A citation-based method for searching scientific literature


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



Times Cited
  Times     Co-cited
Similarity


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
61
100

Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome.
Jeffrey S Buzby, Shirley A Williams, Lana Schaffer, Steven R Head, Diane J Nugent. Cancer Genet 2017
1
100

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Jacob F Degner, John C Marioni, Athma A Pai, Joseph K Pickrell, Everlyne Nkadori, Yoav Gilad, Jonathan K Pritchard. Bioinformatics 2009
314
100

A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth via regulation of MITF.
Jiyeon Choi, Mai Xu, Matthew M Makowski, Tongwu Zhang, Matthew H Law, Michael A Kovacs, Anton Granzhan, Wendy J Kim, Hemang Parikh, Michael Gartside,[...]. Nat Genet 2017
26
100


Landscape of X chromosome inactivation across human tissues.
Taru Tukiainen, Alexandra-Chloé Villani, Angela Yen, Manuel A Rivas, Jamie L Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby,[...]. Nature 2017
284
100

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
100

Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer.
Craig M Bielski, Mark T A Donoghue, Mayur Gadiya, Aphrothiti J Hanrahan, Helen H Won, Matthew T Chang, Philip Jonsson, Alexander V Penson, Alexander Gorelick, Christopher Harris,[...]. Cancer Cell 2018
31
100

Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.
Weiwei Shi, Charlotte K Y Ng, Raymond S Lim, Tingting Jiang, Sushant Kumar, Xiaotong Li, Vikram B Wali, Salvatore Piscuoglio, Mark B Gerstein, Anees B Chagpar,[...]. Cell Rep 2018
42
100

Regulatory variants: from detection to predicting impact.
Elena Rojano, Pedro Seoane, Juan A G Ranea, James R Perkins. Brief Bioinform 2019
26
100

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Jong Kyoung Kim, Aleksandra A Kolodziejczyk, Tomislav Ilicic, Sarah A Teichmann, John C Marioni. Nat Commun 2015
94
100

Biased allelic expression in human primary fibroblast single cells.
Christelle Borel, Pedro G Ferreira, Federico Santoni, Olivier Delaneau, Alexandre Fort, Konstantin Y Popadin, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Michel Guipponi,[...]. Am J Hum Genet 2015
69
100

Monoallelic expression determines oncogenic progression and outcome in benign and malignant brain tumors.
Erin J Walker, Cindy Zhang, Pedro Castelo-Branco, Cynthia Hawkins, Wes Wilson, Nataliya Zhukova, Noa Alon, Ana Novokmet, Berivan Baskin, Peter Ray,[...]. Cancer Res 2012
33
100

Transcriptome genetics using second generation sequencing in a Caucasian population.
Stephen B Montgomery, Micha Sammeth, Maria Gutierrez-Arcelus, Radoslaw P Lach, Catherine Ingle, James Nisbett, Roderic Guigo, Emmanouil T Dermitzakis. Nature 2010
604
100

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden.
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki,[...]. Genome Med 2017
100

Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Joseph K Pickrell, John C Marioni, Athma A Pai, Jacob F Degner, Barbara E Engelhardt, Everlyne Nkadori, Jean-Baptiste Veyrieras, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard. Nature 2010
848
100

Allele-Specific QTL Fine Mapping with PLASMA.
Austin T Wang, Anamay Shetty, Edward O'Connor, Connor Bell, Mark M Pomerantz, Matthew L Freedman, Alexander Gusev. Am J Hum Genet 2020
2
100

Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T.
Laura Duran-Lozano, Gemma Montalban, Sandra Bonache, Alejandro Moles-Fernández, Anna Tenés, Marta Castroviejo-Bermejo, Estela Carrasco, Adrià López-Fernández, Sara Torres-Esquius, Neus Gadea,[...]. Breast Cancer Res Treat 2019
4
100

Integrating GWAS and expression data for functional characterization of disease-associated SNPs: an application to follicular lymphoma.
Lucia Conde, Paige M Bracci, Rhea Richardson, Stephen B Montgomery, Christine F Skibola. Am J Hum Genet 2013
36
100

Cell type-specific genetic regulation of gene expression across human tissues.
Sarah Kim-Hellmuth, François Aguet, Meritxell Oliva, Manuel Muñoz-Aguirre, Silva Kasela, Valentin Wucher, Stephane E Castel, Andrew R Hamel, Ana Viñuela, Amy L Roberts,[...]. Science 2020
34
100

MBASED: allele-specific expression detection in cancer tissues and cell lines.
Oleg Mayba, Houston N Gilbert, Jinfeng Liu, Peter M Haverty, Suchit Jhunjhunwala, Zhaoshi Jiang, Colin Watanabe, Zemin Zhang. Genome Biol 2014
59
100

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk.
Stephane E Castel, Alejandra Cervera, Pejman Mohammadi, François Aguet, Ferran Reverter, Aaron Wolman, Roderic Guigo, Ivan Iossifov, Ana Vasileva, Tuuli Lappalainen. Nat Genet 2018
72
100

A vast resource of allelic expression data spanning human tissues.
Stephane E Castel, François Aguet, Pejman Mohammadi, Kristin G Ardlie, Tuuli Lappalainen. Genome Biol 2020
11
100

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline.
Vitor R C Aguiar, Jônatas César, Olivier Delaneau, Emmanouil T Dermitzakis, Diogo Meyer. PLoS Genet 2019
23
100

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.
Athma A Pai, Carolyn E Cain, Orna Mizrahi-Man, Sherryl De Leon, Noah Lewellen, Jean-Baptiste Veyrieras, Jacob F Degner, Daniel J Gaffney, Joseph K Pickrell, Matthew Stephens,[...]. PLoS Genet 2012
63
100

Leveraging allelic imbalance to refine fine-mapping for eQTL studies.
Jennifer Zou, Farhad Hormozdiari, Brandon Jew, Stephane E Castel, Tuuli Lappalainen, Jason Ernst, Jae Hoon Sul, Eleazar Eskin. PLoS Genet 2019
6
100

Tools and best practices for data processing in allelic expression analysis.
Stephane E Castel, Ami Levy-Moonshine, Pejman Mohammadi, Eric Banks, Tuuli Lappalainen. Genome Biol 2015
127
100

Germline genetic polymorphisms influence tumor gene expression and immune cell infiltration.
Yoong Wearn Lim, Haiyin Chen-Harris, Oleg Mayba, Steve Lianoglou, Arthur Wuster, Tushar Bhangale, Zia Khan, Sanjeev Mariathasan, Anneleen Daemen, Jens Reeder,[...]. Proc Natl Acad Sci U S A 2018
44
100

Genetic regulatory variation in populations informs transcriptome analysis in rare disease.
Pejman Mohammadi, Stephane E Castel, Beryl B Cummings, Jonah Einson, Christina Sousa, Paul Hoffman, Sandra Donkervoort, Zhuoxun Jiang, Payam Mohassel, A Reghan Foley,[...]. Science 2019
27
100

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
100


Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.
Lili Wang, Jean Fan, Joshua M Francis, George Georghiou, Sarah Hergert, Shuqiang Li, Rutendo Gambe, Chensheng W Zhou, Chunxiao Yang, Sheng Xiao,[...]. Genome Res 2017
35
100

Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci.
Maria Gutierrez-Arcelus, Yuriy Baglaenko, Jatin Arora, Susan Hannes, Yang Luo, Tiffany Amariuta, Nikola Teslovich, Deepak A Rao, Joerg Ermann, A Helena Jonsson,[...]. Nat Genet 2020
21
100

Rare variant phasing and haplotypic expression from RNA sequencing with phASER.
Stephane E Castel, Pejman Mohammadi, Wendy K Chung, Yufeng Shen, Tuuli Lappalainen. Nat Commun 2016
38
100

Standardization of Sequencing Coverage Depth in NGS: Recommendation for Detection of Clonal and Subclonal Mutations in Cancer Diagnostics.
Anna Petrackova, Michal Vasinek, Lenka Sedlarikova, Tereza Dyskova, Petra Schneiderova, Tomas Novosad, Tomas Papajik, Eva Kriegova. Front Oncol 2019
21
100

Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison, Jouni Sirén, Adam M Novak, Glenn Hickey, Jordan M Eizenga, Eric T Dawson, William Jones, Shilpa Garg, Charles Markello, Michael F Lin,[...]. Nat Biotechnol 2018
104
100

Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues.
Andrew R Marderstein, Manik Uppal, Akanksha Verma, Bhavneet Bhinder, Zakieh Tayyebi, Jason Mezey, Andrew G Clark, Olivier Elemento. Nat Commun 2020
5
100

Genome-Wide Association Study of Bladder Cancer in a Chinese Cohort Reveals a New Susceptibility Locus at 5q12.3.
Meilin Wang, Zhiqiang Li, Haiyan Chu, Qiang Lv, Dingwei Ye, Qiang Ding, Chuanliang Xu, Jianming Guo, Mulong Du, Jianhua Chen,[...]. Cancer Res 2016
20
100

High-throughput allele-specific expression across 250 environmental conditions.
Gregory A Moyerbrailean, Allison L Richards, Daniel Kurtz, Cynthia A Kalita, Gordon O Davis, Chris T Harvey, Adnan Alazizi, Donovan Watza, Yoram Sorokin, Nancy Hauff,[...]. Genome Res 2016
43
100

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
100

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Livnat Jerby-Arnon, Parin Shah, Michael S Cuoco, Christopher Rodman, Mei-Ju Su, Johannes C Melms, Rachel Leeson, Abhay Kanodia, Shaolin Mei, Jia-Ren Lin,[...]. Cell 2018
297
100

6
100

Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing.
Maria Gutierrez-Arcelus, Halit Ongen, Tuuli Lappalainen, Stephen B Montgomery, Alfonso Buil, Alisa Yurovsky, Julien Bryois, Ismael Padioleau, Luciana Romano, Alexandra Planchon,[...]. PLoS Genet 2015
110
100

Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Helena Kilpinen, Sebastian M Waszak, Andreas R Gschwind, Sunil K Raghav, Robert M Witwicki, Andrea Orioli, Eugenia Migliavacca, Michaël Wiederkehr, Maria Gutierrez-Arcelus, Nikolaos I Panousis,[...]. Science 2013
232
100

Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.
Jean Fan, Hae-Ock Lee, Soohyun Lee, Da-Eun Ryu, Semin Lee, Catherine Xue, Seok Jin Kim, Kihyun Kim, Nikolaos Barkas, Peter J Park,[...]. Genome Res 2018
52
100

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Sebastian M Waszak, Helena Kilpinen, Andreas R Gschwind, Andrea Orioli, Sunil K Raghav, Robert M Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen, Nouria Hernandez,[...]. Bioinformatics 2014
6
100

Allele-specific expression reveals interactions between genetic variation and environment.
David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Douglas F Levinson,[...]. Nat Methods 2017
53
100

Genomic basis for RNA alterations in cancer.
Claudia Calabrese, Natalie R Davidson, Deniz Demircioğlu, Nuno A Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M Soulette,[...]. Nature 2020
85
100

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods.
Jiarui Ding, Xian Adiconis, Sean K Simmons, Monika S Kowalczyk, Cynthia C Hession, Nemanja D Marjanovic, Travis K Hughes, Marc H Wadsworth, Tyler Burks, Lan T Nguyen,[...]. Nat Biotechnol 2020
102
100

WASP: allele-specific software for robust molecular quantitative trait locus discovery.
Bryce van de Geijn, Graham McVicker, Yoav Gilad, Jonathan K Pritchard. Nat Methods 2015
180
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.