Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander V Misharin, Fabian J Theis. Nat Biotechnol 2022
Times Cited: 10
Times Cited: 10
Times Cited
Times Co-cited
Similarity
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
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
60
Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
50
SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
50
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
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
40
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
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
40
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
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
40
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
Krzysztof Polański, Matthew D Young, Zhichao Miao, Kerstin B Meyer, Sarah A Teichmann, Jong-Eun Park. Bioinformatics 2020
40
Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models.
Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef. Mol Syst Biol 2021
Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, Nir Yosef. Mol Syst Biol 2021
40
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama.
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
Brian Hie, Bryan Bryson, Bonnie Berger. Nat Biotechnol 2019
40
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
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
40
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
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
40
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
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
30
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
Joshua D Welch, Velina Kozareva, Ashley Ferreira, Charles Vanderburg, Carly Martin, Evan Z Macosko. Cell 2019
30
A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
30
scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
30
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
Ilya Korsunsky, Nghia Millard, Jean Fan, Kamil Slowikowski, Fan Zhang, Kevin Wei, Yuriy Baglaenko, Michael Brenner, Po-Ru Loh, Soumya Raychaudhuri. Nat Methods 2019
30
Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
30
The single-cell transcriptional landscape of mammalian organogenesis.
Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers,[...]. Nature 2019
Junyue Cao, Malte Spielmann, Xiaojie Qiu, Xingfan Huang, Daniel M Ibrahim, Andrew J Hill, Fan Zhang, Stefan Mundlos, Lena Christiansen, Frank J Steemers,[...]. Nature 2019
30
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
Hoa Thi Nhu Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen. Genome Biol 2020
30
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
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
30
Joint probabilistic modeling of single-cell multi-omic data with totalVI.
Adam Gayoso, Zoë Steier, Romain Lopez, Jeffrey Regier, Kristopher L Nazor, Aaron Streets, Nir Yosef. Nat Methods 2021
Adam Gayoso, Zoë Steier, Romain Lopez, Jeffrey Regier, Kristopher L Nazor, Aaron Streets, Nir Yosef. Nat Methods 2021
30
Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.
Luke Zappia, Belinda Phipson, Alicia Oshlack. PLoS Comput Biol 2018
Luke Zappia, Belinda Phipson, Alicia Oshlack. PLoS Comput Biol 2018
30
Single-cell multimodal omics: the power of many.
Chenxu Zhu, Sebastian Preissl, Bing Ren. Nat Methods 2020
Chenxu Zhu, Sebastian Preissl, Bing Ren. Nat Methods 2020
30
Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
30
Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
20
Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
20
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2.
Harrison Specht, Edward Emmott, Aleksandra A Petelski, R Gray Huffman, David H Perlman, Marco Serra, Peter Kharchenko, Antonius Koller, Nikolai Slavov. Genome Biol 2021
Harrison Specht, Edward Emmott, Aleksandra A Petelski, R Gray Huffman, David H Perlman, Marco Serra, Peter Kharchenko, Antonius Koller, Nikolai Slavov. Genome Biol 2021
20
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
20
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
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
20
Joint analysis of heterogeneous single-cell RNA-seq dataset collections.
Nikolas Barkas, Viktor Petukhov, Daria Nikolaeva, Yaroslav Lozinsky, Samuel Demharter, Konstantin Khodosevich, Peter V Kharchenko. Nat Methods 2019
Nikolas Barkas, Viktor Petukhov, Daria Nikolaeva, Yaroslav Lozinsky, Samuel Demharter, Konstantin Khodosevich, Peter V Kharchenko. Nat Methods 2019
20
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury,[...]. Cell 2016
20
SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references.
Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang. Brief Bioinform 2021
Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang. Brief Bioinform 2021
20
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.
Julie Jerber, Daniel D Seaton, Anna S E Cuomo, Natsuhiko Kumasaka, James Haldane, Juliette Steer, Minal Patel, Daniel Pearce, Malin Andersson, Marc Jan Bonder,[...]. Nat Genet 2021
Julie Jerber, Daniel D Seaton, Anna S E Cuomo, Natsuhiko Kumasaka, James Haldane, Juliette Steer, Minal Patel, Daniel Pearce, Malin Andersson, Marc Jan Bonder,[...]. Nat Genet 2021
20
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
Michael Hagemann-Jensen, Christoph Ziegenhain, Ping Chen, Daniel Ramsköld, Gert-Jan Hendriks, Anton J M Larsson, Omid R Faridani, Rickard Sandberg. Nat Biotechnol 2020
20
muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data.
Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Daniela Calini, Ludovic Collin, Catarina Raposo, Dheeraj Malhotra, Mark D Robinson. Nat Commun 2020
Helena L Crowell, Charlotte Soneson, Pierre-Luc Germain, Daniela Calini, Ludovic Collin, Catarina Raposo, Dheeraj Malhotra, Mark D Robinson. Nat Commun 2020
20
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
Darren A Cusanovich, Riza Daza, Andrew Adey, Hannah A Pliner, Lena Christiansen, Kevin L Gunderson, Frank J Steemers, Cole Trapnell, Jay Shendure. Science 2015
20
Tumour evolution inferred by single-cell sequencing.
Nicholas Navin, Jude Kendall, Jennifer Troge, Peter Andrews, Linda Rodgers, Jeanne McIndoo, Kerry Cook, Asya Stepansky, Dan Levy, Diane Esposito,[...]. Nature 2011
Nicholas Navin, Jude Kendall, Jennifer Troge, Peter Andrews, Linda Rodgers, Jeanne McIndoo, Kerry Cook, Asya Stepansky, Dan Levy, Diane Esposito,[...]. Nature 2011
20
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
Nathan Lawlor, Joshy George, Mohan Bolisetty, Romy Kursawe, Lili Sun, V Sivakamasundari, Ina Kycia, Paul Robson, Michael L Stitzel. Genome Res 2017
20
20
High-definition spatial transcriptomics for in situ tissue profiling.
Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro,[...]. Nat Methods 2019
Sanja Vickovic, Gökcen Eraslan, Fredrik Salmén, Johanna Klughammer, Linnea Stenbeck, Denis Schapiro, Tarmo Äijö, Richard Bonneau, Ludvig Bergenstråhle, José Fernandéz Navarro,[...]. Nat Methods 2019
20
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
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
20
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
Fuchou Tang, Catalin Barbacioru, Yangzhou Wang, Ellen Nordman, Clarence Lee, Nanlan Xu, Xiaohui Wang, John Bodeau, Brian B Tuch, Asim Siddiqui,[...]. Nat Methods 2009
20
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
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
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
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
20
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
Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R Zhang, Mingyao Li. Nat Commun 2019
20
Spatially mapped single-cell chromatin accessibility.
Casey A Thornton, Ryan M Mulqueen, Kristof A Torkenczy, Andrew Nishida, Eve G Lowenstein, Andrew J Fields, Frank J Steemers, Wenri Zhang, Heather L McConnell, Randy L Woltjer,[...]. Nat Commun 2021
Casey A Thornton, Ryan M Mulqueen, Kristof A Torkenczy, Andrew Nishida, Eve G Lowenstein, Andrew J Fields, Frank J Steemers, Wenri Zhang, Heather L McConnell, Randy L Woltjer,[...]. Nat Commun 2021
20
MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.
Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C Marioni, Oliver Stegle. Genome Biol 2020
Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C Marioni, Oliver Stegle. Genome Biol 2020
20
voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
Charity W Law, Yunshun Chen, Wei Shi, Gordon K Smyth. Genome Biol 2014
20
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
20
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
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
20
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.