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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for Andrea Blasco at 2020-08-05 11:32:02 -0400
%% Saved with string encoding Unicode (UTF-8)
@article{good2013crowdsourcing,
title={Crowdsourcing for bioinformatics},
author={Good, Benjamin M and Su, Andrew I},
journal={Bioinformatics},
volume={29},
number={16},
pages={1925--1933},
year={2013},
publisher={Oxford University Press}
}
@article{gaujoux2013cellmix,
Author = {Gaujoux, Renaud and Seoighe, Cathal},
Date-Added = {2020-08-05 11:31:49 -0400},
Date-Modified = {2020-08-05 11:31:49 -0400},
Journal = {Bioinformatics},
Number = {17},
Pages = {2211--2212},
Publisher = {Oxford University Press},
Title = {CellMix: a comprehensive toolbox for gene expression deconvolution},
Volume = {29},
Year = {2013}}
@article{shen2013computational,
Author = {Shen-Orr, Shai S and Gaujoux, Renaud},
Date-Added = {2019-12-09 09:07:30 -0500},
Date-Modified = {2019-12-09 09:07:30 -0500},
Journal = {Current opinion in immunology},
Number = {5},
Pages = {571--578},
Publisher = {Elsevier},
Title = {Computational deconvolution: extracting cell type-specific information from heterogeneous samples},
Volume = {25},
Year = {2013},
Bdsk-File-1 = {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}}
@article{zaitsev2019complete,
Author = {Zaitsev, Konstantin and Bambouskova, Monika and Swain, Amanda and Artyomov, Maxim N},
Date-Added = {2019-11-07 11:55:41 -0500},
Date-Modified = {2019-11-07 11:55:41 -0500},
Journal = {Nature communications},
Number = {1},
Pages = {2209},
Publisher = {Nature Publishing Group},
Title = {Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures},
Volume = {10},
Year = {2019}}
@article{newman2015robust,
Author = {Newman, Aaron M and Liu, Chih Long and Green, Michael R and Gentles, Andrew J and Feng, Weiguo and Xu, Yue and Hoang, Chuong D and Diehn, Maximilian and Alizadeh, Ash A},
Date-Added = {2019-11-07 11:55:04 -0500},
Date-Modified = {2019-11-07 11:55:04 -0500},
Journal = {Nature methods},
Number = {5},
Pages = {453},
Publisher = {Nature Publishing Group},
Title = {Robust enumeration of cell subsets from tissue expression profiles},
Volume = {12},
Year = {2015}}
@article{lamb2006connectivity,
Author = {Lamb, Justin and Crawford, Emily D and Peck, David and Modell, Joshua W and Blat, Irene C and Wrobel, Matthew J and Lerner, Jim and Brunet, Jean-Philippe and Subramanian, Aravind and Ross, Kenneth N and others},
Date-Added = {2019-11-05 13:14:47 -0500},
Date-Modified = {2019-11-05 13:14:47 -0500},
Journal = {science},
Number = {5795},
Pages = {1929--1935},
Publisher = {American Association for the Advancement of Science},
Title = {The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease},
Volume = {313},
Year = {2006}}
@article{lloyd1982least,
Author = {Lloyd, Stuart},
Date-Added = {2019-10-25 10:28:05 -0400},
Date-Modified = {2019-10-25 10:28:05 -0400},
Journal = {IEEE transactions on information theory},
Number = {2},
Pages = {129--137},
Publisher = {IEEE},
Title = {Least squares quantization in PCM},
Volume = {28},
Year = {1982}}
@article{hie2019efficient,
Author = {Hie, Brian and Bryson, Bryan and Berger, Bonnie},
Date-Added = {2019-10-22 13:05:17 -0400},
Date-Modified = {2019-10-22 13:05:17 -0400},
Journal = {Nature biotechnology},
Number = {6},
Pages = {685},
Publisher = {Nature Publishing Group},
Title = {Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
Volume = {37},
Year = {2019}}
@article{deng2019scalable,
Author = {Deng, Yue and Bao, Feng and Dai, Qionghai and Wu, Lani F and Altschuler, Steven J},
Date-Added = {2019-10-22 13:04:40 -0400},
Date-Modified = {2019-10-22 13:04:40 -0400},
Journal = {Nature methods},
Number = {4},
Pages = {311},
Publisher = {Nature Publishing Group},
Title = {Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning},
Volume = {16},
Year = {2019}}
@article{cleary2017efficient,
Author = {Cleary, Brian and Cong, Le and Cheung, Anthea and Lander, Eric S and Regev, Aviv},
Date-Added = {2019-10-22 13:03:27 -0400},
Date-Modified = {2019-10-22 13:03:27 -0400},
Journal = {Cell},
Number = {6},
Pages = {1424--1436},
Publisher = {Elsevier},
Title = {Efficient generation of transcriptomic profiles by random composite measurements},
Volume = {171},
Year = {2017}}
@inproceedings{ronneberger2015u,
Author = {Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
Booktitle = {International Conference on Medical image computing and computer-assisted intervention},
Date-Added = {2019-10-09 14:42:05 -0400},
Date-Modified = {2019-10-09 14:42:05 -0400},
Organization = {Springer},
Pages = {234--241},
Title = {U-net: Convolutional networks for biomedical image segmentation},
Year = {2015}}
@article{terstappen2007target,
Author = {Terstappen, Georg C and Schl{\"u}pen, Christina and Raggiaschi, Roberto and Gaviraghi, Giovanni},
Date-Added = {2019-10-07 08:54:54 -0400},
Date-Modified = {2019-10-07 08:54:54 -0400},
Journal = {Nature Reviews Drug Discovery},
Number = {11},
Pages = {891},
Publisher = {Nature Publishing Group},
Title = {Target deconvolution strategies in drug discovery},
Volume = {6},
Year = {2007}}
@article{maaten2008visualizing,
Author = {Maaten, Laurens van der and Hinton, Geoffrey},
Date-Added = {2019-10-06 09:32:00 -0400},
Date-Modified = {2019-10-06 09:32:00 -0400},
Journal = {Journal of machine learning research},
Number = {Nov},
Pages = {2579--2605},
Title = {Visualizing data using t-SNE},
Volume = {9},
Year = {2008}}
@article{musa2017review,
Author = {Musa, Aliyu and Ghoraie, Laleh Soltan and Zhang, Shu-Dong and Glazko, Galina and Yli-Harja, Olli and Dehmer, Matthias and Haibe-Kains, Benjamin and Emmert-Streib, Frank},
Date-Added = {2019-10-04 16:03:39 -0400},
Date-Modified = {2019-10-04 16:03:39 -0400},
Journal = {Briefings in bioinformatics},
Number = {3},
Pages = {506--523},
Publisher = {Oxford University Press},
Title = {A review of connectivity map and computational approaches in pharmacogenomics},
Volume = {19},
Year = {2017}}
@article{preibisch2014efficient,
Author = {Preibisch, Stephan and Amat, Fernando and Stamataki, Evangelia and Sarov, Mihail and Singer, Robert H and Myers, Eugene and Tomancak, Pavel},
Date-Added = {2019-10-04 15:55:54 -0400},
Date-Modified = {2019-10-04 15:55:54 -0400},
Journal = {Nature methods},
Number = {6},
Pages = {645},
Publisher = {Nature Publishing Group},
Title = {Efficient Bayesian-based multiview deconvolution},
Volume = {11},
Year = {2014}}
@inproceedings{hunt1971deconvolution,
Author = {Hunt, BR},
Booktitle = {1971 IEEE Conference on Decision and Control},
Date-Added = {2019-10-04 15:55:33 -0400},
Date-Modified = {2019-10-04 15:55:33 -0400},
Organization = {IEEE},
Pages = {367--371},
Title = {Deconvolution of linear systems by constrained regression and its relationship to the Wiener theory},
Year = {1971}}
@article{down2008bayesian,
Author = {Down, Thomas A and Rakyan, Vardhman K and Turner, Daniel J and Flicek, Paul and Li, Heng and Kulesha, Eugene and Graef, Stefan and Johnson, Nathan and Herrero, Javier and Tomazou, Eleni M and others},
Date-Added = {2019-10-04 15:54:41 -0400},
Date-Modified = {2019-10-04 15:54:41 -0400},
Journal = {Nature biotechnology},
Number = {7},
Pages = {779},
Publisher = {Nature Publishing Group},
Title = {A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis},
Volume = {26},
Year = {2008}}
@article{zhong2012gene,
Author = {Zhong, Yi and Liu, Zhandong},
Date-Added = {2019-10-04 15:54:05 -0400},
Date-Modified = {2019-10-04 15:54:05 -0400},
Journal = {Nature methods},
Number = {1},
Pages = {8},
Publisher = {Nature Publishing Group},
Title = {Gene expression deconvolution in linear space},
Volume = {9},
Year = {2012}}
@article{liu2015compound,
Author = {Liu, Chenglin and Su, Jing and Yang, Fei and Wei, Kun and Ma, Jinwen and Zhou, Xiaobo},
Date-Added = {2019-10-04 15:51:53 -0400},
Date-Modified = {2019-10-04 15:51:53 -0400},
Journal = {Molecular BioSystems},
Number = {3},
Pages = {714--722},
Publisher = {Royal Society of Chemistry},
Title = {Compound signature detection on LINCS L1000 big data},
Volume = {11},
Year = {2015}}
@article{blasco2019advancing,
Abstract = {Open data science and algorithm development competitions offer a unique avenue for rapid discovery of better computational strategies. We highlight three examples in computational biology and bioinformatics research in which the use of competitions has yielded significant performance gains over established algorithms. These include algorithms for antibody clustering, imputing gene expression data, and querying the Connectivity Map (CMap). Performance gains are evaluated quantitatively using realistic, albeit sanitized, data sets. The solutions produced through these competitions are then examined with respect to their utility and the prospects for implementation in the field. We present the decision process and competition design considerations that lead to these successful outcomes as a model for researchers who want to use competitions and non-domain crowds as collaborators to further their research.},
Author = {Blasco, Andrea and Endres, Michael G. and Sergeev, Rinat A. and Jonchhe, Anup and Macaluso, N. J. Maximilian and Narayan, Rajiv and Natoli, Ted and Paik, Jin H. and Briney, Bryan and Wu, Chunlei and Su, Andrew I. and Subramanian, Aravind and Lakhani, Karim R.},
Date-Modified = {2019-10-25 10:04:38 -0400},
Doi = {10.1371/journal.pone.0222165},
Journal = {PLOS ONE},
Month = {09},
Number = {9},
Pages = {1-17},
Publisher = {Public Library of Science},
Title = {Advancing computational biology and bioinformatics research through open innovation competitions},
Url = {https://doi.org/10.1371/journal.pone.0222165},
Volume = {14},
Year = {2019},
Bdsk-Url-1 = {https://doi.org/10.1371/journal.pone.0222165}}
@article{lakhani2013prize,
Author = {Lakhani, Karim R and Boudreau, Kevin J and Loh, Po-Ru and Backstrom, Lars and Baldwin, Carliss and Lonstein, Eric and Lydon, Mike and MacCormack, Alan and Arnaout, Ramy A and Guinan, Eva C},
Date-Added = {2019-09-26 13:16:53 -0400},
Date-Modified = {2019-09-26 13:16:53 -0400},
Journal = {Nature biotechnology},
Number = {2},
Pages = {108},
Publisher = {Nature Publishing Group},
Title = {Prize-based contests can provide solutions to computational biology problems},
Volume = {31},
Year = {2013}}
@article{lu2003expression,
Author = {Lu, Peng and Nakorchevskiy, Aleksey and Marcotte, Edward M},
Date-Added = {2019-09-26 12:46:15 -0400},
Date-Modified = {2019-09-26 12:46:15 -0400},
Journal = {Proceedings of the National Academy of Sciences},
Number = {18},
Pages = {10370--10375},
Publisher = {National Acad Sciences},
Title = {Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations},
Volume = {100},
Year = {2003}}
@article{shen2010cell,
Author = {Shen-Orr, Shai S and Tibshirani, Robert and Khatri, Purvesh and Bodian, Dale L and Staedtler, Frank and Perry, Nicholas M and Hastie, Trevor and Sarwal, Minnie M and Davis, Mark M and Butte, Atul J},
Date-Added = {2019-09-26 12:44:45 -0400},
Date-Modified = {2019-09-26 12:44:45 -0400},
Journal = {Nature methods},
Number = {4},
Pages = {287},
Publisher = {Nature Publishing Group},
Title = {Cell type--specific gene expression differences in complex tissues},
Volume = {7},
Year = {2010}}
@article{wang2016extraction,
Author = {Wang, Zichen and Monteiro, Caroline D and Jagodnik, Kathleen M and Fernandez, Nicolas F and Gundersen, Gregory W and Rouillard, Andrew D and Jenkins, Sherry L and Feldmann, Axel S and Hu, Kevin S and McDermott, Michael G and others},
Date-Added = {2019-09-26 12:26:27 -0400},
Date-Modified = {2019-09-26 12:26:27 -0400},
Journal = {Nature communications},
Pages = {12846},
Publisher = {Nature Publishing Group},
Title = {Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd},
Volume = {7},
Year = {2016}}
@article{corsello2017drug,
Author = {Corsello, Steven M and Bittker, Joshua A and Liu, Zihan and Gould, Joshua and McCarren, Patrick and Hirschman, Jodi E and Johnston, Stephen E and Vrcic, Anita and Wong, Bang and Khan, Mariya and others},
Date-Added = {2019-09-26 12:26:14 -0400},
Date-Modified = {2019-09-26 12:26:14 -0400},
Journal = {Nature medicine},
Number = {4},
Pages = {405},
Publisher = {Nature Publishing Group},
Title = {The Drug Repurposing Hub: a next-generation drug library and information resource},
Volume = {23},
Year = {2017}}
@article{subramanian2017next,
Author = {Subramanian, Aravind and Narayan, Rajiv and Corsello, Steven M and Peck, David D and Natoli, Ted E and Lu, Xiaodong and Gould, Joshua and Davis, John F and Tubelli, Andrew A and Asiedu, Jacob K and others},
Date-Added = {2019-09-26 12:25:36 -0400},
Date-Modified = {2019-09-26 12:25:36 -0400},
Journal = {Cell},
Number = {6},
Pages = {1437--1452},
Publisher = {Elsevier},
Title = {A next generation connectivity map: L1000 platform and the first 1,000,000 profiles},
Volume = {171},
Year = {2017}}