A citation-based method for searching scientific literature

Jason D Buenrostro, Beijing Wu, Ulrike M Litzenburger, Dave Ruff, Michael L Gonzales, Michael P Snyder, Howard Y Chang, William J Greenleaf. Nature 2015
Times Cited: 700







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



Times Cited
  Times     Co-cited
Similarity


Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A Cusanovich, Riza Daza, Andrew Adey, Hannah A Pliner, Lena Christiansen, Kevin L Gunderson, Frank J Steemers, Cole Trapnell, Jay Shendure. Science 2015
425
36

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang, William J Greenleaf. Nat Methods 2013
32

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
24

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
24

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.
Darren A Cusanovich, Andrew J Hill, Delasa Aghamirzaie, Riza M Daza, Hannah A Pliner, Joel B Berletch, Galina N Filippova, Xingfan Huang, Lena Christiansen, William S DeWitt,[...]. Cell 2018
173
20

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.
Alicia N Schep, Beijing Wu, Jason D Buenrostro, William J Greenleaf. Nat Methods 2017
190
20

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
Assaf Rotem, Oren Ram, Noam Shoresh, Ralph A Sperling, Alon Goren, David A Weitz, Bradley E Bernstein. Nat Biotechnol 2015
388
18

Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
580
17

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.
Stephen J Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M Stubbs, Heather J Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C Marioni,[...]. Nat Commun 2018
182
16

Joint profiling of chromatin accessibility and gene expression in thousands of single cells.
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, Jose L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen,[...]. Science 2018
203
16

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
15

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.
Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Yanyan Qi, Francesca Meschi, Geoffrey P McDermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, M Ryan Corces,[...]. Nat Biotechnol 2019
104
15

mRNA-Seq whole-transcriptome analysis of a single cell.
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
15

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
14

Model-based analysis of ChIP-Seq (MACS).
Yong Zhang, Tao Liu, Clifford A Meyer, Jérôme Eeckhoute, David S Johnson, Bradley E Bernstein, Chad Nusbaum, Richard M Myers, Myles Brown, Wei Li,[...]. Genome Biol 2008
14

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman-Aiden, Nynke L van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R Lajoie, Peter J Sabo, Michael O Dorschner,[...]. Science 2009
14


Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
Takashi Nagano, Yaniv Lubling, Tim J Stevens, Stefan Schoenfelder, Eitan Yaffe, Wendy Dean, Ernest D Laue, Amos Tanay, Peter Fraser. Nature 2013
727
14

CUT&Tag for efficient epigenomic profiling of small samples and single cells.
Hatice S Kaya-Okur, Steven J Wu, Christine A Codomo, Erica S Pledger, Terri D Bryson, Jorja G Henikoff, Kami Ahmad, Steven Henikoff. Nat Commun 2019
158
14

Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
14


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
528
13

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution.
Samuel G Rodriques, Robert R Stickels, Aleksandrina Goeva, Carly A Martin, Evan Murray, Charles R Vanderburg, Joshua Welch, Linlin M Chen, Fei Chen, Evan Z Macosko. Science 2019
334
13

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.
Caleb A Lareau, Fabiana M Duarte, Jennifer G Chew, Vinay K Kartha, Zach D Burkett, Andrew S Kohlway, Dmitry Pokholok, Martin J Aryee, Frank J Steemers, Ronald Lebofsky,[...]. Nat Biotechnol 2019
73
17

ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Jason D Buenrostro, Beijing Wu, Howard Y Chang, William J Greenleaf. Curr Protoc Mol Biol 2015
906
13

The accessible chromatin landscape of the human genome.
Robert E Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T Maurano, Eric Haugen, Nathan C Sheffield, Andrew B Stergachis, Hao Wang, Benjamin Vernot,[...]. Nature 2012
12

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.
Hannah A Pliner, Jonathan S Packer, José L McFaline-Figueroa, Darren A Cusanovich, Riza M Daza, Delasa Aghamirzaie, Sanjay Srivatsan, Xiaojie Qiu, Dana Jackson, Anna Minkina,[...]. Mol Cell 2018
111
11

Chromatin accessibility and the regulatory epigenome.
Sandy L Klemm, Zohar Shipony, William J Greenleaf. Nat Rev Genet 2019
230
11

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.
Sebastian Preissl, Rongxin Fang, Hui Huang, Yuan Zhao, Ramya Raviram, David U Gorkin, Yanxiao Zhang, Brandon C Sos, Veena Afzal, Diane E Dickel,[...]. Nat Neurosci 2018
90
12


Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.
Jason D Buenrostro, M Ryan Corces, Caleb A Lareau, Beijing Wu, Alicia N Schep, Martin J Aryee, Ravindra Majeti, Howard Y Chang, William J Greenleaf. Cell 2018
166
11

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.
M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside, Nicholas A Sinnott-Armstrong, Sam Vesuna, Ansuman T Satpathy, Adam J Rubin, Kathleen S Montine, Beijing Wu,[...]. Nat Methods 2017
373
11

High-resolution mapping and characterization of open chromatin across the genome.
Alan P Boyle, Sean Davis, Hennady P Shulha, Paul Meltzer, Elliott H Margulies, Zhiping Weng, Terrence S Furey, Gregory E Crawford. Cell 2008
791
11

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Patrik L Ståhl, Fredrik Salmén, Sanja Vickovic, Anna Lundmark, José Fernández Navarro, Jens Magnusson, Stefania Giacomello, Michaela Asp, Jakub O Westholm, Mikael Huss,[...]. Science 2016
478
11

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Christof Angermueller, Stephen J Clark, Heather J Lee, Iain C Macaulay, Mabel J Teng, Tim Xiaoming Hu, Felix Krueger, Sebastien Smallwood, Chris P Ponting, Thierry Voet,[...]. Nat Methods 2016
293
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


Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.
Chongyuan Luo, Christopher L Keown, Laurie Kurihara, Jingtian Zhou, Yupeng He, Junhao Li, Rosa Castanon, Jacinta Lucero, Joseph R Nery, Justin P Sandoval,[...]. Science 2017
166
10

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.
M Ryan Corces, Jason D Buenrostro, Beijing Wu, Peyton G Greenside, Steven M Chan, Julie L Koenig, Michael P Snyder, Jonathan K Pritchard, Anshul Kundaje, William J Greenleaf,[...]. Nat Genet 2016
370
9

The chromatin accessibility landscape of primary human cancers.
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, Jose A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho,[...]. Science 2018
207
9

Molecular Architecture of the Mouse Nervous System.
Amit Zeisel, Hannah Hochgerner, Peter Lönnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Häring, Emelie Braun, Lars E Borm, Gioele La Manno,[...]. Cell 2018
598
9

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples.
Wenfei Jin, Qingsong Tang, Mimi Wan, Kairong Cui, Yi Zhang, Gang Ren, Bing Ni, Jeffrey Sklar, Teresa M Przytycka, Richard Childs,[...]. Nature 2015
169
9

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
244
9

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer.
Kevin Grosselin, Adeline Durand, Justine Marsolier, Adeline Poitou, Elisabetta Marangoni, Fariba Nemati, Ahmed Dahmani, Sonia Lameiras, Fabien Reyal, Olivia Frenoy,[...]. Nat Genet 2019
97
9

Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
9

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
9

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Sébastien A Smallwood, Heather J Lee, Christof Angermueller, Felix Krueger, Heba Saadeh, Julian Peat, Simon R Andrews, Oliver Stegle, Wolf Reik, Gavin Kelsey. Nat Methods 2014
475
9

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
285
9

Assessment of computational methods for the analysis of single-cell ATAC-seq data.
Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E Vinyard, Sara P Garcia, Kendell Clement, Miguel A Andrade-Navarro, Jason D Buenrostro, Luca Pinello. Genome Biol 2019
38
23

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.
Carmen Bravo González-Blas, Liesbeth Minnoye, Dafni Papasokrati, Sara Aibar, Gert Hulselmans, Valerie Christiaens, Kristofer Davie, Jasper Wouters, Stein Aerts. Nat Methods 2019
61
14


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.