A citation-based method for searching scientific literature

Christoph Ziegenhain, Gert-Jan Hendriks, Michael Hagemann-Jensen, Rickard Sandberg. Nat Methods 2022
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Integrated analysis of multimodal single-cell data.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager,[...]. Cell 2021
100

Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data.
Gregor Sturm, Tamas Szabo, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, Francesca Finotello. Bioinformatics 2020
33
50

Single-cell RNA counting at allele and isoform resolution using Smart-seq3.
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J M Larsson, Omid R Faridani, Rickard Sandberg. Nat Biotechnol 2020
160
50

Miniaturization of Smart-seq2 for Single-Cell and Single-Nucleus RNA Sequencing.
Baptiste N Jaeger, Emilio Yángüez, Lorenzo Gesuita, Annina Denoth-Lippuner, Merit Kruse, Theofanis Karayannis, Sebastian Jessberger. STAR Protoc 2020
9
50

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
50

Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
50

Cellsnp-lite: an efficient tool for genotyping single cells.
Xianjie Huang, Yuanhua Huang. Bioinformatics 2021
12
50

RNA velocity of single cells.
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan,[...]. Nature 2018
50


Tn5 transposase and tagmentation procedures for massively scaled sequencing projects.
Simone Picelli, Asa K Björklund, Björn Reinius, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Genome Res 2014
370
50

Miniaturization Technologies for Efficient Single-Cell Library Preparation for Next-Generation Sequencing.
Sergio Mora-Castilla, Cuong To, Soheila Vaezeslami, Robert Morey, Srimeenakshi Srinivasan, Jennifer N Chousal, Heidi Cook-Andersen, Joby Jenkins, Louise C Laurent. J Lab Autom 2016
30
50

Miniaturization and optimization of 384-well compatible RNA sequencing library preparation.
Madeline Y Mayday, Lillian M Khan, Eric D Chow, Matt S Zinter, Joseph L DeRisi. PLoS One 2019
24
50

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs.
Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann. Gigascience 2018
133
50

High-throughput full-length single-cell RNA-seq automation.
Lira Mamanova, Zhichao Miao, Ayesha Jinat, Peter Ellis, Lesley Shirley, Sarah A Teichmann. Nat Protoc 2021
5
50

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K Lau,[...]. Nat Biotechnol 2020
141
50


Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning.
Nicholas J Bernstein, Nicole L Fong, Irene Lam, Margaret A Roy, David G Hendrickson, David R Kelley. Cell Syst 2020
36
50

T cell fate and clonality inference from single-cell transcriptomes.
Michael J T Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, Sarah A Teichmann. Nat Methods 2016
266
50

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
Dave T P Tang, Charles Plessy, Md Salimullah, Ana Maria Suzuki, Raffaella Calligaris, Stefano Gustincich, Piero Carninci. Nucleic Acids Res 2013
41
50

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
David Warde-Farley, Sylva L Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes,[...]. Nucleic Acids Res 2010
50

Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
50

Integrating -omics data into genome-scale metabolic network models: principles and challenges.
Charlotte Ramon, Mattia G Gollub, Jörg Stelling. Essays Biochem 2018
20
50

A single-cell atlas of the normal and malformed human brain vasculature.
Ethan A Winkler, Chang N Kim, Jayden M Ross, Joseph H Garcia, Eugene Gil, Irene Oh, Lindsay Q Chen, David Wu, Joshua S Catapano, Kunal Raygor,[...]. Science 2022
26
50

node2vec: Scalable Feature Learning for Networks.
Aditya Grover, Jure Leskovec. KDD 2016
533
50

An integrated approach to inferring gene-disease associations in humans.
Predrag Radivojac, Kang Peng, Wyatt T Clark, Brandon J Peters, Amrita Mohan, Sean M Boyle, Sean D Mooney. Proteins 2008
104
50

Estimating the support of a high-dimensional distribution.
B Schölkopf, J C Platt, J Shawe-Taylor, A J Smola, R C Williamson. Neural Comput 2001
394
50

Gene prioritization through genomic data fusion.
Stein Aerts, Diether Lambrechts, Sunit Maity, Peter Van Loo, Bert Coessens, Frederik De Smet, Leon-Charles Tranchevent, Bart De Moor, Peter Marynen, Bassem Hassan,[...]. Nat Biotechnol 2006
581
50

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.
Charles J Norsigian, Neha Pusarla, John Luke McConn, James T Yurkovich, Andreas Dräger, Bernhard O Palsson, Zachary King. Nucleic Acids Res 2020
70
50

PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.
Scott R Tyler, Pavana G Rotti, Xingshen Sun, Yaling Yi, Weiliang Xie, Michael C Winter, Miles J Flamme-Wiese, Budd A Tucker, Robert F Mullins, Andrew W Norris,[...]. Cell Rep 2019
26
50

Deep learning based feature-level integration of multi-omics data for breast cancer patients survival analysis.
Li Tong, Jonathan Mitchel, Kevin Chatlin, May D Wang. BMC Med Inform Decis Mak 2020
14
50

Eleven grand challenges in single-cell data science.
David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz,[...]. Genome Biol 2020
301
50

A statistical framework for genomic data fusion.
Gert R G Lanckriet, Tijl De Bie, Nello Cristianini, Michael I Jordan, William Stafford Noble. Bioinformatics 2004
230
50

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis.
Taylor S Adams, Jonas C Schupp, Sergio Poli, Ehab A Ayaub, Nir Neumark, Farida Ahangari, Sarah G Chu, Benjamin A Raby, Giuseppe DeIuliis, Michael Januszyk,[...]. Sci Adv 2020
268
50

Multi-omics integration in the age of million single-cell data.
Zhen Miao, Benjamin D Humphreys, Andrew P McMahon, Junhyong Kim. Nat Rev Nephrol 2021
18
50

Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response.
Yuping Zhang, Sathiya P Narayanan, Rahul Mannan, Gregory Raskind, Xiaoming Wang, Pankaj Vats, Fengyun Su, Noshad Hosseini, Xuhong Cao, Chandan Kumar-Sinha,[...]. Proc Natl Acad Sci U S A 2021
41
50

OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics.
Guangyan Zhou, Zhiqiang Pang, Yao Lu, Jessica Ewald, Jianguo Xia. Nucleic Acids Res 2022
1
100

DeepPVP: phenotype-based prioritization of causative variants using deep learning.
Imane Boudellioua, Maxat Kulmanov, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf. BMC Bioinformatics 2019
28
50

Escher-FBA: a web application for interactive flux balance analysis.
Elliot Rowe, Bernhard O Palsson, Zachary A King. BMC Syst Biol 2018
19
50


Wisdom of crowds for robust gene network inference.
Daniel Marbach, James C Costello, Robert Küffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, Manolis Kellis, James J Collins, Gustavo Stolovitzky. Nat Methods 2012
850
50

An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates.
Jermaine Goveia, Katerina Rohlenova, Federico Taverna, Lucas Treps, Lena-Christin Conradi, Andreas Pircher, Vincent Geldhof, Laura P M H de Rooij, Joanna Kalucka, Liliana Sokol,[...]. Cancer Cell 2020
122
50

Predicting Parkinson's Disease Genes Based on Node2vec and Autoencoder.
Jiajie Peng, Jiaojiao Guan, Xuequn Shang. Front Genet 2019
41
50

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma.
Li Zhang, Chenkai Lv, Yaqiong Jin, Ganqi Cheng, Yibao Fu, Dongsheng Yuan, Yiran Tao, Yongli Guo, Xin Ni, Tieliu Shi. Front Genet 2018
63
50


The complete sequence of a human genome.
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman,[...]. Science 2022
171
50

Analyzing cell-type-specific dynamics of metabolism in kidney repair.
Gangqi Wang, Bram Heijs, Sarantos Kostidis, Ahmed Mahfouz, Rosalie G J Rietjens, Roel Bijkerk, Angela Koudijs, Loïs A K van der Pluijm, Cathelijne W van den Berg, Sébastien J Dumas,[...]. Nat Metab 2022
3
50

Single-Cell Transcriptome Atlas of Murine Endothelial Cells.
Joanna Kalucka, Laura P M H de Rooij, Jermaine Goveia, Katerina Rohlenova, Sébastien J Dumas, Elda Meta, Nadine V Conchinha, Federico Taverna, Laure-Anne Teuwen, Koen Veys,[...]. Cell 2020
345
50

Computational strategies for single-cell multi-omics integration.
Nigatu Adossa, Sofia Khan, Kalle T Rytkönen, Laura L Elo. Comput Struct Biotechnol J 2021
9
50

Proteogenomic and metabolomic characterization of human glioblastoma.
Liang-Bo Wang, Alla Karpova, Marina A Gritsenko, Jennifer E Kyle, Song Cao, Yize Li, Dmitry Rykunov, Antonio Colaprico, Joseph H Rothstein, Runyu Hong,[...]. Cancer Cell 2021
115
50

An integrated network of Arabidopsis growth regulators and its use for gene prioritization.
Ehsan Sabaghian, Zuzanna Drebert, Dirk Inzé, Yvan Saeys. Sci Rep 2015
6
50


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.