A citation-based method for searching scientific literature

Jian Hu, Amelia Schroeder, Kyle Coleman, Chixiang Chen, Benjamin J Auerbach, Mingyao Li. Comput Struct Biotechnol J 2021
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis.
Xiangjie Li, Kui Wang, Yafei Lyu, Huize Pan, Jingxiao Zhang, Dwight Stambolian, Katalin Susztak, Muredach P Reilly, Gang Hu, Mingyao Li. Nat Commun 2020
39
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
739
50

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
50

Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
234
50

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
50

Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction.
Johanna Fitz, Tobias Neumann, Monika Steininger, Eva-Maria Wiedemann, Adriana Cantoran Garcia, Alexander Athanasiadis, Ursula E Schoeberl, Rushad Pavri. Nat Genet 2020
19
50


Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
553
50

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
51
50

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
171
50

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Yong Wang, Jill Waters, Marco L Leung, Anna Unruh, Whijae Roh, Xiuqing Shi, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang,[...]. Nature 2014
600
50

deconvSeq: deconvolution of cell mixture distribution in sequencing data.
Rose Du, Vince Carey, Scott T Weiss. Bioinformatics 2019
13
50

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
171
50

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
564
50

A systematic evaluation of single-cell RNA-sequencing imputation methods.
Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie C Hicks. Genome Biol 2020
22
50

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
654
50

A comprehensive survey of regulatory network inference methods using single-cell RNA sequencing data.
Hung Nguyen, Duc Tran, Bang Tran, Bahadir Pehlivan, Tin Nguyen. Brief Bioinform 2020
6
50

Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq.
Qi Qiu, Peng Hu, Xiaojie Qiu, Kiya W Govek, Pablo G Cámara, Hao Wu. Nat Methods 2020
15
50

Single-cell analyses of renal cell cancers reveal insights into tumor microenvironment, cell of origin, and therapy response.
Yuping Zhang, Sathiya P Narayanan, Rahul Mannan, Gregory Raskind, Xiaoming Wang, Pankaj Vats, Fengyun Su, Noshad Hosseini, Xuhong Cao, Chandan Kumar-Sinha,[...]. Proc Natl Acad Sci U S A 2021
5
50

Single-Cell Multiomics: Multiple Measurements from Single Cells.
Iain C Macaulay, Chris P Ponting, Thierry Voet. Trends Genet 2017
227
50

Accurate estimation of cell composition in bulk expression through robust integration of single-cell information.
Brandon Jew, Marcus Alvarez, Elior Rahmani, Zong Miao, Arthur Ko, Kristina M Garske, Jae Hoon Sul, Kirsi H Pietiläinen, Päivi Pajukanta, Eran Halperin. Nat Commun 2020
33
50

Mapping single-cell data to reference atlases by transfer learning.
Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi,[...]. Nat Biotechnol 2021
5
50

Exploring regulation in tissues with eQTL networks.
Maud Fagny, Joseph N Paulson, Marieke L Kuijjer, Abhijeet R Sonawane, Cho-Yi Chen, Camila M Lopes-Ramos, Kimberly Glass, John Quackenbush, John Platig. Proc Natl Acad Sci U S A 2017
48
50

Design and computational analysis of single-cell RNA-sequencing experiments.
Rhonda Bacher, Christina Kendziorski. Genome Biol 2016
210
50

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
50

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data.
Zehua Liu, Huazhe Lou, Kaikun Xie, Hao Wang, Ning Chen, Oscar M Aparicio, Michael Q Zhang, Rui Jiang, Ting Chen. Nat Commun 2017
44
50

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance.
Xuanyao Liu, Yang I Li, Jonathan K Pritchard. Cell 2019
132
50

Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line.
Enrique I Velazquez-Villarreal, Shamoni Maheshwari, Jon Sorenson, Ian T Fiddes, Vijay Kumar, Yifeng Yin, Michelle G Webb, Claudia Catalanotti, Mira Grigorova, Paul A Edwards,[...]. Commun Biol 2020
9
50

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments.
Quin F Wills, Kenneth J Livak, Alex J Tipping, Tariq Enver, Andrew J Goldson, Darren W Sexton, Chris Holmes. Nat Biotechnol 2013
149
50

In vivo mRNA display enables large-scale proteomics by next generation sequencing.
Panos Oikonomou, Roberto Salatino, Saeed Tavazoie. Proc Natl Acad Sci U S A 2020
5
50

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia.
Federico Gaiti, Ronan Chaligne, Hongcang Gu, Ryan M Brand, Steven Kothen-Hill, Rafael C Schulman, Kirill Grigorev, Davide Risso, Kyu-Tae Kim, Alessandro Pastore,[...]. Nature 2019
80
50

Single-cell genomics: coming of age.
Sten Linnarsson, Sarah A Teichmann. Genome Biol 2016
46
50

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
50

SCOPIT: sample size calculations for single-cell sequencing experiments.
Alexander Davis, Ruli Gao, Nicholas E Navin. BMC Bioinformatics 2019
9
50

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
492
50

Kidney Single-Cell Atlas Reveals Myeloid Heterogeneity in Progression and Regression of Kidney Disease.
Bryan R Conway, Eoin D O'Sullivan, Carolynn Cairns, James O'Sullivan, Daniel J Simpson, Angela Salzano, Katie Connor, Peng Ding, Duncan Humphries, Kevin Stewart,[...]. J Am Soc Nephrol 2020
26
50

A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
319
50

A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics.
Justin Lakkis, David Wang, Yuanchao Zhang, Gang Hu, Kui Wang, Huize Pan, Lyle Ungar, Muredach P Reilly, Xiangjie Li, Mingyao Li. Genome Res 2021
4
50

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis.
Robert C Wirka, Dhananjay Wagh, David T Paik, Milos Pjanic, Trieu Nguyen, Clint L Miller, Ramen Kundu, Manabu Nagao, John Coller, Tiffany K Koyano,[...]. Nat Med 2019
137
50

Missing data and technical variability in single-cell RNA-sequencing experiments.
Stephanie C Hicks, F William Townes, Mingxiang Teng, Rafael A Irizarry. Biostatistics 2018
149
50

Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
J C Lambert, C A Ibrahim-Verbaas, D Harold, A C Naj, R Sims, C Bellenguez, A L DeStafano, J C Bis, G W Beecham, B Grenier-Boley,[...]. Nat Genet 2013
50

Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants.
Margaret K R Donovan, Agnieszka D'Antonio-Chronowska, Matteo D'Antonio, Kelly A Frazer. Nat Commun 2020
29
50

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
74
50

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
465
50

Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types.
Jin Li, Johanna Klughammer, Matthias Farlik, Thomas Penz, Andreas Spittler, Charlotte Barbieux, Ekaterine Berishvili, Christoph Bock, Stefan Kubicek. EMBO Rep 2016
130
50

Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human.
Huize Pan, Chenyi Xue, Benjamin J Auerbach, Jiaxin Fan, Alexander C Bashore, Jian Cui, Dina Y Yang, Sarah B Trignano, Wen Liu, Jianting Shi,[...]. Circulation 2020
41
50

Single-cell mRNA quantification and differential analysis with Census.
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell. Nat Methods 2017
421
50


Systematic identification of trans eQTLs as putative drivers of known disease associations.
Harm-Jan Westra, Marjolein J Peters, Tõnu Esko, Hanieh Yaghootkar, Claudia Schurmann, Johannes Kettunen, Mark W Christiansen, Benjamin P Fairfax, Katharina Schramm, Joseph E Powell,[...]. Nat Genet 2013
50

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
26
50


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.