A citation-based method for searching scientific literature

Dustin J Sokolowski, Mariela Faykoo-Martinez, Lauren Erdman, Huayun Hou, Cadia Chan, Helen Zhu, Melissa M Holmes, Anna Goldenberg, Michael D Wilson. NAR Genom Bioinform 2021
Times Cited: 3







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



Times Cited
  Times     Co-cited
Similarity


Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.
Blue B Lake, Rizi Ai, Gwendolyn E Kaeser, Neeraj S Salathia, Yun C Yung, Rui Liu, Andre Wildberg, Derek Gao, Ho-Lim Fung, Song Chen,[...]. Science 2016
401
33

Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.
Muhammad Farooq Rai, Eric D Tycksen, Linda J Sandell, Robert H Brophy. J Orthop Res 2018
23
33

RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression.
Adam Labadorf, Andrew G Hoss, Valentina Lagomarsino, Jeanne C Latourelle, Tiffany C Hadzi, Joli Bregu, Marcy E MacDonald, James F Gusella, Jiang-Fan Chen, Schahram Akbarian,[...]. PLoS One 2015
86
33


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
33

Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus.
Alexander R Abbas, Kristen Wolslegel, Dhaya Seshasayee, Zora Modrusan, Hilary F Clark. PLoS One 2009
241
33

Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic data.
Yu Kong, Deepa Rastogi, Cathal Seoighe, John M Greally, Masako Suzuki. PLoS One 2019
5
33

Genome-wide association study of multiplex schizophrenia pedigrees.
Douglas F Levinson, Jianxin Shi, Kai Wang, Sang Oh, Brien Riley, Ann E Pulver, Dieter B Wildenauer, Claudine Laurent, Bryan J Mowry, Pablo V Gejman,[...]. Am J Psychiatry 2012
44
33

Deblender: a semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples.
Konstantina Dimitrakopoulou, Elisabeth Wik, Lars A Akslen, Inge Jonassen. BMC Bioinformatics 2018
6
33


RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types.
Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger,[...]. Cell Rep 2019
173
33

Cell Type-Specific Annotation and Fine Mapping of Variants Associated With Brain Disorders.
Abolfazl Doostparast Torshizi, Iuliana Ionita-Laza, Kai Wang. Front Genet 2020
1
100

Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases.
Mariet Allen, Minerva M Carrasquillo, Cory Funk, Benjamin D Heavner, Fanggeng Zou, Curtis S Younkin, Jeremy D Burgess, High-Seng Chai, Julia Crook, James A Eddy,[...]. Sci Data 2016
129
33

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.
Åsa Segerstolpe, Athanasia Palasantza, Pernilla Eliasson, Eva-Marie Andersson, Anne-Christine Andréasson, Xiaoyan Sun, Simone Picelli, Alan Sabirsh, Maryam Clausen, Magnus K Bjursell,[...]. Cell Metab 2016
564
33

CellMix: a comprehensive toolbox for gene expression deconvolution.
Renaud Gaujoux, Cathal Seoighe. Bioinformatics 2013
120
33

Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples.
Ting Gong, Nicole Hartmann, Isaac S Kohane, Volker Brinkmann, Frank Staedtler, Martin Letzkus, Sandrine Bongiovanni, Joseph D Szustakowski. PLoS One 2011
81
33


A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys.
Blue B Lake, Song Chen, Masato Hoshi, Nongluk Plongthongkum, Diane Salamon, Amanda Knoten, Anitha Vijayan, Ramakrishna Venkatesh, Eric H Kim, Derek Gao,[...]. Nat Commun 2019
67
33


Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism.
João Fadista, Petter Vikman, Emilia Ottosson Laakso, Inês Guerra Mollet, Jonathan Lou Esguerra, Jalal Taneera, Petter Storm, Peter Osmark, Claes Ladenvall, Rashmi B Prasad,[...]. Proc Natl Acad Sci U S A 2014
247
33

Regularization Paths for Generalized Linear Models via Coordinate Descent.
Jerome Friedman, Trevor Hastie, Rob Tibshirani. J Stat Softw 2010
33


DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data.
Wanwen Zeng, Xi Chen, Zhana Duren, Yong Wang, Rui Jiang, Wing Hung Wong. Nat Commun 2019
20
33

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.
Blue B Lake, Song Chen, Brandon C Sos, Jean Fan, Gwendolyn E Kaeser, Yun C Yung, Thu E Duong, Derek Gao, Jerold Chun, Peter V Kharchenko,[...]. Nat Biotechnol 2018
299
33

Tumor heterogeneity: causes and consequences.
Andriy Marusyk, Kornelia Polyak. Biochim Biophys Acta 2010
868
33

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
33

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data.
Kai Kang, Qian Meng, Igor Shats, David M Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li, Leping Li. PLoS Comput Biol 2019
13
33

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
33

Single-cell genomics identifies cell type-specific molecular changes in autism.
Dmitry Velmeshev, Lucas Schirmer, Diane Jung, Maximilian Haeussler, Yonatan Perez, Simone Mayer, Aparna Bhaduri, Nitasha Goyal, David H Rowitch, Arnold R Kriegstein. Science 2019
167
33

Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies.
Mohan S Rao, Terry R Van Vleet, Rita Ciurlionis, Wayne R Buck, Scott W Mittelstadt, Eric A G Blomme, Michael J Liguori. Front Genet 2019
44
33

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
33

Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations.
Peng Lu, Aleksey Nakorchevskiy, Edward M Marcotte. Proc Natl Acad Sci U S A 2003
87
33

Gene expression elucidates functional impact of polygenic risk for schizophrenia.
Menachem Fromer, Panos Roussos, Solveig K Sieberts, Jessica S Johnson, David H Kavanagh, Thanneer M Perumal, Douglas M Ruderfer, Edwin C Oh, Aaron Topol, Hardik R Shah,[...]. Nat Neurosci 2016
480
33

Determining cell type abundance and expression from bulk tissues with digital cytometry.
Aaron M Newman, Chloé B Steen, Chih Long Liu, Andrew J Gentles, Aadel A Chaudhuri, Florian Scherer, Michael S Khodadoust, Mohammad S Esfahani, Bogdan A Luca, David Steiner,[...]. Nat Biotechnol 2019
492
33

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection.
Antonio F Pardiñas, Peter Holmans, Andrew J Pocklington, Valentina Escott-Price, Stephan Ripke, Noa Carrera, Sophie E Legge, Sophie Bishop, Darren Cameron, Marian L Hamshere,[...]. Nat Genet 2018
580
33



Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.
Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R Zhang, Mingyao Li. Nat Commun 2019
157
33



A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure.
Maayan Baron, Adrian Veres, Samuel L Wolock, Aubrey L Faust, Renaud Gaujoux, Amedeo Vetere, Jennifer Hyoje Ryu, Bridget K Wagner, Shai S Shen-Orr, Allon M Klein,[...]. Cell Syst 2016
421
33

Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia.
Abolfazl Doostparast Torshizi, Chris Armoskus, Hanwen Zhang, Marc P Forrest, Siwei Zhang, Tade Souaiaia, Oleg V Evgrafov, James A Knowles, Jubao Duan, Kai Wang. Sci Adv 2019
19
33

Digital sorting of complex tissues for cell type-specific gene expression profiles.
Yi Zhong, Ying-Wooi Wan, Kaifang Pang, Lionel M L Chow, Zhandong Liu. BMC Bioinformatics 2013
98
33

Purkinje cell dysfunction and loss in a knock-in mouse model of Huntington disease.
S E Dougherty, J L Reeves, M Lesort, P J Detloff, R M Cowell. Exp Neurol 2013
22
33

Benchmarking of cell type deconvolution pipelines for transcriptomics data.
Francisco Avila Cobos, José Alquicira-Hernandez, Joseph E Powell, Pieter Mestdagh, Katleen De Preter. Nat Commun 2020
26
33

Cell type-specific gene expression differences in complex tissues.
Shai S Shen-Orr, Robert Tibshirani, Purvesh Khatri, Dale L Bodian, Frank Staedtler, Nicholas M Perry, Trevor Hastie, Minnie M Sarwal, Mark M Davis, Atul J Butte. Nat Methods 2010
294
33

Genetic identification of brain cell types underlying schizophrenia.
Nathan G Skene, Julien Bryois, Trygve E Bakken, Gerome Breen, James J Crowley, Héléna A Gaspar, Paola Giusti-Rodriguez, Rebecca D Hodge, Jeremy A Miller, Ana B Muñoz-Manchado,[...]. Nat Genet 2018
201
33

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
202
33

Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling.
Qingnan Liang, Rachayata Dharmat, Leah Owen, Akbar Shakoor, Yumei Li, Sangbae Kim, Albert Vitale, Ivana Kim, Denise Morgan, Shaoheng Liang,[...]. Nat Commun 2019
33
33

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach.
Dirk Repsilber, Sabine Kern, Anna Telaar, Gerhard Walzl, Gillian F Black, Joachim Selbig, Shreemanta K Parida, Stefan H E Kaufmann, Marc Jacobsen. BMC Bioinformatics 2010
58
33


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.