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Method: Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated
- Sindri Emmanúel Antonsson and
- Páll Melsted
Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
...this for scRNA-seq data sets. We compare eight widely used methods used for batch correction of scRNA-seq data sets. We present a novel approach to measure the degree to which the methods alter the data in the process of batch correction, both at the fine scale, comparing distances between cells, as well...
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Method: Sequence-based correction of barcode bias in massively parallel reporter assays
- Dongwon Lee,
- Ashish Kapoor,
- Changhee Lee,
- Michael Mudgett,
- Michael A. Beer,
- and Aravinda Chakravarti
Genome Res. September 2021 31: 1638-1645; Published in Advance July 20, 2021, doi:10.1101/gr.268599.120
...upstream or downstream from a reporter gene tagged by unique DNA sequences. However, tag sequences may themselves affect reporter gene expression and lead to major potential biases in the measured cis-regulatory activity. Here, we present a sequence-based method for correcting tag-sequence-specific effects...
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Method: A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics
- Justin Lakkis,
- David Wang,
- Yuanchao Zhang,
- Gang Hu,
- Kui Wang,
- Huize Pan,
- Lyle Ungar,
- Muredach P. Reilly,
- Xiangjie Li,
- and Mingyao Li
Genome Res. October 2021 31: 1753-1766; Published in Advance May 25, 2021, doi:10.1101/gr.271874.120
..., batch effects are still present in the gene expression space, leaving downstream gene-level analysis susceptible to batch effects. Recent studies have shown that batch effect correction in the gene expression space is much harder than in the embedding space. Methods such as Seurat 3.0 rely on the mutual...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...The aberrant epi of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory Varsha Poondi Krishnan1, Barbara Morone1, Shir Toubiana2, Monika Krzak3,6, Salvatore Fioriniello1, Floriana Della Ragione1...
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Method: Analysis and correction of crosstalk effects in pathway analysis
- Michele Donato,
- Zhonghui Xu,
- Alin Tomoiaga,
- James G. Granneman,
- Robert G. MacKenzie,
- Riyue Bao,
- Nandor Gabor Than,
- Peter H. Westfall,
- Roberto Romero,
- and Sorin Draghici
Genome Res. November 2013 23: 1885-1893; Published in Advance August 9, 2013, doi:10.1101/gr.153551.112
...statistically significant when the crosstalk effects of other pathways are removed. We describe a technique able to detect, quantify, and correct crosstalk effects, as well as identify independent functional modules. We assessed this novel approach on data from four experiments involving three phenotypes...
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Method: Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
- Sara Goodwin,
- James Gurtowski,
- Scott Ethe-Sayers,
- Panchajanya Deshpande,
- Michael C. Schatz,
- and W. Richard McCombie
Genome Res. November 2015 25: 1750-1756; Published in Advance October 7, 2015, doi:10.1101/gr.191395.115
...Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic Sara Goodwin,1 James Gurtowski,1 Scott Ethe-Sayers, Panchajanya Deshpande, Michael C. Schatz, and W. Richard McCombie Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA Monitoring...
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CORRECTION: Correction Genome Res. June 1, 1997 7: 661

...1549-5469 1088-9051 genome;7/6/661 Correction Correction Genome Research 7: 434–440 (1997) A linkage map of the rat derived from three F2 crosses Marie-Thérèse Bihoreau, Dominique Gauguier, Norihiro Kato, Gina Hyne, Klaus Lindpaintner, John P. Rapp, Michael R. James, and G. Mark Lathrop...
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Method: Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac
- Fei Xie,
- Lin Ye,
- Judy C. Chang,
- Ashley I. Beyer,
- Jiaming Wang,
- Marcus O. Muench,
- and Yuet Wai Kan
Genome Res. September 2014 24: 1526-1533; Published in Advance August 5, 2014, doi:10.1101/gr.173427.114
...Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac Fei Xie 1 , Lin Ye 1 , Judy C. Chang 1 , Ashley I. Beyer 2 , Jiaming Wang 1 , 3 , Marcus O. Muench 2 , 3...
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Resource: ECHO: A reference-free short-read error correction algorithm
- Wei-Chun Kao,
- Andrew H. Chan,
- and Yun S. Song
Genome Res. July 2011 21: 1181-1192; Published in Advance April 11, 2011, doi:10.1101/gr.111351.110
...ECHO: A reference-free short-read error correction algorithm Wei-Chun Kao 1 , Andrew H. Chan 1 and Yun S. Song 1 , 2 , 3 1Computer Science Division, University of California, Berkeley, California 94721, USA; 2Department...
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ERRATUM: Correction for Volume 15, p. 1620 Genome Res. February 2006 16: 304

...genome;16/2/304 1088-9051 Correction for Volume 15, p. 1620 Correction for Volume 15, p. 1620 Genome Research 15: 1620–1631 (2005) Genomics of the fungal kingdom: Insights into eukaryotic biology James E. Galagan, Matthew R. Henn, Li-Jun Ma, Christina A. Cuomo, and Bruce Birren The authors wish...

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