A citation-based method for searching scientific literature

Sandra Segura-Bayona, Marina Villamor-Payà, Camille Stephan-Otto Attolini, Lars M Koenig, Maria Sanchiz-Calvo, Simon J Boulton, Travis H Stracker. Cell Rep 2020
Times Cited: 3







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



Times Cited
  Times     Co-cited
Similarity


Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds.
Danwei Huangfu, René Maehr, Wenjun Guo, Astrid Eijkelenboom, Melinda Snitow, Alice E Chen, Douglas A Melton. Nat Biotechnol 2008
66

TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres.
Zhong Deng, Julie Norseen, Andreas Wiedmer, Harold Riethman, Paul M Lieberman. Mol Cell 2009
355
66

Investigating the transcriptional control of cardiovascular development.
Irfan S Kathiriya, Elphège P Nora, Benoit G Bruneau. Circ Res 2015
51
33

PU.1 and C/EBPalpha/beta convert fibroblasts into macrophage-like cells.
Ru Feng, Sabrina C Desbordes, Huafeng Xie, Ester Sanchez Tillo, Fiona Pixley, E Richard Stanley, Thomas Graf. Proc Natl Acad Sci U S A 2008
241
33

Landscape of cohesin-mediated chromatin loops in the human genome.
Fabian Grubert, Rohith Srivas, Damek V Spacek, Maya Kasowski, Mariana Ruiz-Velasco, Nasa Sinnott-Armstrong, Peyton Greenside, Anil Narasimha, Qing Liu, Benjamin Geller,[...]. Nature 2020
27
33

Single-cell RNA-seq identifies a reversible mesodermal activation in abnormally specified epithelia of p63 EEC syndrome.
Eduardo Soares, Quan Xu, Qingqing Li, Jieqiong Qu, Yuxuan Zheng, Henriette H M Raeven, Karina O Brandao, Isabelle Petit, Willem M R van den Akker, Simon J van Heeringen,[...]. Proc Natl Acad Sci U S A 2019
7
33

Ensembl 2019.
Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M Ridwan Amode, Irina M Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu,[...]. Nucleic Acids Res 2019
426
33

ENCODE data at the ENCODE portal.
Cricket A Sloan, Esther T Chan, Jean M Davidson, Venkat S Malladi, J Seth Strattan, Benjamin C Hitz, Idan Gabdank, Aditi K Narayanan, Marcus Ho, Brian T Lee,[...]. Nucleic Acids Res 2016
227
33

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
33

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
Christian H Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P Kumar, Elisabetta Mereu, Brian A Joughin, Oliver Stegle, Douglas A Lauffenburger, Holger Heyn,[...]. Genome Biol 2020
39
33


Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.
Seung Woo Cho, Jin Xu, Ruping Sun, Maxwell R Mumbach, Ava C Carter, Y Grace Chen, Kathryn E Yost, Jeewon Kim, Jing He, Stephanie A Nevins,[...]. Cell 2018
185
33

Proteomics. Tissue-based map of the human proteome.
Mathias Uhlén, Linn Fagerberg, Björn M Hallström, Cecilia Lindskog, Per Oksvold, Adil Mardinoglu, Åsa Sivertsson, Caroline Kampf, Evelina Sjöstedt, Anna Asplund,[...]. Science 2015
33

The AP-2 Transcription Factor APTF-2 Is Required for Neuroblast and Epidermal Morphogenesis in Caenorhabditis elegans Embryogenesis.
Yemima Budirahardja, Pei Yi Tan, Thang Doan, Peter Weisdepp, Ronen Zaidel-Bar. PLoS Genet 2016
4
33

GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions.
Li Fang, Yunjin Li, Lu Ma, Qiyue Xu, Fei Tan, Geng Chen. Nucleic Acids Res 2021
6
33

Towards a knowledge-based Human Protein Atlas.
Mathias Uhlen, Per Oksvold, Linn Fagerberg, Emma Lundberg, Kalle Jonasson, Mattias Forsberg, Martin Zwahlen, Caroline Kampf, Kenneth Wester, Sophia Hober,[...]. Nat Biotechnol 2010
33

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
33

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.
Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark, Avi Ma'ayan. BMC Bioinformatics 2013
33

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
33

Separated at birth? The functional and molecular divergence of OLIG1 and OLIG2.
Dimphna H Meijer, Michael F Kane, Shwetal Mehta, Hongye Liu, Emily Harrington, Christopher M Taylor, Charles D Stiles, David H Rowitch. Nat Rev Neurosci 2012
102
33

A pitfall for machine learning methods aiming to predict across cell types.
Jacob Schreiber, Ritambhara Singh, Jeffrey Bilmes, William Stafford Noble. Genome Biol 2020
7
33

Critical role of p63 in the development of a normal esophageal and tracheobronchial epithelium.
Yaron Daniely, Grace Liao, Darlene Dixon, R Ilona Linnoila, Adriana Lori, Scott H Randell, Moshe Oren, Anton M Jetten. Am J Physiol Cell Physiol 2004
197
33

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
33

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks.
Thomas Moerman, Sara Aibar Santos, Carmen Bravo González-Blas, Jaak Simm, Yves Moreau, Jan Aerts, Stein Aerts. Bioinformatics 2019
59
33

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions.
Heonjong Han, Jae-Won Cho, Sangyoung Lee, Ayoung Yun, Hyojin Kim, Dasom Bae, Sunmo Yang, Chan Yeong Kim, Muyoung Lee, Eunbeen Kim,[...]. Nucleic Acids Res 2018
423
33

corto: a lightweight R package for gene network inference and master regulator analysis.
Daniele Mercatelli, Gonzalo Lopez-Garcia, Federico M Giorgi. Bioinformatics 2020
10
33

Induced pluripotent stem cell lines derived from human somatic cells.
Junying Yu, Maxim A Vodyanik, Kim Smuga-Otto, Jessica Antosiewicz-Bourget, Jennifer L Frane, Shulan Tian, Jeff Nie, Gudrun A Jonsdottir, Victor Ruotti, Ron Stewart,[...]. Science 2007
33

Induction of pluripotent stem cells from adult human fibroblasts by defined factors.
Kazutoshi Takahashi, Koji Tanabe, Mari Ohnuki, Megumi Narita, Tomoko Ichisaka, Kiichiro Tomoda, Shinya Yamanaka. Cell 2007
33


GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments.
Simon J van Heeringen, Gert Jan C Veenstra. Bioinformatics 2011
79
33

Perturbations to uncover gene networks.
Jesper Tegnér, Johan Björkegren. Trends Genet 2007
36
33

Patterning the gastrointestinal epithelium to confer regional-specific functions.
Cayla A Thompson, Ann DeLaForest, Michele A Battle. Dev Biol 2018
29
33

Direct conversion of human fibroblasts into hepatocyte-like cells by ATF5, PROX1, FOXA2, FOXA3, and HNF4A transduction.
Daiki Nakamori, Hiroki Akamine, Kazuo Takayama, Fuminori Sakurai, Hiroyuki Mizuguchi. Sci Rep 2017
33
33

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
206
33


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
33

AP-2 factors act in concert with Notch to orchestrate terminal differentiation in skin epidermis.
Xuan Wang, H Amalia Pasolli, Trevor Williams, Elaine Fuchs. J Cell Biol 2008
64
33


Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C).
Marieke Simonis, Petra Klous, Erik Splinter, Yuri Moshkin, Rob Willemsen, Elzo de Wit, Bas van Steensel, Wouter de Laat. Nat Genet 2006
874
33

Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding.
Andrew D Johnston, Claudia A Simões-Pires, Taylor V Thompson, Masako Suzuki, John M Greally. Nat Commun 2019
12
33


Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.
Daniel Marbach, Sushmita Roy, Ferhat Ay, Patrick E Meyer, Rogerio Candeias, Tamer Kahveci, Christopher A Bristow, Manolis Kellis. Genome Res 2012
67
33

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
Jeffrey M Granja, M Ryan Corces, Sarah E Pierce, S Tansu Bagdatli, Hani Choudhry, Howard Y Chang, William J Greenleaf. Nat Genet 2021
39
33

NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells.
Jason Tchieu, Elizabeth L Calder, Sudha R Guttikonda, Eveline M Gutzwiller, Kelly A Aromolaran, Julius A Steinbeck, Peter A Goldstein, Lorenz Studer. Nat Biotechnol 2019
60
33

Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs.
Qing Liu, Chao Jiang, Jin Xu, Ming-Tao Zhao, Kevin Van Bortle, Xun Cheng, Guangwen Wang, Howard Y Chang, Joseph C Wu, Michael P Snyder. Circ Res 2017
60
33


In vivo reprogramming of wound-resident cells generates skin epithelial tissue.
Masakazu Kurita, Toshikazu Araoka, Tomoaki Hishida, David D O'Keefe, Yuta Takahashi, Akihisa Sakamoto, Masahiro Sakurai, Keiichiro Suzuki, Jun Wu, Mako Yamamoto,[...]. Nature 2018
45
33

SeesawPred: A Web Application for Predicting Cell-fate Determinants in Cell Differentiation.
András Hartmann, Satoshi Okawa, Gaia Zaffaroni, Antonio Del Sol. Sci Rep 2018
4
33

Accurate prediction of cell type-specific transcription factor binding.
Jens Keilwagen, Stefan Posch, Jan Grau. Genome Biol 2019
33
33



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.