A citation-based method for searching scientific literature

Rui Chen, George I Mias, Jennifer Li-Pook-Than, Lihua Jiang, Hugo Y K Lam, Rong Chen, Elana Miriami, Konrad J Karczewski, Manoj Hariharan, Frederick E Dewey, Yong Cheng, Michael J Clark, Hogune Im, Lukas Habegger, Suganthi Balasubramanian, Maeve O'Huallachain, Joel T Dudley, Sara Hillenmeyer, Rajini Haraksingh, Donald Sharon, Ghia Euskirchen, Phil Lacroute, Keith Bettinger, Alan P Boyle, Maya Kasowski, Fabian Grubert, Scott Seki, Marco Garcia, Michelle Whirl-Carrillo, Mercedes Gallardo, Maria A Blasco, Peter L Greenberg, Phyllis Snyder, Teri E Klein, Russ B Altman, Atul J Butte, Euan A Ashley, Mark Gerstein, Kari C Nadeau, Hua Tang, Michael Snyder. Cell 2012
Times Cited: 729







List of co-cited articles
450 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


A longitudinal big data approach for precision health.
Sophia Miryam Schüssler-Fiorenza Rose, Kévin Contrepois, Kegan J Moneghetti, Wenyu Zhou, Tejaswini Mishra, Samson Mataraso, Orit Dagan-Rosenfeld, Ariel B Ganz, Jessilyn Dunn, Daniel Hornburg,[...]. Nat Med 2019
120
14

Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information.
Xiao Li, Jessilyn Dunn, Denis Salins, Gao Zhou, Wenyu Zhou, Sophia Miryam Schüssler-Fiorenza Rose, Dalia Perelman, Elizabeth Colbert, Ryan Runge, Shannon Rego,[...]. PLoS Biol 2017
106
11

A wellness study of 108 individuals using personal, dense, dynamic data clouds.
Nathan D Price, Andrew T Magis, John C Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T McDonald, Ulrike Kusebauch, Christopher L Moss, Yong Zhou,[...]. Nat Biotechnol 2017
173
11

Integrative omics for health and disease.
Konrad J Karczewski, Michael P Snyder. Nat Rev Genet 2018
267
11

Longitudinal multi-omics of host-microbe dynamics in prediabetes.
Wenyu Zhou, M Reza Sailani, Kévin Contrepois, Yanjiao Zhou, Sara Ahadi, Shana R Leopold, Martin J Zhang, Varsha Rao, Monika Avina, Tejaswini Mishra,[...]. Nature 2019
137
10

Multi-omics approaches to disease.
Yehudit Hasin, Marcus Seldin, Aldons Lusis. Genome Biol 2017
499
9

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.
Brian D Piening, Wenyu Zhou, Kévin Contrepois, Hannes Röst, Gucci Jijuan Gu Urban, Tejaswini Mishra, Blake M Hanson, Eddy J Bautista, Shana Leopold, Christine Y Yeh,[...]. Cell Syst 2018
92
8

Glucotypes reveal new patterns of glucose dysregulation.
Heather Hall, Dalia Perelman, Alessandra Breschi, Patricia Limcaoco, Ryan Kellogg, Tracey McLaughlin, Michael Snyder. PLoS Biol 2018
68
10


Revisiting biomarker discovery by plasma proteomics.
Philipp E Geyer, Lesca M Holdt, Daniel Teupser, Matthias Mann. Mol Syst Biol 2017
248
6

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.
Farhana R Pinu, David J Beale, Amy M Paten, Konstantinos Kouremenos, Sanjay Swarup, Horst J Schirra, David Wishart. Metabolites 2019
138
6

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
6

More Is Better: Recent Progress in Multi-Omics Data Integration Methods.
Sijia Huang, Kumardeep Chaudhary, Lana X Garmire. Front Genet 2017
239
6

Multi-omics Data Integration, Interpretation, and Its Application.
Indhupriya Subramanian, Srikant Verma, Shiva Kumar, Abhay Jere, Krishanpal Anamika. Bioinform Biol Insights 2020
98
6

Proteogenomic characterization of human colon and rectal cancer.
Bing Zhang, Jing Wang, Xiaojing Wang, Jing Zhu, Qi Liu, Zhiao Shi, Matthew C Chambers, Lisa J Zimmerman, Kent F Shaddox, Sangtae Kim,[...]. Nature 2014
777
5

A new initiative on precision medicine.
Francis S Collins, Harold Varmus. N Engl J Med 2015
5

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
5


WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder, Steve Horvath. BMC Bioinformatics 2008
5

mixOmics: An R package for 'omics feature selection and multiple data integration.
Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao. PLoS Comput Biol 2017
743
5



Methods of integrating data to uncover genotype-phenotype interactions.
Marylyn D Ritchie, Emily R Holzinger, Ruowang Li, Sarah A Pendergrass, Dokyoon Kim. Nat Rev Genet 2015
395
4

Personalized Nutrition by Prediction of Glycemic Responses.
David Zeevi, Tal Korem, Niv Zmora, David Israeli, Daphna Rothschild, Adina Weinberger, Orly Ben-Yacov, Dar Lador, Tali Avnit-Sagi, Maya Lotan-Pompan,[...]. Cell 2015
884
4

Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry.
Ben C Collins, Christie L Hunter, Yansheng Liu, Birgit Schilling, George Rosenberger, Samuel L Bader, Daniel W Chan, Bradford W Gibson, Anne-Claude Gingras, Jason M Held,[...]. Nat Commun 2017
195
4

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
4

Methods for the integration of multi-omics data: mathematical aspects.
Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone Castellani, Luciano Milanesi. BMC Bioinformatics 2016
147
4


Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nat Protoc 2009
4

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
4

The n-of-1 clinical trial: the ultimate strategy for individualizing medicine?
Elizabeth O Lillie, Bradley Patay, Joel Diamant, Brian Issell, Eric J Topol, Nicholas J Schork. Per Med 2011
275
4

Plasma Proteome Profiling to Assess Human Health and Disease.
Philipp E Geyer, Nils A Kulak, Garwin Pichler, Lesca M Holdt, Daniel Teupser, Matthias Mann. Cell Syst 2016
262
4

10 Years of GWAS Discovery: Biology, Function, and Translation.
Peter M Visscher, Naomi R Wray, Qian Zhang, Pamela Sklar, Mark I McCarthy, Matthew A Brown, Jian Yang. Am J Hum Genet 2017
4

Integrated Omics: Tools, Advances, and Future Approaches.
Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox. J Mol Endocrinol 2018
89
4

Systems genetics approaches to understand complex traits.
Mete Civelek, Aldons J Lusis. Nat Rev Genet 2014
331
4

The sequence of the human genome.
J C Venter, M D Adams, E W Myers, P W Li, R J Mural, G G Sutton, H O Smith, M Yandell, C A Evans, R A Holt,[...]. Science 2001
4

Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring.
Chao Jiang, Xin Wang, Xiyan Li, Jingga Inlora, Ting Wang, Qing Liu, Michael Snyder. Cell 2018
57
7

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
4

Circular RNAs are a large class of animal RNAs with regulatory potency.
Sebastian Memczak, Marvin Jens, Antigoni Elefsinioti, Francesca Torti, Janna Krueger, Agnieszka Rybak, Luisa Maier, Sebastian D Mackowiak, Lea H Gregersen, Mathias Munschauer,[...]. Nature 2013
4

Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma.
Jason D Arroyo, John R Chevillet, Evan M Kroh, Ingrid K Ruf, Colin C Pritchard, Donald F Gibson, Patrick S Mitchell, Christopher F Bennett, Era L Pogosova-Agadjanyan, Derek L Stirewalt,[...]. Proc Natl Acad Sci U S A 2011
4

Clinical assessment incorporating a personal genome.
Euan A Ashley, Atul J Butte, Matthew T Wheeler, Rong Chen, Teri E Klein, Frederick E Dewey, Joel T Dudley, Kelly E Ormond, Aleksandra Pavlovic, Alexander A Morgan,[...]. Lancet 2010
464
4


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 Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
3

A multivariate approach to the integration of multi-omics datasets.
Chen Meng, Bernhard Kuster, Aedín C Culhane, Amin Moghaddas Gholami. BMC Bioinformatics 2014
111
3

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
Charles J Vaske, Stephen C Benz, J Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, Joshua M Stuart. Bioinformatics 2010
447
3

The CPTAC Data Portal: A Resource for Cancer Proteomics Research.
Nathan J Edwards, Mauricio Oberti, Ratna R Thangudu, Shuang Cai, Peter B McGarvey, Shine Jacob, Subha Madhavan, Karen A Ketchum. J Proteome Res 2015
97
3

KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
3

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
3

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Da Wei Huang, Brad T Sherman, Richard A Lempicki. Nucleic Acids Res 2009
3

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
3


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.