A citation-based method for searching scientific literature

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, Douglas A Melton, Itai Yanai. Cell Syst 2016
Times Cited: 476







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



Times Cited
  Times     Co-cited
Similarity


A Single-Cell Transcriptome Atlas of the Human Pancreas.
Mauro J Muraro, Gitanjali Dharmadhikari, Dominic Grün, Nathalie Groen, Tim Dielen, Erik Jansen, Leon van Gurp, Marten A Engelse, Francoise Carlotti, Eelco J P de Koning,[...]. Cell Syst 2016
450
46

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
612
43

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
34

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
29


Single-Cell Transcriptomics of the Human Endocrine Pancreas.
Yue J Wang, Jonathan Schug, Kyoung-Jae Won, Chengyang Liu, Ali Naji, Dana Avrahami, Maria L Golson, Klaus H Kaestner. Diabetes 2016
189
28

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes.
Nathan Lawlor, Joshy George, Mohan Bolisetty, Romy Kursawe, Lili Sun, V Sivakamasundari, Ina Kycia, Paul Robson, Michael L Stitzel. Genome Res 2017
191
26

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes.
Yurong Xin, Jinrang Kim, Haruka Okamoto, Min Ni, Yi Wei, Christina Adler, Andrew J Murphy, George D Yancopoulos, Calvin Lin, Jesper Gromada. Cell Metab 2016
246
24

Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
23

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
21

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
572
20

Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
613
20

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
18

Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
305
17

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
164
17

A benchmark of batch-effect correction methods for single-cell RNA sequencing data.
Hoa Thi Nhu Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen. Genome Biol 2020
197
17

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
241
15

Mapping the Mouse Cell Atlas by Microwell-Seq.
Xiaoping Han, Renying Wang, Yincong Zhou, Lijiang Fei, Huiyu Sun, Shujing Lai, Assieh Saadatpour, Ziming Zhou, Haide Chen, Fang Ye,[...]. Cell 2018
490
14

Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes.
Joan Camunas-Soler, Xiao-Qing Dai, Yan Hang, Austin Bautista, James Lyon, Kunimasa Suzuki, Seung K Kim, Stephen R Quake, Patrick E MacDonald. Cell Metab 2020
87
16

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
14

SC3: consensus clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green,[...]. Nat Methods 2017
527
13

Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns.
Martin Enge, H Efsun Arda, Marco Mignardi, John Beausang, Rita Bottino, Seung K Kim, Stephen R Quake. Cell 2017
203
13

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.
Dominic Grün, Mauro J Muraro, Jean-Charles Boisset, Kay Wiebrands, Anna Lyubimova, Gitanjali Dharmadhikari, Maaike van den Born, Johan van Es, Erik Jansen, Hans Clevers,[...]. Cell Stem Cell 2016
248
13

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
13

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
282
12

Single-cell RNA-seq denoising using a deep count autoencoder.
Gökcen Eraslan, Lukas M Simon, Maria Mircea, Nikola S Mueller, Fabian J Theis. Nat Commun 2019
222
12

Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
12

BBKNN: fast batch alignment of single cell transcriptomes.
Krzysztof Polański, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann, Jong-Eun Park. Bioinformatics 2020
148
12

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
11

scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
218
11

A comparison of automatic cell identification methods for single-cell RNA sequencing data.
Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J T Reinders, Ahmed Mahfouz. Genome Biol 2019
134
11

Charting cellular identity during human in vitro β-cell differentiation.
Adrian Veres, Aubrey L Faust, Henry L Bushnell, Elise N Engquist, Jennifer Hyoje-Ryu Kenty, George Harb, Yeh-Chuin Poh, Elad Sintov, Mads Gürtler, Felicia W Pagliuca,[...]. Nature 2019
175
11

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo,[...]. Science 2017
11

Pseudotime Ordering of Single Human β-Cells Reveals States of Insulin Production and Unfolded Protein Response.
Yurong Xin, Giselle Dominguez Gutierrez, Haruka Okamoto, Jinrang Kim, Ann-Hwee Lee, Christina Adler, Min Ni, George D Yancopoulos, Andrew J Murphy, Jesper Gromada. Diabetes 2018
72
15

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
11

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
11

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
10

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
271
10

Supervised classification enables rapid annotation of cell atlases.
Hannah A Pliner, Jay Shendure, Cole Trapnell. Nat Methods 2019
132
10

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar, Sylvain W Lapan, Irene E Whitney, Nicholas M Tran, Evan Z Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z Levin, James Nemesh, Melissa Goldman,[...]. Cell 2016
520
10

Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
419
10

Human islets contain four distinct subtypes of β cells.
Craig Dorrell, Jonathan Schug, Pamela S Canaday, Holger A Russ, Branden D Tarlow, Maria T Grompe, Tamara Horton, Matthias Hebrok, Philip R Streeter, Klaus H Kaestner,[...]. Nat Commun 2016
189
10

Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
10

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
261
9

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
9

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
192
9

The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, Eric S Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, Peter Campbell, Piero Carninci, Menna Clatworthy,[...]. Elife 2017
787
9

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells.
Alireza Rezania, Jennifer E Bruin, Payal Arora, Allison Rubin, Irina Batushansky, Ali Asadi, Shannon O'Dwyer, Nina Quiskamp, Majid Mojibian, Tobias Albrecht,[...]. Nat Biotechnol 2014
806
9

Generation of functional human pancreatic β cells in vitro.
Felicia W Pagliuca, Jeffrey R Millman, Mads Gürtler, Michael Segel, Alana Van Dervort, Jennifer Hyoje Ryu, Quinn P Peterson, Dale Greiner, Douglas A Melton. Cell 2014
9

The Human Cell Atlas: from vision to reality.
Orit Rozenblatt-Rosen, Michael J T Stubbington, Aviv Regev, Sarah A Teichmann. Nature 2017
238
9


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.