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Hypothesis generation is becoming a crucial time-saving technique which allows biomedical researchers to quickly discover implicit connections between important concepts.
Undiscovered public knowledge
Don R Swanson · 1986
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Using arrowsmith: a computer-assisted approach to formulating and assessing scientific hypotheses
Neil R Smalheiser and Don R Swanson · 1998
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Link analysis of medline titles as an aid to scientific discovery
Don Swanson and Neil Smalheiser · 1998
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Implicit text linkage between medline records: using arrowsmith as an aid to scientific discovery
Don R Swanson and Neil R Smalheiser · 1999
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Latent dirichlet allocation
David M Blei, Andrew Y Ng, and Michael I Jordan · 2003
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Thomas L Griffiths and Mark Steyvers · 2004
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Viral and cellular rna helicases as antiviral targets
Ann D Kwong, B Govinda Rao, and Kuan-Teh Jeang · 2005
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Specialist nlp tools, 2006
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Dynamic topic models
David M Blei and John D Lafferty · 2006
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Graph minimum linear arrangement by multilevel weighted edge contractions
I. Safro, D. Ron, and A. Brandt · 2006
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The human disease network
Kwang-Il Goh, Michael E Cusick, David Valle, Barton Childs, Marc Vidal, and Albert-László Barabási · 2007
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Pharmacophore modeling and molecular docking led to the discovery of inhibitors of human immunodeficiency virus-1 replication targeting the human cellular aspartic acid- glutamic acid- alanine- aspartic acid box polypeptide 3
Giovanni Maga, Federico Falchi, Anna Garbelli, Amalia Belfiore, Myriam Witvrouw, Fabrizio Manetti, and Maurizio Botta · 2008
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Umls reference manual, 2009
2009
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Network properties of complex human disease genes identified through genome-wide association studies
Fredrik Barrenas, Sreenivas Chavali, Petter Holme, Reza Mobini, and Mikael Benson · 2009
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Improving random walk performance
Ilya Safro, Paul D Hovland, Jaewook Shin, and Michelle Mills Strout · 2009
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Arrowsmith two-node search interface: A tutorial on finding meaningful links between two disparate sets of articles in medline
Neil R Smalheiser, Vetle I Torvik, and Wei Zhou · 2009
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Literature mining, ontologies and information visualization for drug repurposing
Christos Andronis, Anuj Sharma, Vassilis Virvilis, Spyros Deftereos, and Aris Persidis · 2011
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Conflicting biomedical assumptions for mathematical modeling: the case of cancer metastasis
Anna Divoli, Eneida A Mendonça, James A Evans, and Andrey Rzhetsky · 2011
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Advancing science through mining libraries, ontologies, and communities
James A Evans and Andrey Rzhetsky · 2011
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Building the process-drug–side effect network to discover the relationship between biological processes and side effects
Sejoon Lee, Kwang H Lee, Min Song, and Doheon Lee · 2011
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Plda+: Parallel latent dirichlet allocation with data placement and pipeline processing
Zhiyuan Liu, Yuzhou Zhang, Edward Y Chang, and Maosong Sun · 2011
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Multiscale approach for the network compression-friendly ordering
Ilya Safro and Boris Temkin · 2011
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Representation of research hypotheses
Scalable nearest neighbor algorithms for high dimensional data
Marius Muja and David G Lowe · 2014
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Automated hypothesis generation based on mining scientific literature
Scott Spangler, Angela D Wilkins, Benjamin J Bachman, Meena Nagarajan, Tajhal Dayaram, Peter Haas, Sam Regenbogen, Curtis R Pickering, Austin Comer, Jeffrey N Myers, et al · 2014
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Human symptoms–disease network
XueZhong Zhou, Jörg Menche, Albert-László Barabási, and Amitabh Sharma · 2014
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Targeting ddx3 with a small molecule inhibitor for lung cancer therapy
Guus M Bol, Farhad Vesuna, Min Xie, Jing Zeng, Khaled Aziz, Nishant Gandhi, Anne Levine, Ashley Irving, Dorian Korz, Saritha Tantravedi, et al · 2015
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Ddx3, a potential target for cancer treatment
Guus Martinus Bol, Min Xie, and Venu Raman · 2015
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Ddx3 modulates cell adhesion and motility and cancer cell metastasis via rac1-mediated signaling pathway
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Larisa N Soldatova and Andrey Rzhetsky · 2011
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The role of ddx3 in regulating snail
Mianen Sun, Ling Song, Tong Zhou, G Yancey Gillespie, and Richard S Jope · 2011
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Finding complex biological relationships in recent pubmed articles using bio-lda
Huijun Wang, Ying Ding, Jie Tang, Xiao Dong, Bing He, Judy Qiu, and David J Wild · 2011
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Ncats launches drug repurposing program, 2012
Malorye Allison · 2012
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Drug repurposing: far beyond new targets for old drugs
TI Oprea and J Mestres · 2012
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Rna helicase ddx3 is a regulatory subunit of casein kinase 1 in wnt– β \beta -catenin signaling
Cristina-Maria Cruciat, Christine Dolde, Reinoud EA de Groot, Bisei Ohkawara, Carmen Reinhard, Hendrik C Korswagen, and Christof Niehrs · 2013
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Efficient estimation of word representations in vector space
Tomas Mikolov, Kai Chen, Greg Corrado, and Jeffrey Dean · 2013
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HH Chen, HI Yu, WC Cho, and WY Tarn · 2015
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Tradition and innovation in scientists’ research strategies
Jacob G Foster, Andrey Rzhetsky, and James A Evans · 2015
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A network comprising short and long noncoding rnas and rna helicase controls mouse retina architecture
Jacek Krol, Ilona Krol, Claudia Patricia Patino Alvarez, Michele Fiscella, Andreas Hierlemann, Botond Roska, and Witold Filipowicz · 2015
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Ketorolac salt is a newly discovered ddx3 inhibitor to treat oral cancer
Sabindra K Samal, Samapika Routray, Ganesh Kumar Veeramachaneni, Rupesh Dash, and Mahendran Botlagunta · 2015
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Accelerating Discovery: Mining Unstructured Information for Hypothesis Generation
Scott Spangler · 2015
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Pubmed, 2016
2016
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Enriching word vectors with subword information
Piotr Bojanowski, Edouard Grave, Armand Joulin, and Tomas Mikolov · 2016
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Scalable dynamic topic modeling with clustered latent dirichlet allocation (clda)
Chris Gropp, Alexander Herzog, Ilya Safro, Paul W Wilson, and Amy W Apon · 2016
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Bag of tricks for efficient text classification
Armand Joulin, Edouard Grave, Piotr Bojanowski, and Tomas Mikolov · 2016
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The prognostic effect of ddx3 upregulation in distant breast cancer metastases
Marise R Heerma van Voss, Willemijne AME Schrijver, Natalie D ter Hoeve, Laurien D Hoefnagel, Quirine F Manson, Elsken van der Wall, Venu Raman, Paul J van Diest, Dutch Distant Breast Cancer Metastases Consortium, et al · 2016
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Moliere: Automatic biomedical hypothesis generation system. medline knowledge graph. implementation, 2017
Justin Sybrandt and Ilya Safro · 2017
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