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Avi Ma'ayan
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2020 – today
- 2024
- [j58]Giacomo B. Marino, Daniel J. B. Clarke, Alexander Lachmann, Eden Z. Deng, Avi Ma'ayan:
RummaGEO: Automatic mining of human and mouse gene sets from GEO. Patterns 5(10): 101072 (2024) - 2023
- [j57]Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan:
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database J. Biol. Databases Curation 2023 (2023) - [j56]John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan:
Enrichr-KG: bridging enrichment analysis across multiple libraries. Nucleic Acids Res. 51(W1): 168-179 (2023) - [j55]Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan:
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. Nucleic Acids Res. 51(W1): 213-224 (2023) - 2022
- [j54]Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan:
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. Bioinform. 38(8): 2356-2357 (2022) - [j53]Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan:
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinform. 23(1): 76 (2022) - [j52]Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke, Avi Ma'ayan:
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinform. 23(1): 374 (2022) - [j51]John Erol Evangelista, Daniel J. B. Clarke, Zhuorui Xie, Alexander Lachmann, Minji Jeon, Kerwin Chen, Kathleen M. Jagodnik, Sherry L. Jenkins, Maxim V. Kuleshov, Megan L. Wojciechowicz, Stephan C. Schürer, Mario Medvedovic, Avi Ma'ayan:
SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 50(W1): 697-709 (2022) - 2021
- [j50]Eryk Kropiwnicki, John Erol Evangelista, Daniel J. Stein, Daniel J. B. Clarke, Alexander Lachmann, Maxim V. Kuleshov, Minji Jeon, Kathleen M. Jagodnik, Avi Ma'ayan:
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. Database J. Biol. Databases Curation 2021 (2021) - [j49]Maxim V. Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan:
KEA3: improved kinase enrichment analysis via data integration. Nucleic Acids Res. 49(Webserver-Issue): 304-316 (2021) - [j48]Daniel J. B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman, Serena Zhang, Christine Yoon, Tahmid Ahamed, Samantha Bhuiyan, Minxuan Cheng, Julie Karam, Kathleen M. Jagodnik, Ingrid Shu, Alexander Lachmann, Sam Ayling, Sherry L. Jenkins, Avi Ma'ayan:
Appyters: Turning Jupyter Notebooks into data-driven web apps. Patterns 2(3): 100213 (2021) - 2020
- [j47]Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan:
EnrichrBot: Twitter bot tracking tweets about human genes. Bioinform. 36(12): 3932-3934 (2020) - [j46]Vasileios Stathias, John Paul Turner, Amar Koleti, Dusica Vidovic, Daniel J. Cooper, Mehdi Fazel-Najafabadi, Marcin Pilarczyk, Raymond Terryn, Caty Chung, Afoma Umeano, Daniel J. B. Clarke, Alexander Lachmann, John Erol Evangelista, Avi Ma'ayan, Mario Medvedovic, Stephan C. Schürer:
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Nucleic Acids Res. 48(Database-Issue): D431-D439 (2020) - [j45]Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller:
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. Nucleic Acids Res. 48(Webserver-Issue): W85-W93 (2020) - [j44]Maxim V. Kuleshov, Daniel J. Stein, Daniel J. B. Clarke, Eryk Kropiwnicki, Kathleen M. Jagodnik, Alon Bartal, John Erol Evangelista, Jason Hom, Minxuan Cheng, Allison Bailey, Abigail Zhou, Laura B. Ferguson, Alexander Lachmann, Avi Ma'ayan:
The COVID-19 Drug and Gene Set Library. Patterns 1(6): 100090 (2020)
2010 – 2019
- 2019
- [j43]Randall J. Ellis, Zichen Wang, Nicholas Genes, Avi Ma'ayan:
Predicting opioid dependence from electronic health records with machine learning. BioData Min. 12(1): 3:1-3:19 (2019) - [j42]Zichen Wang, Edward He, Kevin Sani, Kathleen M. Jagodnik, Moshe C. Silverstein, Avi Ma'ayan:
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. Bioinform. 35(7): 1247-1248 (2019) - [j41]Maxim V. Kuleshov, Jennifer E. L. Diaz, Zachary N. Flamholz, Alexandra B. Keenan, Alexander Lachmann, Megan L. Wojciechowicz, Ross L. Cagan, Avi Ma'ayan:
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. Nucleic Acids Res. 47(Webserver-Issue): W183-W190 (2019) - [j40]Alexandra B. Keenan, Denis Torre, Alexander Lachmann, Ariel K. Leong, Megan L. Wojciechowicz, Vivian Utti, Kathleen M. Jagodnik, Eryk Kropiwnicki, Zichen Wang, Avi Ma'ayan:
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 47(Webserver-Issue): W212-W224 (2019) - [j39]Alexander Lachmann, Brian M. Schilder, Megan L. Wojciechowicz, Denis Torre, Maxim V. Kuleshov, Alexandra B. Keenan, Avi Ma'ayan:
Geneshot: search engine for ranking genes from arbitrary text queries. Nucleic Acids Res. 47(Webserver-Issue): W571-W577 (2019) - 2018
- [j38]Khader Shameer, Benjamin S. Glicksberg, Rachel Hodos, Kipp W. Johnson, Marcus A. Badgeley, Ben Readhead, Max S. Tomlinson, Timothy O'Connor, Riccardo Miotto, Brian A. Kidd, Rong Chen, Avi Ma'ayan, Joel T. Dudley:
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. Briefings Bioinform. 19(4): 656-678 (2018) - [j37]Zichen Wang, Alexander Lachmann, Alexandra B. Keenan, Avi Ma'ayan:
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. Bioinform. 34(12): 2150-2152 (2018) - [j36]Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J. Cooper, John Paul Turner, Dusica Vidovic, Michele Forlin, Tanya T. Kelley, Alessandro D'Urso, Bryce K. Allen, Denis Torre, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Al Mahi, Marcin Pilarczyk, Nicholas A. Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'ayan, Ajay Pillai, Stephan C. Schürer:
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. Nucleic Acids Res. 46(Database-Issue): D558-D566 (2018) - [j35]Daniel J. B. Clarke, Maxim V. Kuleshov, Brian M. Schilder, Denis Torre, Mary E. Duffy, Alexandra B. Keenan, Alexander Lachmann, Axel S. Feldmann, Gregory W. Gundersen, Moshe C. Silverstein, Zichen Wang, Avi Ma'ayan:
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Res. 46(Webserver-Issue): W171-W179 (2018) - [j34]Simon Koplev, Katie Lin, Anders B. Dohlman, Avi Ma'ayan:
Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. PLoS Comput. Biol. 14(1) (2018) - [c7]Avi Ma'ayan:
The Art of Connectivity Mapping. BCB 2018: 563 - [c6]Rachel Hodos, Ping Zhang, Hao-Chih Lee, Qiaonan Duan, Zichen Wang, Neil R. Clark, Avi Ma'ayan, Fei Wang, Brian A. Kidd, Jianying Hu, David A. Sontag, Joel Dudley:
Cell-specific prediction and application of drug-induced gene expression . PSB 2018: 32-43 - 2017
- [j33]Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schürer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi K. Madduri, Ajay Pillai, Avi Ma'ayan:
Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. J. Biomed. Informatics 71: 49-57 (2017) - [j32]Zichen Wang, Li Li, Benjamin S. Glicksberg, Ariel Israel, Joel T. Dudley, Avi Ma'ayan:
Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. J. Biomed. Informatics 76: 59-68 (2017) - [j31]Dac-Trung Nguyen, Stephen L. Mathias, Cristian Bologa, Søren Brunak, Nicolas F. Fernandez, Anna Gaulton, Anne Hersey, Jayme Holmes, Lars Juhl Jensen, Anneli Karlsson, Guixia Liu, Avi Ma'ayan, Geetha Mandava, Subramani Mani, Saurabh Mehta, John P. Overington, Juhee Patel, Andrew D. Rouillard, Stephan C. Schürer, Timothy Sheils, Anton Simeonov, Larry A. Sklar, Noel Southall, Oleg Ursu, Dusica Vidovic, Anna Waller, Jeremy J. Yang, Ajit Jadhav, Tudor I. Oprea, Rajarshi Guha:
Pharos: Collating protein information to shed light on the druggable genome. Nucleic Acids Res. 45(Database-Issue): D995-D1002 (2017) - 2016
- [j30]Andrew D. Rouillard, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan:
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database J. Biol. Databases Curation 2016 (2016) - [j29]Zichen Wang, Neil R. Clark, Avi Ma'ayan:
Drug-induced adverse events prediction with the LINCS L1000 data. Bioinform. 32(15): 2338-2345 (2016) - [j28]Gregory W. Gundersen, Kathleen M. Jagodnik, Holly Woodland, Nicolas F. Fernandez, Kevin Sani, Anders B. Dohlman, Peter Man-Un Ung, Caroline D. Monteiro, Avner Schlessinger, Avi Ma'ayan:
GEN3VA: aggregation and analysis of gene expression signatures from related studies. BMC Bioinform. 17: 461:1-461:12 (2016) - [j27]Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gundersen, Avi Ma'ayan:
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44(Webserver-Issue): W90-W97 (2016) - [i2]Avi Ma'ayan, Neil R. Clark:
Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations. CoRR abs/1601.01653 (2016) - [i1]Zichen Wang, Avi Ma'ayan:
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. F1000Research 5: 1574 (2016) - 2015
- [j26]Gregory W. Gundersen, Matthew R. Jones, Andrew D. Rouillard, Yan Kou, Caroline D. Monteiro, Axel S. Feldmann, Kevin S. Hu, Avi Ma'ayan:
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinform. 31(18): 3060-3062 (2015) - [j25]Zichen Wang, Neil R. Clark, Avi Ma'ayan:
Dynamics of the discovery process of protein-protein interactions from low content studies. BMC Syst. Biol. 9: 26 (2015) - [j24]Andrew D. Rouillard, Zichen Wang, Avi Ma'ayan:
Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". Comput. Biol. Chem. 59: 123-138 (2015) - [c5]Neil R. Clark, Maciej Szymkiewicz, Zichen Wang, Caroline D. Monteiro, Matthew R. Jones, Avi Ma'ayan:
Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. BIBM 2015: 256-262 - 2014
- [j23]Qiaonan Duan, Zichen Wang, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Cyril H. Benes, Avi Ma'ayan:
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Bioinform. 30(22): 3289-3290 (2014) - [j22]Neil R. Clark, Kevin S. Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma'ayan:
The characteristic direction: a geometrical approach to identify differentially expressed genes. BMC Bioinform. 15: 79 (2014) - [j21]Qiaonan Duan, Corey Flynn, Mario Niepel, Marc Hafner, Jeremy Muhlich, Nicolas F. Fernandez, Andrew D. Rouillard, Christopher M. Tan, Edward Y. Chen, Todd R. Golub, Peter K. Sorger, Aravind Subramanian, Avi Ma'ayan:
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res. 42(Webserver-Issue): 449-460 (2014) - [j20]Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor Lemischka, Avi Ma'ayan:
Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells. PLoS Comput. Biol. 10(8) (2014) - 2013
- [j19]Huilei Xu, Caroline Baroukh, Ruth Dannenfelser, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor Lemischka, Avi Ma'ayan:
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database J. Biol. Databases Curation 2013 (2013) - [j18]Christopher M. Tan, Edward Y. Chen, Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan:
Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinform. 29(15): 1872-1878 (2013) - [j17]Edward Y. Chen, Christopher M. Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R. Clark, Avi Ma'ayan:
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform. 14: 128 (2013) - [c4]Yan Kou, Edward Y. Chen, Neil R. Clark, Qiaonan Duan, Christopher M. Tan, Avi Ma'ayan:
ChEA2: Gene-Set Libraries from ChIP-X Experiments to Decode the Transcription Regulome. CD-ARES 2013: 416-430 - 2012
- [j16]Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, Avi Ma'ayan:
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. Bioinform. 28(1): 105-111 (2012) - [j15]Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan:
Genes2FANs: connecting genes through functional association networks. BMC Bioinform. 13: 156 (2012) - [j14]Neil R. Clark, Ruth Dannenfelser, Christopher M. Tan, Michael E. Komosinski, Avi Ma'ayan:
Sets2Networks: network inference from repeated observations of sets. BMC Syst. Biol. 6: 89 (2012) - [c3]Simon Gordonov, Avi Ma'ayan:
Connecting clusters of patient to drug responses of cell lines to suggest personalized therapeutics for breast cancer. BIBM Workshops 2012: 529-534 - 2011
- [j13]Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan:
FNV: light-weight flash-based network and pathway viewer. Bioinform. 27(8): 1181-1182 (2011) - [j12]Amin R. Mazloom, Ruth Dannenfelser, Neil R. Clark, Arsen V. Grigoryan, Kathryn M. Linder, Timothy Cardozo, Julia C. Bond, Aislyn D. W. Boran, Ravi Iyengar, Anna Malovannaya, Rainer B. Lanz, Avi Ma'ayan:
Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. PLoS Comput. Biol. 7(12) (2011) - [j11]Ryan L. Webb, Avi Ma'ayan:
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format. Source Code Biol. Medicine 6: 5 (2011) - [j10]Caroline Baroukh, Sherry L. Jenkins, Ruth Dannenfelser, Avi Ma'ayan:
Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. Source Code Biol. Medicine 6: 15 (2011) - [c2]Huilei Xu, Avi Ma'ayan:
Visualization of Patient Samples by Dimensionality Reduction of Genome-Wide Measurements. USAB 2011: 15-22 - 2010
- [j9]Ben D. MacArthur, Alexander Lachmann, Ihor Lemischka, Avi Ma'ayan:
GATE: software for the analysis and visualization of high-dimensional time series expression data. Bioinform. 26(1): 143-144 (2010) - [j8]Alexander Lachmann, Huilei Xu, Jayanth Krishnan, Seth I. Berger, Amin R. Mazloom, Avi Ma'ayan:
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinform. 26(19): 2438-2444 (2010) - [j7]Alexander Lachmann, Avi Ma'ayan:
Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinform. 11: 87 (2010) - [j6]Huilei Xu, Ihor Lemischka, Avi Ma'ayan:
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. BMC Syst. Biol. 4: 173 (2010) - [c1]Marylens Hernandez, Alexander Lachmann, Shan Zhao, Kunhong Xiao, Avi Ma'ayan:
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network. BIBE 2010: 180-184
2000 – 2009
- 2009
- [j5]Alexander Lachmann, Avi Ma'ayan:
KEA: kinase enrichment analysis. Bioinform. 25(5): 684-686 (2009) - [j4]Avi Ma'ayan, Sherry L. Jenkins, Ryan L. Webb, Seth I. Berger, Sudarshan P. Purushothaman, Noura S. Abul-Husn, Jeremy M. Posner, Tony Flores, Ravi Iyengar:
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. BMC Syst. Biol. 3: 10 (2009) - 2008
- [j3]Avi Ma'ayan:
PubMedAlertMe - Standalone Windows-based PubMed SDI software application. Comput. Biol. Medicine 38(5): 620-622 (2008) - 2007
- [j2]Seth I. Berger, Ravi Iyengar, Avi Ma'ayan:
AVIS: AJAX viewer of interactive signaling networks. Bioinform. 23(20): 2803-2805 (2007) - [j1]Seth I. Berger, Jeremy M. Posner, Avi Ma'ayan:
Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinform. 8 (2007)
Coauthor Index
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last updated on 2024-10-18 19:30 CEST by the dblp team
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