A citation-based method for searching scientific literature

Michael Thompson, Maika Matsumoto, Tianqi Ma, Anne Senabouth, Nathan J Palpant, Joseph E Powell, Quan Nguyen. Front Genet 2021
Times Cited: 1







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



Times Cited
  Times     Co-cited
Similarity


A single-cell molecular map of mouse gastrulation and early organogenesis.
Blanca Pijuan-Sala, Jonathan A Griffiths, Carolina Guibentif, Tom W Hiscock, Wajid Jawaid, Fernando J Calero-Nieto, Carla Mulas, Ximena Ibarra-Soria, Richard C V Tyser, Debbie Lee Lian Ho,[...]. Nature 2019
203
100

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
100

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
100

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z Yeung, William M Mauck, Peter Smibert, Rahul Satija. Genome Biol 2018
209
100

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation.
Clayton E Friedman, Quan Nguyen, Samuel W Lukowski, Abbigail Helfer, Han Sheng Chiu, Jason Miklas, Shiri Levy, Shengbao Suo, Jing-Dong Jackie Han, Pierre Osteil,[...]. Cell Stem Cell 2018
100
100

A human cell atlas of fetal gene expression.
Junyue Cao, Diana R O'Day, Hannah A Pliner, Paul D Kingsley, Mei Deng, Riza M Daza, Michael A Zager, Kimberly A Aldinger, Ronnie Blecher-Gonen, Fan Zhang,[...]. Science 2020
63
100

Single-Cell Transcriptomics Meets Lineage Tracing.
Lennart Kester, Alexander van Oudenaarden. Cell Stem Cell 2018
154
100

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets.
Yingxin Lin, Shila Ghazanfar, Kevin Y X Wang, Johann A Gagnon-Bartsch, Kitty K Lo, Xianbin Su, Ze-Guang Han, John T Ormerod, Terence P Speed, Pengyi Yang,[...]. Proc Natl Acad Sci U S A 2019
44
100


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
489
100

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action.
James M McFarland, Brenton R Paolella, Allison Warren, Kathryn Geiger-Schuller, Tsukasa Shibue, Michael Rothberg, Olena Kuksenko, William N Colgan, Andrew Jones, Emily Chambers,[...]. Nat Commun 2020
21
100

Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer.
Anthony R Cillo, Cornelius H L Kürten, Tracy Tabib, Zengbiao Qi, Sayali Onkar, Ting Wang, Angen Liu, Umamaheswar Duvvuri, Seungwon Kim, Ryan J Soose,[...]. Immunity 2020
98
100

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
17
100


Characterization of cell fate probabilities in single-cell data with Palantir.
Manu Setty, Vaidotas Kiseliovas, Jacob Levine, Adam Gayoso, Linas Mazutis, Dana Pe'er. Nat Biotechnol 2019
80
100

Computational principles and challenges in single-cell data integration.
Ricard Argelaguet, Anna S E Cuomo, Oliver Stegle, John C Marioni. Nat Biotechnol 2021
12
100

Inference and analysis of cell-cell communication using CellChat.
Suoqin Jin, Christian F Guerrero-Juarez, Lihua Zhang, Ivan Chang, Raul Ramos, Chen-Hsiang Kuan, Peggy Myung, Maksim V Plikus, Qing Nie. Nat Commun 2021
65
100

Comprehensive single-cell transcriptional profiling of a multicellular organism.
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers,[...]. Science 2017
465
100

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices.
Christopher S McGinnis, David M Patterson, Juliane Winkler, Daniel N Conrad, Marco Y Hein, Vasudha Srivastava, Jennifer L Hu, Lyndsay M Murrow, Jonathan S Weissman, Zena Werb,[...]. Nat Methods 2019
105
100


The NIH Roadmap Epigenomics Mapping Consortium.
Bradley E Bernstein, John A Stamatoyannopoulos, Joseph F Costello, Bing Ren, Aleksandar Milosavljevic, Alexander Meissner, Manolis Kellis, Marco A Marra, Arthur L Beaudet, Joseph R Ecker,[...]. Nat Biotechnol 2010
100

Genotype-free demultiplexing of pooled single-cell RNA-seq.
Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang,[...]. Genome Biol 2019
10
100

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles.
Zhenjia Wang, Mete Civelek, Clint L Miller, Nathan C Sheffield, Michael J Guertin, Chongzhi Zang. Bioinformatics 2018
32
100

Single-Cell Resolution of Temporal Gene Expression during Heart Development.
Daniel M DeLaughter, Alexander G Bick, Hiroko Wakimoto, David McKean, Joshua M Gorham, Irfan S Kathiriya, John T Hinson, Jason Homsy, Jesse Gray, William Pu,[...]. Dev Cell 2016
195
100

Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice.
Weike Pei, Xi Wang, Jens Rössler, Thorsten B Feyerabend, Thomas Höfer, Hans-Reimer Rodewald. Nat Protoc 2019
9
100

Concepts and limitations for learning developmental trajectories from single cell genomics.
Sophie Tritschler, Maren Büttner, David S Fischer, Marius Lange, Volker Bergen, Heiko Lickert, Fabian J Theis. Development 2019
61
100

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
149
100

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
732
100


Multilineage communication regulates human liver bud development from pluripotency.
J Gray Camp, Keisuke Sekine, Tobias Gerber, Henry Loeffler-Wirth, Hans Binder, Malgorzata Gac, Sabina Kanton, Jorge Kageyama, Georg Damm, Daniel Seehofer,[...]. Nature 2017
225
100

Sfaira accelerates data and model reuse in single cell genomics.
David S Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos, Sophie Tritschler, Olle Holmberg, Hananeh Aliee, Fabian J Theis. Genome Biol 2021
1
100

Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters.
Christian Umkehrer, Felix Holstein, Laura Formenti, Julian Jude, Kimon Froussios, Tobias Neumann, Shona M Cronin, Lisa Haas, Jesse J Lipp, Thomas R Burkard,[...]. Nat Biotechnol 2021
13
100

BATMAN: Fast and Accurate Integration of Single-Cell RNA-Seq Datasets via Minimum-Weight Matching.
Igor Mandric, Brian L Hill, Malika K Freund, Michael Thompson, Eran Halperin. iScience 2020
3
100

Lineage tracing on transcriptional landscapes links state to fate during differentiation.
Caleb Weinreb, Alejo Rodriguez-Fraticelli, Fernando D Camargo, Allon M Klein. Science 2020
133
100

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
374
100


SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
812
100

EpiMogrify Models H3K4me3 Data to Identify Signaling Molecules that Improve Cell Fate Control and Maintenance.
Uma S Kamaraj, Joseph Chen, Khairunnisa Katwadi, John F Ouyang, Yu Bo Yang Sun, Yu Ming Lim, Xiaodong Liu, Lusy Handoko, Jose M Polo, Enrico Petretto,[...]. Cell Syst 2020
3
100

Inferring population dynamics from single-cell RNA-sequencing time series data.
David S Fischer, Anna K Fiedler, Eric M Kernfeld, Ryan M J Genga, Aimée Bastidas-Ponce, Mostafa Bakhti, Heiko Lickert, Jan Hasenauer, Rene Maehr, Fabian J Theis. Nat Biotechnol 2019
38
100

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
242
100

Reconstitution of prospermatogonial specification in vitro from human induced pluripotent stem cells.
Young Sun Hwang, Shinnosuke Suzuki, Yasunari Seita, Jumpei Ito, Yuka Sakata, Hirofumi Aso, Kei Sato, Brian P Hermann, Kotaro Sasaki. Nat Commun 2020
14
100

Recording development with single cell dynamic lineage tracing.
Aaron McKenna, James A Gagnon. Development 2019
53
100

Predicting cell-to-cell communication networks using NATMI.
Rui Hou, Elena Denisenko, Huan Ting Ong, Jordan A Ramilowski, Alistair R R Forrest. Nat Commun 2020
11
100

An unsupervised method for physical cell interaction profiling of complex tissues.
Nathanael Andrews, Jason T Serviss, Natalie Geyer, Agneta B Andersson, Ewa Dzwonkowska, Iva Šutevski, Rosan Heijboer, Ninib Baryawno, Marco Gerling, Martin Enge. Nat Methods 2021
3
100

CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics.
Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C Rivera-Gonzalez, Xue Yang, Yuhei Kirita, Samantha A Morris. Genome Biol 2019
21
100

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
319
100

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells.
Drew Neavin, Quan Nguyen, Maciej S Daniszewski, Helena H Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W Lukowski, Duncan E Crombie, Grace E Lidgerwood,[...]. Genome Biol 2021
6
100


Generalizing RNA velocity to transient cell states through dynamical modeling.
Volker Bergen, Marius Lange, Stefan Peidli, F Alexander Wolf, Fabian J Theis. Nat Biotechnol 2020
202
100

COMUNET: a tool to explore and visualize intercellular communication.
Maria Solovey, Antonio Scialdone. Bioinformatics 2020
3
100


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.