A citation-based method for searching scientific literature

András Szolek, Benjamin Schubert, Christopher Mohr, Marc Sturm, Magdalena Feldhahn, Oliver Kohlbacher. Bioinformatics 2014
Times Cited: 343







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



Times Cited
  Times     Co-cited
Similarity


NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.
Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters, Morten Nielsen. J Immunol 2017
652
27


Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes.
Sachet A Shukla, Michael S Rooney, Mohini Rajasagi, Grace Tiao, Philip M Dixon, Michael S Lawrence, Jonathan Stevens, William J Lane, Jamie L Dellagatta, Scott Steelman,[...]. Nat Biotechnol 2015
364
20

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution.
Nicholas McGranahan, Rachel Rosenthal, Crispin T Hiley, Andrew J Rowan, Thomas B K Watkins, Gareth A Wilson, Nicolai J Birkbak, Selvaraju Veeriah, Peter Van Loo, Javier Herrero,[...]. Cell 2017
589
20

Molecular and genetic properties of tumors associated with local immune cytolytic activity.
Michael S Rooney, Sachet A Shukla, Catherine J Wu, Gad Getz, Nir Hacohen. Cell 2015
18

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.
Kristian Cibulskis, Michael S Lawrence, Scott L Carter, Andrey Sivachenko, David Jaffe, Carrie Sougnez, Stacey Gabriel, Matthew Meyerson, Eric S Lander, Gad Getz. Nat Biotechnol 2013
18

An immunogenic personal neoantigen vaccine for patients with melanoma.
Patrick A Ott, Zhuting Hu, Derin B Keskin, Sachet A Shukla, Jing Sun, David J Bozym, Wandi Zhang, Adrienne Luoma, Anita Giobbie-Hurder, Lauren Peter,[...]. Nature 2017
17

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.
Nicholas McGranahan, Andrew J S Furness, Rachel Rosenthal, Sofie Ramskov, Rikke Lyngaa, Sunil Kumar Saini, Mariam Jamal-Hanjani, Gareth A Wilson, Nicolai J Birkbak, Crispin T Hiley,[...]. Science 2016
16

Neoantigens in cancer immunotherapy.
Ton N Schumacher, Robert D Schreiber. Science 2015
16

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens.
Jasreet Hundal, Beatriz M Carreno, Allegra A Petti, Gerald P Linette, Obi L Griffith, Elaine R Mardis, Malachi Griffith. Genome Med 2016
216
16

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
16

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy.
Diego Chowell, Luc G T Morris, Claud M Grigg, Jeffrey K Weber, Robert M Samstein, Vladimir Makarov, Fengshen Kuo, Sviatoslav M Kendall, David Requena, Nadeem Riaz,[...]. Science 2018
538
15

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
15

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
15

The Immune Landscape of Cancer.
Vésteinn Thorsson, David L Gibbs, Scott D Brown, Denise Wolf, Dante S Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F Gao, Christopher L Plaisier, James A Eddy,[...]. Immunity 2018
14

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.
Derin B Keskin, Annabelle J Anandappa, Jing Sun, Itay Tirosh, Nathan D Mathewson, Shuqiang Li, Giacomo Oliveira, Anita Giobbie-Hurder, Kristen Felt, Evisa Gjini,[...]. Nature 2019
630
13

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer.
Ugur Sahin, Evelyna Derhovanessian, Matthias Miller, Björn-Philipp Kloke, Petra Simon, Martin Löwer, Valesca Bukur, Arbel D Tadmor, Ulrich Luxemburger, Barbara Schrörs,[...]. Nature 2017
13

Genetic basis for clinical response to CTLA-4 blockade in melanoma.
Alexandra Snyder, Vladimir Makarov, Taha Merghoub, Jianda Yuan, Jesse M Zaretsky, Alexis Desrichard, Logan A Walsh, Michael A Postow, Phillip Wong, Teresa S Ho,[...]. N Engl J Med 2014
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
13

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
Eliezer M Van Allen, Diana Miao, Bastian Schilling, Sachet A Shukla, Christian Blank, Lisa Zimmer, Antje Sucker, Uwe Hillen, Marnix H Geukes Foppen, Simone M Goldinger,[...]. Science 2015
13

GSVA: gene set variation analysis for microarray and RNA-seq data.
Sonja Hänzelmann, Robert Castelo, Justin Guinney. BMC Bioinformatics 2013
13

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Kai Wang, Mingyao Li, Hakon Hakonarson. Nucleic Acids Res 2010
13

Near-optimal probabilistic RNA-seq quantification.
Nicolas L Bray, Harold Pimentel, Páll Melsted, Lior Pachter. Nat Biotechnol 2016
13

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis.
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir,[...]. Lancet Oncol 2017
506
12

Signatures of mutational processes in human cancer.
Ludmil B Alexandrov, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, Niccolò Bolli, Ake Borg, Anne-Lise Børresen-Dale,[...]. Nature 2013
12

xCell: digitally portraying the tissue cellular heterogeneity landscape.
Dvir Aran, Zicheng Hu, Atul J Butte. Genome Biol 2017
12

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
Freddie Bray, Jacques Ferlay, Isabelle Soerjomataram, Rebecca L Siegel, Lindsey A Torre, Ahmedin Jemal. CA Cancer J Clin 2018
11

HLA typing from RNA-Seq sequence reads.
Sebastian Boegel, Martin Löwer, Michael Schäfer, Thomas Bukur, Jos de Graaf, Valesca Boisguérin, Ozlem Türeci, Mustafa Diken, John C Castle, Ugur Sahin. Genome Med 2012
138
11

Derivation of HLA types from shotgun sequence datasets.
René L Warren, Gina Choe, Douglas J Freeman, Mauro Castellarin, Sarah Munro, Richard Moore, Robert A Holt. Genome Med 2012
115
11

Robust enumeration of cell subsets from tissue expression profiles.
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh. Nat Methods 2015
11

Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer.
Naiyer A Rizvi, Matthew D Hellmann, Alexandra Snyder, Pia Kvistborg, Vladimir Makarov, Jonathan J Havel, William Lee, Jianda Yuan, Phillip Wong, Teresa S Ho,[...]. Science 2015
11

MHC-II neoantigens shape tumour immunity and response to immunotherapy.
Elise Alspach, Danielle M Lussier, Alexander P Miceli, Ilya Kizhvatov, Michel DuPage, Adrienne M Luoma, Wei Meng, Cheryl F Lichti, Ekaterina Esaulova, Anthony N Vomund,[...]. Nature 2019
332
11

MuPeXI: prediction of neo-epitopes from tumor sequencing data.
Anne-Mette Bjerregaard, Morten Nielsen, Sine Reker Hadrup, Zoltan Szallasi, Aron Charles Eklund. Cancer Immunol Immunother 2017
100
10

IPD-IMGT/HLA Database.
James Robinson, Dominic J Barker, Xenia Georgiou, Michael A Cooper, Paul Flicek, Steven G E Marsh. Nucleic Acids Res 2020
993
10

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer.
Eric Tran, Paul F Robbins, Yong-Chen Lu, Todd D Prickett, Jared J Gartner, Li Jia, Anna Pasetto, Zhili Zheng, Satyajit Ray, Eric M Groh,[...]. N Engl J Med 2016
686
10

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy.
Razvan Cristescu, Robin Mogg, Mark Ayers, Andrew Albright, Erin Murphy, Jennifer Yearley, Xinwei Sher, Xiao Qiao Liu, Hongchao Lu, Michael Nebozhyn,[...]. Science 2018
10

Tumor Mutational Burden and Response Rate to PD-1 Inhibition.
Mark Yarchoan, Alexander Hopkins, Elizabeth M Jaffee. N Engl J Med 2017
10

The Molecular Signatures Database (MSigDB) hallmark gene set collection.
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, Pablo Tamayo. Cell Syst 2015
10

Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs.
Christopher T Saunders, Wendy S W Wong, Sajani Swamy, Jennifer Becq, Lisa J Murray, R Keira Cheetham. Bioinformatics 2012
993
10

Tumor mutational load predicts survival after immunotherapy across multiple cancer types.
Robert M Samstein, Chung-Han Lee, Alexander N Shoushtari, Matthew D Hellmann, Ronglai Shen, Yelena Y Janjigian, David A Barron, Ahmet Zehir, Emmet J Jordan, Antonio Omuro,[...]. Nat Genet 2019
10


Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.
F Favero, T Joshi, A M Marquard, N J Birkbak, M Krzystanek, Q Li, Z Szallasi, A C Eklund. Ann Oncol 2015
315
10

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.
Chao Xie, Zhen Xuan Yeo, Marie Wong, Jason Piper, Tao Long, Ewen F Kirkness, William H Biggs, Ken Bloom, Stephen Spellman, Cynthia Vierra-Green,[...]. Proc Natl Acad Sci U S A 2017
69
13


Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype.
Daehwan Kim, Joseph M Paggi, Chanhee Park, Christopher Bennett, Steven L Salzberg. Nat Biotechnol 2019
9

limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
9

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, Barbara Hill, Matthew L Meyerson, Rameen Beroukhim, Gad Getz. Genome Biol 2011
9

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing.
Daniel C Koboldt, Qunyuan Zhang, David E Larson, Dong Shen, Michael D McLellan, Ling Lin, Christopher A Miller, Elaine R Mardis, Li Ding, Richard K Wilson. Genome Res 2012
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
9

Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer.
Eric Tran, Simon Turcotte, Alena Gros, Paul F Robbins, Yong-Chen Lu, Mark E Dudley, John R Wunderlich, Robert P Somerville, Katherine Hogan, Christian S Hinrichs,[...]. Science 2014
9


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.