SearchResearch
Beta
Hello! Describe your research question and I'll help you find matching datasets across 2,944 studies from AnVIL, BDC, CRDC, and KFDRC.

Comprehensive Analysis of the Immunogenomics of Triple Negative Breast Cancer Brain Metastases from LCCC1419

Request Access

The Sequence Alignment/Map format and SAMtools

Heng Li, R. Handsaker, Alec Wysoker, et al. (2009). Bioinformatics. Cited 54,792 times. https://doi.org/10.1093/bioinformatics/btp352

GSVA: gene set variation analysis for microarray and RNA-Seq data

Sonja Hänzelmann, R. Castelo, J. Guinney. (2013). BMC Bioinformatics. Cited 11,195 times. https://doi.org/10.1186/1471-2105-14-7

Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

Rob Patro, Geet Duggal, M. Love, et al. (2017). Nature methods. Cited 8,162 times. https://doi.org/10.1038/nmeth.4197

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love, Wolfgang Huber, Simon Anders. (2014). Genome Biology. Cited 6,870 times. https://doi.org/10.1186/s13059-014-0550-8

Robust enumeration of cell subsets from tissue expression profiles

Aaron M. Newman, C. Liu, M. Green, et al. (2015). Nature methods. Cited 4,788 times. https://doi.org/10.1038/nmeth.3337

Determining cell-type abundance and expression from bulk tissues with digital cytometry

Aaron M. Newman, C. Steen, C. Liu, et al. (2019). Nature biotechnology. Cited 3,280 times. https://doi.org/10.1038/s41587-019-0114-2

GENCODE reference annotation for the human and mouse genomes

A. Frankish, M. Diekhans, Anne-Maud Ferreira, et al. (2018). Nucleic Acids Research. Cited 2,646 times. https://doi.org/10.1093/nar/gky955

MiXCR: software for comprehensive adaptive immunity profiling

D. A. Bolotin, S. Poslavsky, Igor Mitrophanov, et al. (2015). Nature Methods. Cited 1,465 times. https://doi.org/10.1038/nmeth.3364

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

V. Jurtz, S. Paul, M. Andreatta, et al. (2017). The Journal of Immunology. Cited 1,062 times. https://doi.org/10.4049/jimmunol.1700893

Comprehensive assessment of T-cell receptor beta-chain diversity in alphabeta T cells.

H. Robins, P. Campregher, S. Srivastava, et al. (2009). Blood. Cited 1,049 times. https://doi.org/10.1182/blood-2009-04-217604

Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities between Tumors and Wounds

Howard Y. Chang, Julie B. Sneddon, Ash A. Alizadeh, et al. (2004). PLoS Biology. Cited 973 times. https://doi.org/10.1371/journal.pbio.0020007

Using synthetic templates to design an unbiased multiplex PCR assay

C. Carlson, R. Emerson, A. Sherwood, et al. (2013). Nature Communications. Cited 555 times. https://doi.org/10.1038/ncomms3680

heatmaply: an R package for creating interactive cluster heatmaps for online publishing

Tal Galili, Alan O'Callaghan, J. Sidi, et al. (2017). Bioinformatics. Cited 490 times. https://doi.org/10.1093/bioinformatics/btx657

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.

M. Rajasagi, S. Shukla, E. Fritsch, et al. (2014). Blood. Cited 315 times. https://doi.org/10.1182/blood-2014-04-567933

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

Wei Zhao, Xiaping He, K. Hoadley, et al. (2014). BMC Genomics. Cited 294 times. https://doi.org/10.1186/1471-2164-15-419

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

Yu Bai, M. Ni, Blerta Cooper, et al. (2014). BMC Genomics. Cited 105 times. https://doi.org/10.1186/1471-2164-15-325

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer

Lisle E. Mose, Sara R. Selitsky, L. Bixby, et al. (2016). Bioinformatics. Cited 61 times. https://doi.org/10.1093/bioinformatics/btw526

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

A. Picornell, I. Echavarría, E. Alvarez, et al. (2019). BMC Genomics. Cited 44 times. https://doi.org/10.1186/s12864-019-5849-0

Improved T-cell Receptor Diversity Estimates Associate with Survival and Response to Anti–PD-1 Therapy

Dante S. Bortone, M. Woodcock, J. Parker, et al. (2020). Cancer Immunology Research. Cited 17 times. https://doi.org/10.1158/2326-6066.CIR-20-0398