buttons: - - type: preprint - link: https://doi.org/10.1101/2020.11.06.371963 -- id: doi:10.1371/journal.pcbi.1009290 - title: 'miQC: An adaptive probabilistic framework for quality control of single-cell - RNA-sequencing data' + plugin: orcid.py + file: orcid.yaml +- id: doi:10.1101/2022.12.04.519045 + title: Performance of computational algorithms to deconvolve heterogeneous bulk + tumor tissue depends on experimental factors authors: - Ariel A. Hippen - - Matias M. Falco + - Dalia K. Omran - Lukas M. Weber - - Erdogan Pekcan Erkan - - Kaiyang Zhang - - Jennifer Anne Doherty - - "Anna V\xE4h\xE4rautio" - - Casey S. Greene + - Euihye Jung + - Ronny Drapkin + - Jennifer A. Doherty - Stephanie C. 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Greene publisher: Cold Spring Harbor Laboratory - date: '2021-06-29' - link: https://doi.org/10.1101/2021.06.23.21259416 + date: '2022-12-05' + link: https://doi.org/10.1101/2022.12.04.519045 orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.1128/mSystems.00122-21 - title: Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention - and Treatment +- id: doi:10.1016/j.gpb.2022.09.011 + title: 'SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional + Responses' authors: - - Ronan Lordan - - Halie M. Rando + - Alexandra J. Lee + - Dallas L. Mould + - Jake Crawford + - Dongbo Hu + - Rani K. Powers + - Georgia Doing + - James C. Costello + - Deborah A. Hogan - Casey S. Greene - publisher: mSystems - date: '2021-06-29' - link: https://doi.org/10.1128/msystems.00122-21 + publisher: Genomics, Proteomics & Bioinformatics + date: '2022-10-01' + link: https://doi.org/10.1016/j.gpb.2022.09.011 orcid: 0000-0001-8713-9213 member: casey-greene plugin: sources.py file: sources.yaml - image: https://greenelab.github.io/covid19-review/images/N000-overview.png - tags: - - COVID19 -- id: doi:10.1101/2021.06.21.449261 - title: Analysis of science journalism reveals gender and regional disparities in - coverage + image: https://raw.githubusercontent.com/greenelab/generic-expression-patterns/master/figure_generation/output/figure_2.png + buttons: + - type: preprint + link: https://doi.org/10.1101/2021.05.24.445440 +- id: doi:10.1371/journal.pcbi.1009757 + title: Ten simple rules for large-scale data processing authors: - - Natalie R. Davidson - - Casey S. Greene - publisher: Cold Spring Harbor Laboratory - date: '2021-06-22' - link: https://doi.org/10.1101/2021.06.21.449261 + - Arkarachai Fungtammasan + - Alexandra Lee + - Jaclyn Taroni + - Kurt Wheeler + - Chen-Shan Chin + - Sean Davis + - Casey Greene + publisher: PLOS Computational Biology + date: '2022-02-10' + link: https://doi.org/10.1371/journal.pcbi.1009757 orcid: 0000-0001-8713-9213 member: casey-greene plugin: sources.py file: sources.yaml - image: https://user-images.githubusercontent.com/542643/122943080-f1e45d00-d333-11eb-8b8c-d481ebc554e5.png -- id: doi:10.1101/2021.05.26.445900 - title: 'GenomicSuperSignature: interpretation of RNA-seq experiments through robust, - efficient comparison to public databases' + image: https://user-images.githubusercontent.com/542643/153752465-a788f7d3-707c-4804-91f5-04ad1aebaed4.png +- id: doi:10.1101/2022.06.22.497194 + title: The Effects of Nonlinear Signal on Expression-Based Prediction Performance authors: - - Sehyun Oh - - Ludwig Geistlinger - - Marcel Ramos - - Daniel Blankenberg - - Marius van den Beek - - Jaclyn N. Taroni - - Vincent Carey - - Casey Greene - - Levi Waldron - - Sean Davis + - Benjamin J. Heil + - Jake Crawford + - Casey S. Greene publisher: Cold Spring Harbor Laboratory - date: '2021-05-27' - link: https://doi.org/10.1101/2021.05.26.445900 + date: '2022-06-26' + link: https://doi.org/10.1101/2022.06.22.497194 orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.1101/2021.05.24.445440 - title: Generative neural networks separate common and specific transcriptional responses +- id: doi:10.48550/arxiv.2203.13946 + title: Using genome-wide expression compendia to study microorganisms authors: - Alexandra J. Lee - - Dallas L. Mould - - Jake Crawford - - Dongbo Hu - - Rani K. Powers + - Taylor Reiter - Georgia Doing - - James C. Costello + - Julia Oh - Deborah A. Hogan - Casey S. 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Greene publisher: Cold Spring Harbor Laboratory - date: '2021-05-24' - link: https://doi.org/10.1101/2021.05.24.445440 + date: '2021-10-28' + link: https://doi.org/10.1101/2021.10.27.466140 orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.5281/zenodo.4677667 - title: Response to NOT-OD-21-066 - Racial EDI in Biomedical Research Workforce +- id: doi:10.1101/2022.04.09.487671 + title: 'wenda_gpu: fast domain adaptation for genomic data' authors: - - Monica Munoz-Torres - - Melissa Haendel - - Sean Davis - - Lawrence Hunter - - Andrew Neumann - - Nicole Vasilevsky - - Tursynay Issabekova - - Janine Higgins - - Judy Regensteiner - - Casey Greene - - Samuel Volchenboum - - Anita Walden - - Mary Ann Tuli - - Deepak Unni - - Halie Rando - - Shawn T. O'Neil - - Matthew H. Brush - publisher: Zenodo - date: '2021-04-09' - link: https://doi.org/10.5281/zenodo.4677667 + - Ariel A. Hippen + - Jake Crawford + - Jacob R. Gardner + - Casey S. 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Greene - publisher: Cold Spring Harbor Laboratory - date: '2021-03-04' - link: https://doi.org/10.1101/2021.03.04.433874 + - Anne E Carpenter + - Casey S Greene + - Piero Carnici + - Benilton S Carvalho + - Michiel de Hoon + - Stacey Finley + - Kim-Anh Le Cao + - Jerry SH Lee + - Luigi Marchionni + - Suzanne Sindi + - Fabian J Theis + - Gregory P Way + - Jean YH Yang + - Elana J Fertig + publisher: arXiv + date: '2021-01-01' + link: https://doi.org/gt6s6r orcid: 0000-0001-8713-9213 member: casey-greene plugin: orcid.py file: orcid.yaml -- id: doi:10.1101/2021.03.03.433798 - title: 'miQC: An adaptive probabilistic framework for quality control of single-cell - RNA-sequencing data' +- id: doi:10.48550/arxiv.2109.08633 + title: An Open-Publishing Response to the COVID-19 Infodemic authors: - - Ariel A. Hippen - - Matias M. Falco - - Lukas M. Weber - - Erdogan Pekcan Erkan - - Kaiyang Zhang - - Jennifer Anne Doherty - - "Anna V\xE4h\xE4rautio" + - Halie M. Rando + - Simina M. 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Greene - publisher: Genome Biology - date: '2020-05-11' - link: https://doi.org/10.1186/s13059-020-02021-3 + publisher: Cell Systems + date: '2021-09-01' + link: https://doi.org/10.1016/j.cels.2021.07.007 orcid: 0000-0001-8713-9213 member: casey-greene plugin: sources.py file: sources.yaml - image: https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2Fs13059-020-02021-3/MediaObjects/13059_2020_2021_Fig1_HTML.png?as=webp + image: https://raw.githubusercontent.com/greenelab/iscb-diversity/20d21504463c0487aa844be0ff236b3a51c70fa4/figs/2020-01-31_groupings.png buttons: - type: preprint - link: https://doi.org/10.1101/573782 + link: https://doi.org/10.1101/2020.04.14.927251 + - type: manubot + link: https://greenelab.github.io/iscb-diversity-manuscript/ - type: source - link: https://github.com/greenelab/biobombe - - type: website - link: https://greenelab.github.io/BioBombe/ + link: https://github.com/greenelab/iscb-diversity + text: iscb-diversity + - type: source + link: https://github.com/greenelab/wiki-nationality-estimate + text: wiki-nationality-estimate + - type: source + link: https://github.com/dhimmel/pubmedpy + text: pubmedpy tags: - machine learning - - genomics -- id: doi:10.1101/2020.11.06.371963 - title: Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer - facilitates effective experimental design + - diversity +- id: doi:10.1186/s13059-021-02468-y + title: 'Author Correction: Community-wide hackathons to identify central themes + in single-cell multi-omics' authors: - - Lukas M. Weber - - Ariel A. Hippen - - Peter F. Hickey - - Kristofer C. Berrett - - Jason Gertz - - Jennifer Anne Doherty + - "Kim-Anh L\xEA Cao" + - Al J. Abadi + - Emily F. Davis-Marcisak + - Lauren Hsu + - Arshi Arora + - Alexis Coullomb + - Atul Deshpande + - Yuzhou Feng + - Pratheepa Jeganathan + - Melanie Loth + - Chen Meng + - Wancen Mu + - Vera Pancaldi + - Kris Sankaran + - Dario Righelli + - Amrit Singh + - Joshua S. Sodicoff + - "Genevieve L. Stein-O\u2019Brien" + - Ayshwarya Subramanian + - Joshua D. Welch + - Yue You + - Ricard Argelaguet + - Vincent J. Carey + - Ruben Dries - Casey S. Greene - - Stephanie C. Hicks - publisher: Cold Spring Harbor Laboratory - date: '2020-11-07' - link: https://doi.org/10.1101/2020.11.06.371963 + - Susan Holmes + - Michael I. Love + - Matthew E. Ritchie + - Guo-Cheng Yuan + - Aedin C. 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Greene - - Deepashree Venkatesh Prasad - - Xiaoqian Jiang + - Lauren M. Sanders + - Jason H. Yang + - Ryan T. Scott + - Amina Ann Qutub + - Hector Garcia Martin + - Daniel C. Berrios + - Jaden J. A. Hastings + - Jon Rask + - Graham Mackintosh + - Adrienne L. Hoarfrost + - Stuart Chalk + - John Kalantari + - Kia Khezeli + - Erik L. Antonsen + - Joel Babdor + - Richard Barker + - Sergio E. Baranzini + - Afshin Beheshti + - Guillermo M. Delgado-Aparicio + - Benjamin S. Glicksberg - Casey S. Greene - publisher: Nature Reviews Genetics - date: '2020-07-21' - link: https://doi.org/10.1038/s41576-020-0257-5 + - Melissa Haendel + - Arif A. Hamid + - Philip Heller + - Daniel Jamieson + - Katelyn J. Jarvis + - Svetlana V. Komarova + - Matthieu Komorowski + - Prachi Kothiyal + - Ashish Mahabal + - Uri Manor + - Christopher E. Mason + - Mona Matar + - George I. Mias + - Jack Miller + - Jerry G. 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Kucherlapati - - Stephen Baylin - - Leslie Cope - - Ludmila Danilova - - Moiz S. Bootwalla - - Phillip H. Lai - - Dennis T. Maglinte - - David J. Van Den Berg - - Daniel J. Weisenberger - - J. Todd Auman - - Saianand Balu - - Tom Bodenheimer - - Cheng Fan - - Katherine A. Hoadley - - Alan P. Hoyle - - Stuart R. Jefferys - - Corbin D. Jones - - Shaowu Meng - - Piotr A. Mieczkowski - - Lisle E. Mose - - Amy H. Perou - - Charles M. Perou - - Jeffrey Roach - - Yan Shi - - Janae V. Simons - - Tara Skelly - - Matthew G. Soloway - - Donghui Tan - - Umadevi Veluvolu - - Huihui Fan - - Toshinori Hinoue - - Peter W. Laird - - Hui Shen - - Wanding Zhou - - Michelle Bellair - - Kyle Chang - - Kyle Covington - - Chad J. Creighton - - Huyen Dinh - - HarshaVardhan Doddapaneni - - Lawrence A. Donehower - - Jennifer Drummond - - Richard A. 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Ramirez - - Lisa Wise - - Erik Zmuda - - Niall Corcoran - - Tony Costello - - Christopher Hovens - - Andre L. Carvalho - - Ana C. de Carvalho - - "Jos\xE9 H. Fregnani" - - Adhemar Longatto-Filho - - Rui M. Reis - - Cristovam Scapulatempo-Neto - - Henrique C.S. Silveira - - Daniel O. Vidal - - Andrew Burnette - - Jennifer Eschbacher - - Beth Hermes - - Ardene Noss - - Rosy Singh - - Matthew L. Anderson - - Patricia D. Castro - - Michael Ittmann - - David Huntsman - - Bernard Kohl - - Xuan Le - - Richard Thorp - - Chris Andry - - Elizabeth R. Duffy - - Vladimir Lyadov - - Oxana Paklina - - Galiya Setdikova - - Alexey Shabunin - - Mikhail Tavobilov - - Christopher McPherson - - Ronald Warnick - - Ross Berkowitz - - Daniel Cramer - - Colleen Feltmate - - Neil Horowitz - - Adam Kibel - - Michael Muto - - Chandrajit P. Raut - - Andrei Malykh - - Jill S. Barnholtz-Sloan - - Wendi Barrett - - Karen Devine - - Jordonna Fulop - - Quinn T. Ostrom - - Kristen Shimmel - - Yingli Wolinsky - - Andrew E. Sloan - - Agostino De Rose - - Felice Giuliante - - Marc Goodman - - Beth Y. Karlan - - Curt H. Hagedorn - - John Eckman - - Jodi Harr - - Jerome Myers - - Kelinda Tucker - - Leigh Anne Zach - - Brenda Deyarmin - - Hai Hu - - Leonid Kvecher - - Caroline Larson - - Richard J. Mural - - Stella Somiari - - Ales Vicha - - Tomas Zelinka - - Joseph Bennett - - Mary Iacocca - - Brenda Rabeno - - Patricia Swanson - - Mathieu Latour - - Louis Lacombe - - "Bernard T\xEAtu" - - Alain Bergeron - - Mary McGraw - - Susan M. Staugaitis - - John Chabot - - Hanina Hibshoosh - - Antonia Sepulveda - - Tao Su - - Timothy Wang - - Olga Potapova - - Olga Voronina - - Laurence Desjardins - - Odette Mariani - - Sergio Roman-Roman - - Xavier Sastre - - Marc-Henri Stern - - Feixiong Cheng - - Sabina Signoretti - - Andrew Berchuck - - Darell Bigner - - Eric Lipp - - Jeffrey Marks - - Shannon McCall - - Roger McLendon - - Angeles Secord - - Alexis Sharp - - Madhusmita Behera - - Daniel J. Brat - - Amy Chen - - Keith Delman - - Seth Force - - Fadlo Khuri - - Kelly Magliocca - - Shishir Maithel - - Jeffrey J. Olson - - Taofeek Owonikoko - - Alan Pickens - - Suresh Ramalingam - - Dong M. Shin - - Gabriel Sica - - Erwin G. Van Meir - - Hongzheng Zhang - - Wil Eijckenboom - - Ad Gillis - - Esther Korpershoek - - Leendert Looijenga - - Wolter Oosterhuis - - Hans Stoop - - Kim E. van Kessel - - Ellen C. Zwarthoff - - Chiara Calatozzolo - - Lucia Cuppini - - Stefania Cuzzubbo - - Francesco DiMeco - - Gaetano Finocchiaro - - Luca Mattei - - Alessandro Perin - - Bianca Pollo - - Chu Chen - - John Houck - - Pawadee Lohavanichbutr - - Arndt Hartmann - - Christine Stoehr - - Robert Stoehr - - Helge Taubert - - Sven Wach - - Bernd Wullich - - Witold Kycler - - Dawid Murawa - - Maciej Wiznerowicz - - Ki Chung - - W. Jeffrey Edenfield - - Julie Martin - - Eric Baudin - - Glenn Bubley - - Raphael Bueno - - Assunta De Rienzo - - William G. Richards - - Steven Kalkanis - - Tom Mikkelsen - - Houtan Noushmehr - - Lisa Scarpace - - Nicolas Girard - - Marta Aymerich - - Elias Campo - - "Eva Gin\xE9" - - "Armando L\xF3pez Guillermo" - - Nguyen Van Bang - - Phan Thi Hanh - - Bui Duc Phu - - Yufang Tang - - Howard Colman - - Kimberley Evason - - Peter R. Dottino - - John A. Martignetti - - Hani Gabra - - Hartmut Juhl - - Teniola Akeredolu - - Serghei Stepa - - Dave Hoon - - Keunsoo Ahn - - Koo Jeong Kang - - Felix Beuschlein - - Anne Breggia - - Michael Birrer - - Debra Bell - - Mitesh Borad - - Alan H. Bryce - - Erik Castle - - Vishal Chandan - - John Cheville - - John A. Copland - - Michael Farnell - - Thomas Flotte - - Nasra Giama - - Thai Ho - - Michael Kendrick - - Jean-Pierre Kocher - - Karla Kopp - - Catherine Moser - - David Nagorney - - "Daniel O\u2019Brien" - - "Brian Patrick O\u2019Neill" - - Tushar Patel - - Gloria Petersen - - Florencia Que - - Michael Rivera - - Lewis Roberts - - Robert Smallridge - - Thomas Smyrk - - Melissa Stanton - - R. Houston Thompson - - Michael Torbenson - - Ju Dong Yang - - Lizhi Zhang - - Fadi Brimo - - Jaffer A. Ajani - - Ana Maria Angulo Gonzalez - - Carmen Behrens - - Jolanta Bondaruk - - Russell Broaddus - - Bogdan Czerniak - - Bita Esmaeli - - Junya Fujimoto - - Jeffrey Gershenwald - - Charles Guo - - Alexander J. Lazar - - Christopher Logothetis - - Funda Meric-Bernstam - - Cesar Moran - - Lois Ramondetta - - David Rice - - Anil Sood - - Pheroze Tamboli - - Timothy Thompson - - Patricia Troncoso - - Anne Tsao - - Ignacio Wistuba - - Candace Carter - - Lauren Haydu - - Peter Hersey - - Valerie Jakrot - - Hojabr Kakavand - - Richard Kefford - - Kenneth Lee - - Georgina Long - - Graham Mann - - Michael Quinn - - Robyn Saw - - Richard Scolyer - - Kerwin Shannon - - Andrew Spillane - - Jonathan Stretch - - Maria Synott - - John Thompson - - James Wilmott - - Hikmat Al-Ahmadie - - Timothy A. Chan - - Ronald Ghossein - - Anuradha Gopalan - - Douglas A. Levine - - Victor Reuter - - Samuel Singer - - Bhuvanesh Singh - - Nguyen Viet Tien - - Thomas Broudy - - Cyrus Mirsaidi - - Praveen Nair - - Paul Drwiega - - Judy Miller - - Jennifer Smith - - Howard Zaren - - Joong-Won Park - - Nguyen Phi Hung - - Electron Kebebew - - W. Marston Linehan - - Adam R. Metwalli - - Karel Pacak - - Peter A. Pinto - - Mark Schiffman - - Laura S. Schmidt - - Cathy D. Vocke - - Nicolas Wentzensen - - Robert Worrell - - Hannah Yang - - Marc Moncrieff - - Chandra Goparaju - - Jonathan Melamed - - Harvey Pass - - Natalia Botnariuc - - Irina Caraman - - Mircea Cernat - - Inga Chemencedji - - Adrian Clipca - - Serghei Doruc - - Ghenadie Gorincioi - - Sergiu Mura - - Maria Pirtac - - Irina Stancul - - Diana Tcaciuc - - Monique Albert - - Iakovina Alexopoulou - - Angel Arnaout - - John Bartlett - - Jay Engel - - Sebastien Gilbert - - Jeremy Parfitt - - Harman Sekhon - - George Thomas - - Doris M. Rassl - - Robert C. Rintoul - - Carlo Bifulco - - Raina Tamakawa - - Walter Urba - - Nicholas Hayward - - Henri Timmers - - Anna Antenucci - - Francesco Facciolo - - Gianluca Grazi - - Mirella Marino - - Roberta Merola - - Ronald de Krijger - - Anne-Paule Gimenez-Roqueplo - - "Alain Pich\xE9" - - Simone Chevalier - - Ginette McKercher - - Kivanc Birsoy - - Gene Barnett - - Cathy Brewer - - Carol Farver - - Theresa Naska - - Nathan A. Pennell - - Daniel Raymond - - Cathy Schilero - - Kathy Smolenski - - Felicia Williams - - Carl Morrison - - Jeffrey A. Borgia - - Michael J. Liptay - - Mark Pool - - Christopher W. Seder - - Kerstin Junker - - Larsson Omberg - - Mikhail Dinkin - - George Manikhas - - Domenico Alvaro - - Maria Consiglia Bragazzi - - Vincenzo Cardinale - - Guido Carpino - - Eugenio Gaudio - - David Chesla - - Sandra Cottingham - - Michael Dubina - - Fedor Moiseenko - - Renumathy Dhanasekaran - - Karl-Friedrich Becker - - Klaus-Peter Janssen - - Julia Slotta-Huspenina - - Mohamed H. Abdel-Rahman - - Dina Aziz - - Sue Bell - - Colleen M. Cebulla - - Amy Davis - - Rebecca Duell - - J. Bradley Elder - - Joe Hilty - - Bahavna Kumar - - James Lang - - Norman L. Lehman - - Randy Mandt - - Phuong Nguyen - - Robert Pilarski - - Karan Rai - - Lynn Schoenfield - - Kelly Senecal - - Paul Wakely - - Paul Hansen - - Ronald Lechan - - James Powers - - Arthur Tischler - - William E. Grizzle - - Katherine C. Sexton - - Alison Kastl - - Joel Henderson - - Sima Porten - - Jens Waldmann - - Martin Fassnacht - - Sylvia L. Asa - - Dirk Schadendorf - - Marta Couce - - Markus Graefen - - Hartwig Huland - - Guido Sauter - - Thorsten Schlomm - - Ronald Simon - - Pierre Tennstedt - - Oluwole Olabode - - Mark Nelson - - Oliver Bathe - - Peter R. Carroll - - June M. Chan - - Philip Disaia - - Pat Glenn - - Robin K. Kelley - - Charles N. Landen - - Joanna Phillips - - Michael Prados - - Jeffry Simko - - Karen Smith-McCune - - Scott VandenBerg - - Kevin Roggin - - Ashley Fehrenbach - - Ady Kendler - - Suzanne Sifri - - Ruth Steele - - Antonio Jimeno - - Francis Carey - - Ian Forgie - - Massimo Mannelli - - Michael Carney - - Brenda Hernandez - - Benito Campos - - Christel Herold-Mende - - Christin Jungk - - Andreas Unterberg - - Andreas von Deimling - - Aaron Bossler - - Joseph Galbraith - - Laura Jacobus - - Michael Knudson - - Tina Knutson - - Deqin Ma - - Mohammed Milhem - - Rita Sigmund - - Andrew K. Godwin - - Rashna Madan - - Howard G. Rosenthal - - Clement Adebamowo - - Sally N. Adebamowo - - Alex Boussioutas - - David Beer - - Thomas Giordano - - Anne-Marie Mes-Masson - - Fred Saad - - Therese Bocklage - - Lisa Landrum - - Robert Mannel - - Kathleen Moore - - Katherine Moxley - - Russel Postier - - Joan Walker - - Rosemary Zuna - - Michael Feldman - - Federico Valdivieso - - Rajiv Dhir - - James Luketich - - Edna M. Mora Pinero - - Mario Quintero-Aguilo - - Carlos Gilberto Carlotti - - "Jose Sebasti\xE3o Dos Santos" - - Rafael Kemp - - Ajith Sankarankuty - - Daniela Tirapelli - - James Catto - - Kathy Agnew - - Elizabeth Swisher - - Jenette Creaney - - Bruce Robinson - - Carl Simon Shelley - - Eryn M. Godwin - - Sara Kendall - - Cassaundra Shipman - - Carol Bradford - - Thomas Carey - - Andrea Haddad - - Jeffey Moyer - - Lisa Peterson - - Mark Prince - - Laura Rozek - - Gregory Wolf - - Rayleen Bowman - - Kwun M. Fong - - Ian Yang - - Robert Korst - - W. Kimryn Rathmell - - J. Leigh Fantacone-Campbell - - Jeffrey A. Hooke - - Albert J. Kovatich - - Craig D. Shriver - - John DiPersio - - Bettina Drake - - Ramaswamy Govindan - - Sharon Heath - - Timothy Ley - - Brian Van Tine - - Peter Westervelt - - Mark A. Rubin - - Jung Il Lee - - "Nat\xE1lia D. Aredes" - - Armaz Mariamidze - publisher: Cell Reports - date: '2018-04-01' - link: https://doi.org/10.1016/j.celrep.2018.03.046 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: sources.py - file: sources.yaml - image: https://els-jbs-prod-cdn.jbs.elsevierhealth.com/cms/attachment/4c2909b3-3e15-4723-a8b2-1f94166415e6/fx1.jpg - buttons: - - type: source - link: https://github.com/greenelab/pancancer/blob/master/ras_analysis.sh -- id: doi:10.6084/M9.FIGSHARE.6982919 - title: MultiPLIER Fileset - authors: - - Jaclyn Taroni - - Casey Greene - publisher: figshare - date: '2019-01-01' - link: https://doi.org/10.6084/m9.figshare.6982919 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.6084/m9.figshare.6982919.v1 - title: MultiPLIER Fileset - authors: - - Jaclyn Taroni - - Casey Greene - publisher: figshare - date: '2018-01-01' - link: https://doi.org/10.6084/m9.figshare.6982919.v1 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1016/j.cell.2018.03.035 - title: Oncogenic Signaling Pathways in The Cancer Genome Atlas - authors: - - Francisco Sanchez-Vega - - Marco Mina - - Joshua Armenia - - Walid K. Chatila - - Augustin Luna - - Konnor C. La - - Sofia Dimitriadoy - - David L. Liu - - Havish S. Kantheti - - Sadegh Saghafinia - - Debyani Chakravarty - - Foysal Daian - - Qingsong Gao - - Matthew H. Bailey - - Wen-Wei Liang - - Steven M. Foltz - - Ilya Shmulevich - - Li Ding - - Zachary Heins - - Angelica Ochoa - - Benjamin Gross - - Jianjiong Gao - - Hongxin Zhang - - Ritika Kundra - - Cyriac Kandoth - - Istemi Bahceci - - Leonard Dervishi - - Ugur Dogrusoz - - Wanding Zhou - - Hui Shen - - Peter W. Laird - - Gregory P. Way - - Casey S. Greene - - Han Liang - - Yonghong Xiao - - Chen Wang - - Antonio Iavarone - - Alice H. Berger - - Trever G. Bivona - - Alexander J. Lazar - - Gary D. Hammer - - Thomas Giordano - - Lawrence N. Kwong - - Grant McArthur - - Chenfei Huang - - Aaron D. Tward - - Mitchell J. Frederick - - Frank McCormick - - Matthew Meyerson - - Eliezer M. Van Allen - - Andrew D. Cherniack - - Giovanni Ciriello - - Chris Sander - - Nikolaus Schultz - - Samantha J. Caesar-Johnson - - John A. Demchok - - Ina Felau - - Melpomeni Kasapi - - Martin L. Ferguson - - Carolyn M. Hutter - - Heidi J. Sofia - - Roy Tarnuzzer - - Zhining Wang - - Liming Yang - - Jean C. Zenklusen - - Jiashan (Julia) Zhang - - Sudha Chudamani - - Jia Liu - - Laxmi Lolla - - Rashi Naresh - - Todd Pihl - - Qiang Sun - - Yunhu Wan - - Ye Wu - - Juok Cho - - Timothy DeFreitas - - Scott Frazer - - Nils Gehlenborg - - Gad Getz - - David I. Heiman - - Jaegil Kim - - Michael S. Lawrence - - Pei Lin - - Sam Meier - - Michael S. Noble - - Gordon Saksena - - Doug Voet - - Hailei Zhang - - Brady Bernard - - Nyasha Chambwe - - Varsha Dhankani - - Theo Knijnenburg - - Roger Kramer - - Kalle Leinonen - - Yuexin Liu - - Michael Miller - - Sheila Reynolds - - Ilya Shmulevich - - Vesteinn Thorsson - - Wei Zhang - - Rehan Akbani - - Bradley M. Broom - - Apurva M. Hegde - - Zhenlin Ju - - Rupa S. Kanchi - - Anil Korkut - - Jun Li - - Han Liang - - Shiyun Ling - - Wenbin Liu - - Yiling Lu - - Gordon B. Mills - - Kwok-Shing Ng - - Arvind Rao - - Michael Ryan - - Jing Wang - - John N. Weinstein - - Jiexin Zhang - - Adam Abeshouse - - Joshua Armenia - - Debyani Chakravarty - - Walid K. Chatila - - Ino de Bruijn - - Jianjiong Gao - - Benjamin E. Gross - - Zachary J. Heins - - Ritika Kundra - - Konnor La - - Marc Ladanyi - - Augustin Luna - - Moriah G. Nissan - - Angelica Ochoa - - Sarah M. Phillips - - Ed Reznik - - Francisco Sanchez-Vega - - Chris Sander - - Nikolaus Schultz - - Robert Sheridan - - S. Onur Sumer - - Yichao Sun - - Barry S. Taylor - - Jioajiao Wang - - Hongxin Zhang - - Pavana Anur - - Myron Peto - - Paul Spellman - - Christopher Benz - - Joshua M. Stuart - - Christopher K. Wong - - Christina Yau - - D. Neil Hayes - - Joel S. Parker - - Matthew D. Wilkerson - - Adrian Ally - - Miruna Balasundaram - - Reanne Bowlby - - Denise Brooks - - Rebecca Carlsen - - Eric Chuah - - Noreen Dhalla - - Robert Holt - - Steven J.M. Jones - - Katayoon Kasaian - - Darlene Lee - - Yussanne Ma - - Marco A. Marra - - Michael Mayo - - Richard A. Moore - - Andrew J. Mungall - - Karen Mungall - - A. Gordon Robertson - - Sara Sadeghi - - Jacqueline E. Schein - - Payal Sipahimalani - - Angela Tam - - Nina Thiessen - - Kane Tse - - Tina Wong - - Ashton C. Berger - - Rameen Beroukhim - - Andrew D. Cherniack - - Carrie Cibulskis - - Stacey B. Gabriel - - Galen F. Gao - - Gavin Ha - - Matthew Meyerson - - Steven E. Schumacher - - Juliann Shih - - Melanie H. Kucherlapati - - Raju S. Kucherlapati - - Stephen Baylin - - Leslie Cope - - Ludmila Danilova - - Moiz S. Bootwalla - - Phillip H. Lai - - Dennis T. Maglinte - - David J. Van Den Berg - - Daniel J. Weisenberger - - J. Todd Auman - - Saianand Balu - - Tom Bodenheimer - - Cheng Fan - - Katherine A. Hoadley - - Alan P. Hoyle - - Stuart R. Jefferys - - Corbin D. Jones - - Shaowu Meng - - Piotr A. Mieczkowski - - Lisle E. Mose - - Amy H. Perou - - Charles M. Perou - - Jeffrey Roach - - Yan Shi - - Janae V. Simons - - Tara Skelly - - Matthew G. Soloway - - Donghui Tan - - Umadevi Veluvolu - - Huihui Fan - - Toshinori Hinoue - - Peter W. Laird - - Hui Shen - - Wanding Zhou - - Michelle Bellair - - Kyle Chang - - Kyle Covington - - Chad J. Creighton - - Huyen Dinh - - HarshaVardhan Doddapaneni - - Lawrence A. Donehower - - Jennifer Drummond - - Richard A. Gibbs - - Robert Glenn - - Walker Hale - - Yi Han - - Jianhong Hu - - Viktoriya Korchina - - Sandra Lee - - Lora Lewis - - Wei Li - - Xiuping Liu - - Margaret Morgan - - Donna Morton - - Donna Muzny - - Jireh Santibanez - - Margi Sheth - - Eve Shinbrot - - Linghua Wang - - Min Wang - - David A. Wheeler - - Liu Xi - - Fengmei Zhao - - Julian Hess - - Elizabeth L. Appelbaum - - Matthew Bailey - - Matthew G. Cordes - - Li Ding - - Catrina C. Fronick - - Lucinda A. Fulton - - Robert S. Fulton - - Cyriac Kandoth - - Elaine R. Mardis - - Michael D. McLellan - - Christopher A. Miller - - Heather K. Schmidt - - Richard K. Wilson - - Daniel Crain - - Erin Curley - - Johanna Gardner - - Kevin Lau - - David Mallery - - Scott Morris - - Joseph Paulauskis - - Robert Penny - - Candace Shelton - - Troy Shelton - - Mark Sherman - - Eric Thompson - - Peggy Yena - - Jay Bowen - - Julie M. Gastier-Foster - - Mark Gerken - - Kristen M. Leraas - - Tara M. Lichtenberg - - Nilsa C. Ramirez - - Lisa Wise - - Erik Zmuda - - Niall Corcoran - - Tony Costello - - Christopher Hovens - - Andre L. Carvalho - - Ana C. de Carvalho - - "Jos\xE9 H. Fregnani" - - Adhemar Longatto-Filho - - Rui M. Reis - - Cristovam Scapulatempo-Neto - - Henrique C.S. Silveira - - Daniel O. Vidal - - Andrew Burnette - - Jennifer Eschbacher - - Beth Hermes - - Ardene Noss - - Rosy Singh - - Matthew L. Anderson - - Patricia D. Castro - - Michael Ittmann - - David Huntsman - - Bernard Kohl - - Xuan Le - - Richard Thorp - - Chris Andry - - Elizabeth R. Duffy - - Vladimir Lyadov - - Oxana Paklina - - Galiya Setdikova - - Alexey Shabunin - - Mikhail Tavobilov - - Christopher McPherson - - Ronald Warnick - - Ross Berkowitz - - Daniel Cramer - - Colleen Feltmate - - Neil Horowitz - - Adam Kibel - - Michael Muto - - Chandrajit P. Raut - - Andrei Malykh - - Jill S. Barnholtz-Sloan - - Wendi Barrett - - Karen Devine - - Jordonna Fulop - - Quinn T. Ostrom - - Kristen Shimmel - - Yingli Wolinsky - - Andrew E. Sloan - - Agostino De Rose - - Felice Giuliante - - Marc Goodman - - Beth Y. Karlan - - Curt H. Hagedorn - - John Eckman - - Jodi Harr - - Jerome Myers - - Kelinda Tucker - - Leigh Anne Zach - - Brenda Deyarmin - - Hai Hu - - Leonid Kvecher - - Caroline Larson - - Richard J. Mural - - Stella Somiari - - Ales Vicha - - Tomas Zelinka - - Joseph Bennett - - Mary Iacocca - - Brenda Rabeno - - Patricia Swanson - - Mathieu Latour - - Louis Lacombe - - "Bernard T\xEAtu" - - Alain Bergeron - - Mary McGraw - - Susan M. Staugaitis - - John Chabot - - Hanina Hibshoosh - - Antonia Sepulveda - - Tao Su - - Timothy Wang - - Olga Potapova - - Olga Voronina - - Laurence Desjardins - - Odette Mariani - - Sergio Roman-Roman - - Xavier Sastre - - Marc-Henri Stern - - Feixiong Cheng - - Sabina Signoretti - - Andrew Berchuck - - Darell Bigner - - Eric Lipp - - Jeffrey Marks - - Shannon McCall - - Roger McLendon - - Angeles Secord - - Alexis Sharp - - Madhusmita Behera - - Daniel J. Brat - - Amy Chen - - Keith Delman - - Seth Force - - Fadlo Khuri - - Kelly Magliocca - - Shishir Maithel - - Jeffrey J. Olson - - Taofeek Owonikoko - - Alan Pickens - - Suresh Ramalingam - - Dong M. Shin - - Gabriel Sica - - Erwin G. Van Meir - - Hongzheng Zhang - - Wil Eijckenboom - - Ad Gillis - - Esther Korpershoek - - Leendert Looijenga - - Wolter Oosterhuis - - Hans Stoop - - Kim E. van Kessel - - Ellen C. Zwarthoff - - Chiara Calatozzolo - - Lucia Cuppini - - Stefania Cuzzubbo - - Francesco DiMeco - - Gaetano Finocchiaro - - Luca Mattei - - Alessandro Perin - - Bianca Pollo - - Chu Chen - - John Houck - - Pawadee Lohavanichbutr - - Arndt Hartmann - - Christine Stoehr - - Robert Stoehr - - Helge Taubert - - Sven Wach - - Bernd Wullich - - Witold Kycler - - Dawid Murawa - - Maciej Wiznerowicz - - Ki Chung - - W. Jeffrey Edenfield - - Julie Martin - - Eric Baudin - - Glenn Bubley - - Raphael Bueno - - Assunta De Rienzo - - William G. Richards - - Steven Kalkanis - - Tom Mikkelsen - - Houtan Noushmehr - - Lisa Scarpace - - Nicolas Girard - - Marta Aymerich - - Elias Campo - - "Eva Gin\xE9" - - "Armando L\xF3pez Guillermo" - - Nguyen Van Bang - - Phan Thi Hanh - - Bui Duc Phu - - Yufang Tang - - Howard Colman - - Kimberley Evason - - Peter R. Dottino - - John A. Martignetti - - Hani Gabra - - Hartmut Juhl - - Teniola Akeredolu - - Serghei Stepa - - Dave Hoon - - Keunsoo Ahn - - Koo Jeong Kang - - Felix Beuschlein - - Anne Breggia - - Michael Birrer - - Debra Bell - - Mitesh Borad - - Alan H. Bryce - - Erik Castle - - Vishal Chandan - - John Cheville - - John A. Copland - - Michael Farnell - - Thomas Flotte - - Nasra Giama - - Thai Ho - - Michael Kendrick - - Jean-Pierre Kocher - - Karla Kopp - - Catherine Moser - - David Nagorney - - "Daniel O\u2019Brien" - - "Brian Patrick O\u2019Neill" - - Tushar Patel - - Gloria Petersen - - Florencia Que - - Michael Rivera - - Lewis Roberts - - Robert Smallridge - - Thomas Smyrk - - Melissa Stanton - - R. Houston Thompson - - Michael Torbenson - - Ju Dong Yang - - Lizhi Zhang - - Fadi Brimo - - Jaffer A. Ajani - - Ana Maria Angulo Gonzalez - - Carmen Behrens - - Jolanta Bondaruk - - Russell Broaddus - - Bogdan Czerniak - - Bita Esmaeli - - Junya Fujimoto - - Jeffrey Gershenwald - - Charles Guo - - Alexander J. Lazar - - Christopher Logothetis - - Funda Meric-Bernstam - - Cesar Moran - - Lois Ramondetta - - David Rice - - Anil Sood - - Pheroze Tamboli - - Timothy Thompson - - Patricia Troncoso - - Anne Tsao - - Ignacio Wistuba - - Candace Carter - - Lauren Haydu - - Peter Hersey - - Valerie Jakrot - - Hojabr Kakavand - - Richard Kefford - - Kenneth Lee - - Georgina Long - - Graham Mann - - Michael Quinn - - Robyn Saw - - Richard Scolyer - - Kerwin Shannon - - Andrew Spillane - - Jonathan Stretch - - Maria Synott - - John Thompson - - James Wilmott - - Hikmat Al-Ahmadie - - Timothy A. Chan - - Ronald Ghossein - - Anuradha Gopalan - - Douglas A. Levine - - Victor Reuter - - Samuel Singer - - Bhuvanesh Singh - - Nguyen Viet Tien - - Thomas Broudy - - Cyrus Mirsaidi - - Praveen Nair - - Paul Drwiega - - Judy Miller - - Jennifer Smith - - Howard Zaren - - Joong-Won Park - - Nguyen Phi Hung - - Electron Kebebew - - W. Marston Linehan - - Adam R. Metwalli - - Karel Pacak - - Peter A. Pinto - - Mark Schiffman - - Laura S. Schmidt - - Cathy D. Vocke - - Nicolas Wentzensen - - Robert Worrell - - Hannah Yang - - Marc Moncrieff - - Chandra Goparaju - - Jonathan Melamed - - Harvey Pass - - Natalia Botnariuc - - Irina Caraman - - Mircea Cernat - - Inga Chemencedji - - Adrian Clipca - - Serghei Doruc - - Ghenadie Gorincioi - - Sergiu Mura - - Maria Pirtac - - Irina Stancul - - Diana Tcaciuc - - Monique Albert - - Iakovina Alexopoulou - - Angel Arnaout - - John Bartlett - - Jay Engel - - Sebastien Gilbert - - Jeremy Parfitt - - Harman Sekhon - - George Thomas - - Doris M. Rassl - - Robert C. 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Moore - publisher: Advances in Artificial Life. Darwin Meets von Neumann - date: '2011-01-01' - link: https://doi.org/10.1007/978-3-642-21314-4_36 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1007/978-3-642-21283-3_39 - title: An Open-Ended Computational Evolution Strategy for Evolving Parsimonious - Solutions to Human Genetics Problems - authors: - - Casey S. Greene - - Douglas P. Hill - - Jason H. Moore - publisher: Advances in Artificial Life. 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Moore - publisher: Proceedings of the 12th annual conference on Genetic and evolutionary - computation - date: '2010-07-07' - link: https://doi.org/10.1145/1830483.1830523 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1016/j.semnephrol.2010.07.002 - title: Integrative Systems Biology for Data-Driven Knowledge Discovery - authors: - - Casey S. Greene - - Olga G. Troyanskaya - publisher: Seminars in Nephrology - date: '2010-09-01' - link: https://doi.org/10.1016/j.semnephrol.2010.07.002 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1093/bioinformatics/btq009 - title: Multifactor dimensionality reduction for graphics processing units enables - genome-wide testing of epistasis in sporadic ALS - authors: - - Casey S. Greene - - Nicholas A. Sinnott-Armstrong - - Daniel S. Himmelstein - - Paul J. Park - - Jason H. Moore - - Brent T. 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Tyler - - Bill C. White - - Casey S. Greene - - Peter C. Andrews - - Richard Cowper-Sa - - Jason H. Moore - publisher: 2009 IEEE Congress on Evolutionary Computation - date: '2009-05-01' - link: https://doi.org/10.1109/cec.2009.4983308 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1145/1569901.1570160 - title: Environmental noise improves epistasis models of genetic data discovered - using a computational evolution system - authors: - - Casey S. Greene - - Douglas P. Hill - - Jason H. Moore - publisher: Proceedings of the 11th Annual conference on Genetic and evolutionary - computation - date: '2009-07-08' - link: https://doi.org/10.1145/1569901.1570160 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1371/journal.pone.0005639 - title: Failure to Replicate a Genetic Association May Provide Important Clues About - Genetic Architecture - authors: - - Casey S. Greene - - Nadia M. Penrod - - Scott M. Williams - - Jason H. Moore - publisher: PLoS ONE - date: '2009-06-02' - link: https://doi.org/10.1371/journal.pone.0005639 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1109/CEC.2009.4983027 - title: 'Nature-inspired algorithms for the genetic analysis of epistasis in common - human diseases: Theoretical assessment of wrapper vs. filter approaches' - authors: - - Casey S. Greene - - Jeff Kiralis - - Jason H. Moore - publisher: 2009 IEEE Congress on Evolutionary Computation - date: '2009-05-01' - link: https://doi.org/10.1109/cec.2009.4983027 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1007/978-3-642-01184-9_9 - title: Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis - of Epistasis in Human Disease - authors: - - Casey S. Greene - - Jason M. Gilmore - - Jeff Kiralis - - Peter C. Andrews - - Jason H. Moore - publisher: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - date: '2009-01-01' - link: https://doi.org/10.1007/978-3-642-01184-9_9 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1109/CEC.2009.4983093 - title: Sensible initialization using expert knowledge for genome-wide analysis of - epistasis using genetic programming - authors: - - Casey S. Greene - - Bill C. White - - Jason H. Moore - publisher: 2009 IEEE Congress on Evolutionary Computation - date: '2009-05-01' - link: https://doi.org/10.1109/cec.2009.4983093 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.4018/978-1-60566-705-8.ch007 - title: Solving Complex Problems in Human Genetics using Nature-Inspired Algorithms - Requires Strategies which Exploit Domain-Specific Knowledge - authors: - - Casey S. Greene - - Jason H. Moore - publisher: Nature-Inspired Informatics for Intelligent Applications and Knowledge - Discovery - date: '' - link: https://doi.org/10.4018/978-1-60566-705-8.ch007 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1186/1756-0381-2-5 - title: Spatially Uniform ReliefF (SURF) for computationally-efficient filtering - of gene-gene interactions - authors: - - Casey S Greene - - Nadia M Penrod - - Jeff Kiralis - - Jason H Moore - publisher: BioData Mining - date: '2009-09-22' - link: https://doi.org/10.1186/1756-0381-2-5 - orcid: 0000-0001-8713-9213 - member: casey-greene - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1145/1527063.1527064 - title: Solving complex problems in human genetics using GP - authors: - - Casey S. Greene - - Jason H. 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Clambey - - Jennifer Backus - - Andrew Dumit - - Von Samedi - - Andrew Bubak - - Casey Greene - - Timothy Waxweiler - - Sanjana Mehrotra - - Shilpa Bhatia - - Jacob Gadwa - - Thomas Bickett - - Miles Piper - - Kareem Fakhoury - - Arthur Liu - - Joshua Petit - - Daniel Bowles - - Ashesh Thaker - - Kimberly Atiyeh - - Julie Goddard - - Robert Hoyer - - Adrie Van Bokhoven - - Kimberly Jordan - - Antonio Jimeno - - "Angelo D\u2019Alessandro" - - David Raben - - Jessica D. McDermott - - Sana D. 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Himmelstein - - Brett K. Beaulieu-Jones - - Alexandr A. Kalinin - - Brian T. Do - - Gregory P. Way - - Enrico Ferrero - - Paul-Michael Agapow - - Michael Zietz - - Michael M. Hoffman - - Wei Xie - - Gail L. Rosen - - Benjamin J. Lengerich - - Johnny Israeli - - Jack Lanchantin - - Stephen Woloszynek - - Anne E. Carpenter - - Avanti Shrikumar - - Jinbo Xu - - Evan M. Cofer - - Christopher A. Lavender - - Srinivas C. Turaga - - Amr M. Alexandari - - Zhiyong Lu - - David J. Harris - - Dave DeCaprio - - Yanjun Qi - - Anshul Kundaje - - Yifan Peng - - Laura K. Wiley - - Marwin H. S. Segler - - Simina M. Boca - - S. Joshua Swamidass - - Austin Huang - - Anthony Gitter - - Casey S. Greene - publisher: Journal of The Royal Society Interface - date: '2018-04-01' - link: https://doi.org/10.1098/rsif.2017.0387 - image: https://royalsocietypublishing.org/cms/asset/1b0430b1-5a66-4523-83be-29b435eddf86/rsif20170387f01.jpg - buttons: - - type: preprint - link: https://doi.org/10.1101/142760 - - type: source - link: http://github.com/greenelab/deep-review + - Jaclyn Taroni + - Casey Greene + publisher: figshare + date: '2018-01-01' + link: https://doi.org/10.6084/m9.figshare.6982919.v1 + orcid: 0000-0001-8713-9213 + member: casey-greene + plugin: orcid.py + file: orcid.yaml +- id: doi:10.1534/g3.118.200867 + title: NewDrosophilaLong-Term Memory Genes Revealed by Assessing Computational + Function Prediction Methods + authors: + - Balint Z Kacsoh + - Stephen Barton + - Yuxiang Jiang + - Naihui Zhou + - Sean D Mooney + - Iddo Friedberg + - Predrag Radivojac + - Casey S Greene + - Giovanni Bosco + publisher: G3 Genes|Genomes|Genetics + date: '2019-01-01' + link: https://doi.org/10.1534/g3.118.200867 + orcid: 0000-0001-8713-9213 + member: casey-greene plugin: sources.py file: sources.yaml -- id: doi:10.1016/j.celrep.2018.03.076 - title: Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The - Cancer Genome Atlas + image: https://www.g3journal.org/content/ggg/9/1/251/F2.medium.gif + buttons: + - type: preprint + link: https://doi.org/10.1101/414565 +- id: doi:10.1016/j.cell.2018.03.035 + title: Oncogenic Signaling Pathways in The Cancer Genome Atlas authors: - - Theo A. Knijnenburg - - Linghua Wang - - Michael T. Zimmermann - - Nyasha Chambwe - - Galen F. Gao - - Andrew D. Cherniack - - Huihui Fan - - Hui Shen - - Gregory P. Way - - Casey S. Greene - - Yuexin Liu - - Rehan Akbani - - Bin Feng - - Lawrence A. Donehower - - Chase Miller - - Yang Shen - - Mostafa Karimi - - Haoran Chen - - Pora Kim - - Peilin Jia - - Eve Shinbrot - - Shaojun Zhang - - Jianfang Liu - - Hai Hu + - Francisco Sanchez-Vega + - Marco Mina + - Joshua Armenia + - Walid K. Chatila + - Augustin Luna + - Konnor C. La + - Sofia Dimitriadoy + - David L. Liu + - Havish S. Kantheti + - Sadegh Saghafinia + - Debyani Chakravarty + - Foysal Daian + - Qingsong Gao - Matthew H. Bailey - - Christina Yau - - Denise Wolf - - Zhongming Zhao - - John N. Weinstein - - Lei Li + - Wen-Wei Liang + - Steven M. Foltz + - Ilya Shmulevich - Li Ding - - Gordon B. 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Asa - - Dirk Schadendorf - - Marta Couce - - Markus Graefen - - Hartwig Huland - - Guido Sauter - - Thorsten Schlomm - - Ronald Simon - - Pierre Tennstedt - - Oluwole Olabode - - Mark Nelson - - Oliver Bathe - - Peter R. Carroll - - June M. Chan - - Philip Disaia - - Pat Glenn - - Robin K. Kelley - - Charles N. Landen - - Joanna Phillips - - Michael Prados - - Jeffry Simko - - Karen Smith-McCune - - Scott VandenBerg - - Kevin Roggin - - Ashley Fehrenbach - - Ady Kendler - - Suzanne Sifri - - Ruth Steele - - Antonio Jimeno - - Francis Carey - - Ian Forgie - - Massimo Mannelli - - Michael Carney - - Brenda Hernandez - - Benito Campos - - Christel Herold-Mende - - Christin Jungk - - Andreas Unterberg - - Andreas von Deimling - - Aaron Bossler - - Joseph Galbraith - - Laura Jacobus - - Michael Knudson - - Tina Knutson - - Deqin Ma - - Mohammed Milhem - - Rita Sigmund - - Andrew K. Godwin - - Rashna Madan - - Howard G. Rosenthal - - Clement Adebamowo - - Sally N. Adebamowo - - Alex Boussioutas - - David Beer - - Thomas Giordano - - Anne-Marie Mes-Masson - - Fred Saad - - Therese Bocklage - - Lisa Landrum - - Robert Mannel - - Kathleen Moore - - Katherine Moxley - - Russel Postier - - Joan Walker - - Rosemary Zuna - - Michael Feldman - - Federico Valdivieso - - Rajiv Dhir - - James Luketich - - Edna M. Mora Pinero - - Mario Quintero-Aguilo - - Carlos Gilberto Carlotti - - "Jose Sebasti\xE3o Dos Santos" - - Rafael Kemp - - Ajith Sankarankuty - - Daniela Tirapelli - - James Catto - - Kathy Agnew - - Elizabeth Swisher - - Jenette Creaney - - Bruce Robinson - - Carl Simon Shelley - - Eryn M. Godwin - - Sara Kendall - - Cassaundra Shipman - - Carol Bradford - - Thomas Carey - - Andrea Haddad - - Jeffey Moyer - - Lisa Peterson - - Mark Prince - - Laura Rozek - - Gregory Wolf - - Rayleen Bowman - - Kwun M. Fong - - Ian Yang - - Robert Korst - - W. Kimryn Rathmell - - J. Leigh Fantacone-Campbell - - Jeffrey A. Hooke - - Albert J. Kovatich - - Craig D. 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