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: 408







List of co-cited articles
1016 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


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
552
46

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
385
40

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
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
31

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
164
23

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
221
22


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
170
20

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
494
18

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
184
17

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
62
27

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
467
16

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
422
16

SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
759
16

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
688
15

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
15

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
222
14

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
140
14

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
12

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
228
12

scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
187
12

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
12

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
756
12

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
12

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
137
12

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
151
11

Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function.
H Efsun Arda, Lingyu Li, Jennifer Tsai, Eduardo A Torre, Yenny Rosli, Heshan Peiris, Robert C Spitale, Chunhua Dai, Xueying Gu, Kun Qu,[...]. Cell Metab 2016
125
11

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
11

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
11

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
133
11

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

SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
656
10

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
228
10

Recapitulating endocrine cell clustering in culture promotes maturation of human stem-cell-derived β cells.
Gopika G Nair, Jennifer S Liu, Holger A Russ, Stella Tran, Michael S Saxton, Richard Chen, Charity Juang, Mei-Lan Li, Vinh Q Nguyen, Simone Giacometti,[...]. Nat Cell Biol 2019
142
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
246
9

The unique cytoarchitecture of human pancreatic islets has implications for islet cell function.
Over Cabrera, Dora M Berman, Norma S Kenyon, Camillo Ricordi, Per-Olof Berggren, Alejandro Caicedo. Proc Natl Acad Sci U S A 2006
737
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

Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
540
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.
Anoop P Patel, Itay Tirosh, John J Trombetta, Alex K Shalek, Shawn M Gillespie, Hiroaki Wakimoto, Daniel P Cahill, Brian V Nahed, William T Curry, Robert L Martuza,[...]. Science 2014
9

Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.
Chun Zeng, Francesca Mulas, Yinghui Sui, Tiffany Guan, Nathanael Miller, Yuliang Tan, Fenfen Liu, Wen Jin, Andrea C Carrano, Mark O Huising,[...]. Cell Metab 2017
68
13

Controlled induction of human pancreatic progenitors produces functional beta-like cells in vitro.
Holger A Russ, Audrey V Parent, Jennifer J Ringler, Thomas G Hennings, Gopika G Nair, Mayya Shveygert, Tingxia Guo, Sapna Puri, Leena Haataja, Vincenzo Cirulli,[...]. EMBO J 2015
296
9

Acquisition of Dynamic Function in Human Stem Cell-Derived β Cells.
Leonardo Velazco-Cruz, Jiwon Song, Kristina G Maxwell, Madeleine M Goedegebuure, Punn Augsornworawat, Nathaniel J Hogrebe, Jeffrey R Millman. Stem Cell Reports 2019
107
9

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
155
9

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
65
13

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
178
9

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
9

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
414
8

Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
190
8

Single-Cell Mass Cytometry Analysis of the Human Endocrine Pancreas.
Yue J Wang, Maria L Golson, Jonathan Schug, Daniel Traum, Chengyang Liu, Kumar Vivek, Craig Dorrell, Ali Naji, Alvin C Powers, Kyong-Mi Chang,[...]. Cell Metab 2016
90
8


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.