A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Aravind Subramanian,Rajiv Narayan,Steven M. Corsello,Steven M. Corsello,David Peck,Ted Natoli,Xiaodong Lu,Joshua Gould,John F. Davis,Andrew A. Tubelli,Jacob K. Asiedu,David L. Lahr,Jodi E. Hirschman,Zihan Liu,Melanie Donahue,Bina Julian,Mariya Khan,David Wadden,Ian Smith,Daniel D. Lam,Arthur Liberzon,Courtney Toder,Mukta Bagul,Marek Orzechowski,Oana M. Enache,Federica Piccioni,Sarah A. Johnson,Nicholas J. Lyons,Alice H. Berger,Alice H. Berger,Alykhan F. Shamji,Angela N. Brooks,Angela N. Brooks,Anita Vrcic,Corey Flynn,Jacqueline Rosains,David Y. Takeda,David Y. Takeda,Roger Hu,Desiree Davison,Justin Lamb,Kristin Ardlie,Larson Hogstrom,Peyton Greenside,Nathanael S. Gray,Nathanael S. Gray,Paul A. Clemons,Serena J. Silver,Xiaoyun Wu,Wen-Ning Zhao,Wen-Ning Zhao,Willis Read-Button,Xiaohua Wu,Stephen J. Haggarty,Stephen J. Haggarty,Lucienne Ronco,Jesse S. Boehm,Stuart L. Schreiber,Stuart L. Schreiber,Stuart L. Schreiber,John G. Doench,Joshua A. Bittker,David E. Root,Bang Wong,Todd R. Golub +64 more
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TLDR
The expanded CMap is reported, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that is shown to be highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts.About:
This article is published in Cell.The article was published on 2017-11-30 and is currently open access. It has received 1943 citations till now.read more
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Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19
Deisy Morselli Gysi,Italo Faria do Valle,Marinka Zitnik,Asher Ameli,Xiao Gan,Onur Varol,Susan Dina Ghiassian,J. J. Patten,Robert A. Davey,Joseph Loscalzo,Albert-László Barabási +10 more
TL;DR: Three network-based drug repurposing strategies are deployed, relying on network proximity, diffusion, and AI-based metrics, allowing to rank all approved drugs based on their likely efficacy for COVID-19 patients, and aggregate all predictions, to arrive at 81 promising repurpose candidates.
Journal ArticleDOI
Network medicine framework for identifying drug-repurposing opportunities for COVID-19.
Deisy Morselli Gysi,Deisy Morselli Gysi,Italo Faria do Valle,Marinka Zitnik,Asher Ameli,Xiao Gan,Xiao Gan,Onur Varol,Helia N. Sanchez,Rebecca M. Baron,Dina Ghiassian,Joseph Loscalzo,Albert-László Barabási,Albert-László Barabási,Albert-László Barabási +14 more
TL;DR: In this article, the authors deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2.
Journal ArticleDOI
The quest to slow ageing through drug discovery
TL;DR: The most promising interventions to slow ageing are examined and group them into two tiers based on the robustness of the preclinical, and some clinical, results, in which the top tier includes rapamycin, senolytics, metformin, acarbose, spermidine, NAD + enhancers and lithium.
Journal ArticleDOI
Proteogenomic and metabolomic characterization of human glioblastoma
Liang-Bo Wang,Alla Karpova,Marina A. Gritsenko,Jennifer E. Kyle,Song Cao,Yize Li,Dmitry Rykunov,Antonio Colaprico,Antonio Colaprico,Joseph H. Rothstein,Runyu Hong,Vasileios Stathias,MacIntosh Cornwell,Francesca Petralia,Yige Wu,Boris Reva,Karsten Krug,Pietro Pugliese,Emily Kawaler,Lindsey K. Olsen,Wen-Wei Liang,Xiaoyu Song,Yongchao Dou,Michael C. Wendl,Wagma Caravan,Wenke Liu,Daniel Cui Zhou,Jiayi Ji,Chia-Feng Tsai,Vladislav A. Petyuk,Jamie Moon,Weiping Ma,Rosalie K. Chu,Karl K. Weitz,Ronald J. Moore,Matthew E. Monroe,Rui Zhao,Xiaolu Yang,Xiaolu Yang,Seungyeul Yoo,Azra Krek,Alexis Demopoulos,Houxiang Zhu,Matthew A. Wyczalkowski,Joshua F. McMichael,Brittany Henderson,Caleb M. Lindgren,Hannah Boekweg,Shuangjia Lu,Jessika Baral,Lijun Yao,Kelly L. Stratton,Lisa M. Bramer,Erika M. Zink,Sneha P. Couvillion,Kent J. Bloodsworth,Shankha Satpathy,Weiva Sieh,Simina M. Boca,Stephan C. Schürer,Feng Chen,Maciej Wiznerowicz,Maciej Wiznerowicz,Karen A. Ketchum,Emily S. Boja,Christopher R. Kinsinger,Ana I. Robles,Tara Hiltke,Mathangi Thiagarajan,Alexey I. Nesvizhskii,Bing Zhang,D. R. Mani,Michele Ceccarelli,Xi Chen,Xi Chen,Sandra Cottingham,Qing Kay Li,Albert H. Kim,David Fenyö,Kelly V. Ruggles,Henry Rodriguez,Mehdi Mesri,Samuel H. Payne,Adam C. Resnick,Pei Wang,Richard D. Smith,Antonio Iavarone,Milan G. Chheda,Jill S. Barnholtz-Sloan,Karin D. Rodland,Karin D. Rodland,Tao Liu,Li Ding,Anupriya Agarwal,Mitual Amin,Eunkyung An,Matthew L. Anderson,David W. Andrews,Thomas L. Bauer,Chet Birger,Michael J. Birrer,Lili Blumenberg,William Bocik,Uma Borate,Melissa Borucki,Meghan C. Burke,Shuang Cai,Anna Calinawan,Steven A. Carr,Sandra Cerda,Daniel W. Chan,Alyssa Charamut,Lin Chen,David Chesla,Arul M. Chinnaiyan,Shrabanti Chowdhury,Marcin Cieślik,David J. Clark,Houston Culpepper,Tomasz Czernicki,Fulvio D'Angelo,Jacob J. Day,Stephanie De Young,Emek Demir,Saravana M. Dhanasekaran,Rajiv Dhir,Marcin J. Domagalski,Brian J. Druker,Elizabeth R. Duffy,Maureen Dyer,Nathan Edwards,Robert Edwards,Kimberly Elburn,Matthew J. Ellis,Jennifer M. Eschbacher,Alicia Francis,Stacey Gabriel,Nikolay Gabrovski,Luciano Garofano,Gad Getz,Michael A. Gillette,Andrew K. Godwin,Denis A. Golbin,Ziad Hanhan,Linda Hannick,Pushpa Hariharan,Barbara Hindenach,Katherine A. Hoadley,Galen Hostetter,Chen Huang,Eric J. Jaehnig,Scott D. Jewell,Nan Ji,Corbin D. Jones,Alcida Karz,Wojciech Kaspera,Lyndon Kim,Ramani B. Kothadia,Chandan Kumar-Sinha,Jonathan T. Lei,Felipe D. Leprevost,Kai Li,Yuxing Liao,Jena Lilly,Hongwei Liu,Jan Lubinski,Rashna Madan,William W. Maggio,Ewa P. Malc,Anna Malovannaya,Sailaja Mareedu,Sanford P. Markey,Annette Marrero-Oliveras,Nina Martinez,Nicollette Maunganidze,Jason E. McDermott,Peter B. McGarvey,John McGee,Piotr A. Mieczkowski,Simona Migliozzi,Francesmary Modugno,Rebecca I. Montgomery,Chelsea J. Newton,Gilbert S. Omenn,Umut Ozbek,Oxana Paklina,Amanda G. Paulovich,Amy M. Perou,Alexander R. Pico,Paul D. Piehowski,Dimitris G. Placantonakis,Larisa Polonskaya,Olga Potapova,Barbara Pruetz,Liqun Qi,Shakti Ramkissoon,Adam C. Resnick,Shannon Richey,Gregory J. Riggins,Karna Robinson,Nancy Roche,Daniel C. Rohrer,Brian R. Rood,Larissa Rossell,Sara R. Savage,Eric E. Schadt,Yan Shi,Zhiao Shi,Yvonne Shutack,Shilpi Singh,Tara Skelly,Lori J. Sokoll,Jakub Stawicki,Stephen E. Stein,James Suh,Wojciech Szopa,Dave Tabor,Donghui Tan,Darlene Tansil,Ratna R. Thangudu,Cristina E. Tognon,Elie Traer,Shirley Tsang,Jeffrey W. Tyner,Ki Sung Um,Dana R. Valley,Suhas Vasaikar,Negin Vatanian,Uma Velvulou,Michael Vernon,Weiqing Wan,Junmei Wang,Alex Webster,Bo Wen,Jeffrey R. Whiteaker,George D. Wilson,Yuriy Zakhartsev,Robert Zelt,Hui Zhang,Liwei Zhang,Zhen Zhang,Grace Zhao,Jun Zhu +242 more
TL;DR: This article identified key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors.
Journal ArticleDOI
Genome-wide CRISPR/Cas9 library screening identified PHGDH as a critical driver for Sorafenib resistance in HCC
Lai Wei,Lai Wei,Derek Lee,Derek Lee,Cheuk-Ting Law,Cheuk-Ting Law,Misty Shuo Zhang,Misty Shuo Zhang,Jialing Shen,Jialing Shen,Don Wai-Ching Chin,Don Wai-Ching Chin,Allen Zhang,Allen Zhang,Felice Ho-Ching Tsang,Felice Ho-Ching Tsang,Ceci Lok-Sze Wong,Ceci Lok-Sze Wong,Irene Oi-Lin Ng,Irene Oi-Lin Ng,Carmen Chak-Lui Wong,Carmen Chak-Lui Wong,Chun-Ming Wong,Chun-Ming Wong +23 more
TL;DR: It is shown that phosphoglycerate dehydrogenase, a key enzyme in the serine synthesis pathway, drives sorafenib resistance, which is a major clinical challenge to overcome TKI drug resistance in HCC.
References
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Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal Article
Visualizing Data using t-SNE
TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
Journal ArticleDOI
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Journal ArticleDOI
Adjusting batch effects in microarray expression data using empirical Bayes methods
TL;DR: This paper proposed parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples.
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