A citation-based method for searching scientific literature

Helena Kilpinen, Angela Goncalves, Andreas Leha, Vackar Afzal, Kaur Alasoo, Sofie Ashford, Sendu Bala, Dalila Bensaddek, Francesco Paolo Casale, Oliver J Culley, Petr Danecek, Adam Faulconbridge, Peter W Harrison, Annie Kathuria, Davis McCarthy, Shane A McCarthy, Ruta Meleckyte, Yasin Memari, Nathalie Moens, Filipa Soares, Alice Mann, Ian Streeter, Chukwuma A Agu, Alex Alderton, Rachel Nelson, Sarah Harper, Minal Patel, Alistair White, Sharad R Patel, Laura Clarke, Reena Halai, Christopher M Kirton, Anja Kolb-Kokocinski, Philip Beales, Ewan Birney, Davide Danovi, Angus I Lamond, Willem H Ouwehand, Ludovic Vallier, Fiona M Watt, Richard Durbin, Oliver Stegle, Daniel J Gaffney. Nature 2017
Times Cited: 279







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



Times Cited
  Times     Co-cited
Similarity



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
21

Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.
Ivan Carcamo-Orive, Gabriel E Hoffman, Paige Cundiff, Noam D Beckmann, Sunita L D'Souza, Joshua W Knowles, Achchhe Patel, Dimitri Papatsenko, Fahim Abbasi, Gerald M Reaven,[...]. Cell Stem Cell 2017
153
18


Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.
Christopher DeBoever, He Li, David Jakubosky, Paola Benaglio, Joaquin Reyna, Katrina M Olson, Hui Huang, William Biggs, Efren Sandoval, Matteo D'Antonio,[...]. Cell Stem Cell 2017
95
14

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Anna S E Cuomo, Daniel D Seaton, Davis J McCarthy, Iker Martinez, Marc Jan Bonder, Jose Garcia-Bernardo, Shradha Amatya, Pedro Madrigal, Abigail Isaacson, Florian Buettner,[...]. Nat Commun 2020
78
17

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs.
Courtney K Burrows, Nicholas E Banovich, Bryan J Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K Pritchard, Yoav Gilad. PLoS Genet 2016
82
15

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
13

Molecular and functional variation in iPSC-derived sensory neurons.
Jeremy Schwartzentruber, Stefanie Foskolou, Helena Kilpinen, Julia Rodrigues, Kaur Alasoo, Andrew J Knights, Minal Patel, Angela Goncalves, Rita Ferreira, Caroline Louise Benn,[...]. Nat Genet 2018
116
12


Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential.
Aija Kyttälä, Roksana Moraghebi, Cristina Valensisi, Johannes Kettunen, Colin Andrus, Kalyan Kumar Pasumarthy, Mahito Nakanishi, Ken Nishimura, Manami Ohtaka, Jere Weltner,[...]. Stem Cell Reports 2016
146
12

Genetic background drives transcriptional variation in human induced pluripotent stem cells.
Foad Rouhani, Natsuhiko Kumasaka, Miguel Cardoso de Brito, Allan Bradley, Ludovic Vallier, Daniel Gaffney. PLoS Genet 2014
189
12

Cerebral organoids model human brain development and microcephaly.
Madeline A Lancaster, Magdalena Renner, Carol-Anne Martin, Daniel Wenzel, Louise S Bicknell, Matthew E Hurles, Tessa Homfray, Josef M Penninger, Andrew P Jackson, Juergen A Knoblich. Nature 2013
11

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
10

Induced pluripotent stem cell technology: a decade of progress.
Yanhong Shi, Haruhisa Inoue, Joseph C Wu, Shinya Yamanaka. Nat Rev Drug Discov 2017
689
10

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
52
19

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.
Athanasia D Panopoulos, Matteo D'Antonio, Paola Benaglio, Roy Williams, Sherin I Hashem, Bernhard M Schuldt, Christopher DeBoever, Angelo D Arias, Melvin Garcia, Bradley C Nelson,[...]. Stem Cell Reports 2017
79
11

Embryonic stem cell lines derived from human blastocysts.
J A Thomson, J Itskovitz-Eldor, S S Shapiro, M A Waknitz, J J Swiergiel, V S Marshall, J M Jones. Science 1998
9

Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations.
Florian T Merkle, Sulagna Ghosh, Nolan Kamitaki, Jana Mitchell, Yishai Avior, Curtis Mello, Seva Kashin, Shila Mekhoubad, Dusko Ilic, Maura Charlton,[...]. Nature 2017
271
9

Reproducibility of Molecular Phenotypes after Long-Term Differentiation to Human iPSC-Derived Neurons: A Multi-Site Omics Study.
Viola Volpato, James Smith, Cynthia Sandor, Janina S Ried, Anna Baud, Adam Handel, Sarah E Newey, Frank Wessely, Moustafa Attar, Emma Whiteley,[...]. Stem Cell Reports 2018
85
10

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
9

Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture.
Louise C Laurent, Igor Ulitsky, Ileana Slavin, Ha Tran, Andrew Schork, Robert Morey, Candace Lynch, Julie V Harness, Sunray Lee, Maria J Barrero,[...]. Cell Stem Cell 2011
624
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
8

Autologous Induced Stem-Cell-Derived Retinal Cells for Macular Degeneration.
Michiko Mandai, Akira Watanabe, Yasuo Kurimoto, Yasuhiko Hirami, Chikako Morinaga, Takashi Daimon, Masashi Fujihara, Hiroshi Akimaru, Noriko Sakai, Yumiko Shibata,[...]. N Engl J Med 2017
752
8

Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency.
Bao-Yang Hu, Jason P Weick, Junying Yu, Li-Xiang Ma, Xiao-Qing Zhang, James A Thomson, Su-Chun Zhang. Proc Natl Acad Sci U S A 2010
714
8

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response.
Kaur Alasoo, Julia Rodrigues, Subhankar Mukhopadhyay, Andrew J Knights, Alice L Mann, Kousik Kundu, Christine Hale, Gordon Dougan, Daniel J Gaffney. Nat Genet 2018
117
8

Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach.
Matteo D'Antonio, Paola Benaglio, David Jakubosky, William W Greenwald, Hiroko Matsui, Margaret K R Donovan, He Li, Erin N Smith, Agnieszka D'Antonio-Chronowska, Kelly A Frazer. Cell Rep 2018
44
18



The human-induced pluripotent stem cell initiative-data resources for cellular genetics.
Ian Streeter, Peter W Harrison, Adam Faulconbridge, Paul Flicek, Helen Parkinson, Laura Clarke. Nucleic Acids Res 2017
52
13

Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling.
Stuart M Chambers, Christopher A Fasano, Eirini P Papapetrou, Mark Tomishima, Michel Sadelain, Lorenz Studer. Nat Biotechnol 2009
7

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression.
Benjamin J Schmiedel, Divya Singh, Ariel Madrigal, Alan G Valdovino-Gonzalez, Brandie M White, Jose Zapardiel-Gonzalo, Brendan Ha, Gokmen Altay, Jason A Greenbaum, Graham McVicker,[...]. Cell 2018
297
7

Transcriptome and genome sequencing uncovers functional variation in humans.
Tuuli Lappalainen, Michael Sammeth, Marc R Friedländer, Peter A C 't Hoen, Jean Monlong, Manuel A Rivas, Mar Gonzàlez-Porta, Natalja Kurbatova, Thasso Griebel, Pedro G Ferreira,[...]. Nature 2013
7

Bayesian test for colocalisation between pairs of genetic association studies using summary statistics.
Claudia Giambartolomei, Damjan Vukcevic, Eric E Schadt, Lude Franke, Aroon D Hingorani, Chris Wallace, Vincent Plagnol. PLoS Genet 2014
909
7

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.
Hyun Min Kang, Meena Subramaniam, Sasha Targ, Michelle Nguyen, Lenka Maliskova, Elizabeth McCarthy, Eunice Wan, Simon Wong, Lauren Byrnes, Cristina M Lanata,[...]. Nat Biotechnol 2018
341
7

Donor-dependent variations in hepatic differentiation from human-induced pluripotent stem cells.
Masatoshi Kajiwara, Takashi Aoi, Keisuke Okita, Ryosuke Takahashi, Haruhisa Inoue, Naoya Takayama, Hiroshi Endo, Koji Eto, Junya Toguchida, Shinji Uemoto,[...]. Proc Natl Acad Sci U S A 2012
223
7


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
7

Population-scale proteome variation in human induced pluripotent stem cells.
Bogdan Andrei Mirauta, Daniel D Seaton, Dalila Bensaddek, Alejandro Brenes, Marc Jan Bonder, Helena Kilpinen, Oliver Stegle, Angus I Lamond. Elife 2020
20
35

Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.
Monique G P van der Wijst, Harm Brugge, Dylan H de Vries, Patrick Deelen, Morris A Swertz, Lude Franke. Nat Genet 2018
139
7

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage.
Katherine Amps, Peter W Andrews, George Anyfantis, Lyle Armstrong, Stuart Avery, Hossein Baharvand, Julie Baker, Duncan Baker, Maria B Munoz, Stephen Beil,[...]. Nat Biotechnol 2011
382
7

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.
Alessandra Vigilante, Anna Laddach, Nathalie Moens, Ruta Meleckyte, Andreas Leha, Arsham Ghahramani, Oliver J Culley, Annie Kathuria, Chloe Hurling, Alice Vickers,[...]. Cell Rep 2019
18
33

A cellular model for sporadic ALS using patient-derived induced pluripotent stem cells.
Matthew F Burkhardt, Fernando J Martinez, Sarah Wright, Carla Ramos, Dmitri Volfson, Michael Mason, Jeff Garnes, Vu Dang, Jeffery Lievers, Uzma Shoukat-Mumtaz,[...]. Mol Cell Neurosci 2013
197
6

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
Jessica Mariani, Gianfilippo Coppola, Ping Zhang, Alexej Abyzov, Lauren Provini, Livia Tomasini, Mariangela Amenduni, Anna Szekely, Dean Palejev, Michael Wilson,[...]. Cell 2015
621
6

Multiplex genome engineering using CRISPR/Cas systems.
Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu, Wenyan Jiang, Luciano A Marraffini,[...]. Science 2013
6

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
6

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells.
Jose M Polo, Susanna Liu, Maria Eugenia Figueroa, Warakorn Kulalert, Sarah Eminli, Kah Yong Tan, Effie Apostolou, Matthias Stadtfeld, Yushan Li, Toshi Shioda,[...]. Nat Biotechnol 2010
851
6

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A Doudna, Emmanuelle Charpentier. Science 2012
6

Need for high-resolution Genetic Analysis in iPSC: Results and Lessons from the ForIPS Consortium.
Bernt Popp, Mandy Krumbiegel, Janina Grosch, Annika Sommer, Steffen Uebe, Zacharias Kohl, Sonja Plötz, Michaela Farrell, Udo Trautmann, Cornelia Kraus,[...]. Sci Rep 2018
43
13

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
6


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.