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Method: Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
- Zhaozhao Zhao,
- Qiushi Xu,
- Ran Wei,
- Weixu Wang,
- Dong Ding,
- Yu Yang,
- Jun Yao,
- Liye Zhang,
- Yue-Qing Hu,
- Gang Wei,
- and Ting Ni
Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
...information, and considers most of the interference factors to improve the identification of IpA events (Supplemental Fig. S15). We also compared IPAFinder with APAlyzer, which analyzes intronic polyadenylation by using RNA-seq data based on known poly(A) sites (such as those annotated in the Poly...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...first (She et al. 2009).To collect transcriptome evidence, we downloaded the RNA-seq data from NCBI's BioProject database (https://www.ncbi.nlm.nih.gov/bioproject/) under accession number PRJNA230881 (tissues include whole embryo, adult gonad, brain, tail, and pooled organs) and mapped them...
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Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
- Steffen Erkelenz,
- Stephan Theiss,
- Wolfgang Kaisers,
- Johannes Ptok,
- Lara Walotka,
- Lisa Müller,
- Frank Hillebrand,
- Anna-Lena Brillen,
- Michael Sladek,
- and Heiner Schaal
Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
...Ranking noncanonical 5′ splice site usage by -wide RNA-seq analysis and splicing reporter assays Steffen Erkelenz1,4,5, Stephan Theiss2,4, Wolfgang Kaisers3, Johannes Ptok1, Lara Walotka1, Lisa Müller1, Frank Hillebrand1, Anna-Lena Brillen1, Michael Sladek1 and Heiner Schaal1 1Institute of Virology...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
.... S10A–C). The lack of reactivity among the monoclonal antibodies highlights the possibility of false-negative results with ELISA-based screening methods since MMR-82 was obviously a positive binder to MeV-F.Germline-specific repertoire analysis of antibody sequences confirm B cell class and allows...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...short-read RNA-seq as a modularized software that contains chimeric read extraction, fusion transcripts identification, expression quantification, gene fusion annotation, and interactive visualization. To benchmark existing tools, we collected or generated comprehensive simulation data sets to reflect...
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Method: Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
- Samuel T. Horsfield,
- Basil C.T. Fok,
- Yuhan Fu,
- Paul Turner,
- John A. Lees,
- and Nicholas J. Croucher
Genome Res. April 2025 35: 1025-1040; Published in Advance March 4, 2025, doi:10.1101/gr.279435.124
...,000 bases (targeting 20 kb of 2.2 Mb pneumococcal (∼ 1%) in a 0.01 dilution) in a mixed sample. Taken together, these results indicate that targeting CBL for the identification and serotyping of S. pneumoniae is a viable alternative to whole- enrichment in complex microbial samples.View larger version...
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Method: RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens
- Nuri A. Temiz,
- Branden S. Moriarity,
- Natalie K. Wolf,
- Jesse D. Riordan,
- Adam J. Dupuy,
- David A. Largaespada,
- and Aaron L. Sarver
Genome Res. January 2016 26: 119-129; Published in Advance November 9, 2015, doi:10.1101/gr.188649.114
...to knock down genes in cells utilizing small interfering RNA. While unexpected, this functionality is not surprising due to the harnessing of evolutionary tumor selection in forward genetic screens. Pth,Ptprd, andTgfbr1were identifiedonlyafterRNA-seq-based analysis approaches described here, and each gene...
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Method: MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq
- Jonathon T. Hill,
- Bradley L. Demarest,
- Brent W. Bisgrove,
- Bushra Gorsi,
- Yi-Chu Su,
- and H. Joseph Yost
Genome Res. April 2013 23: 687-697; Published in Advance January 8, 2013, doi:10.1101/gr.146936.112
...it to map two novel ENU-induced cardiovascular mutants, with mutations found in the ctr9 and cds2 genes. MMAPPR can be directly applied to other model organisms, such as Drosophila and Caenorhabditis elegans , that are amenable to both forward genetic screens and pooled RNA-seq experiments. Thus...
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Research: RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas
- Zhao-Shi Bao,
- Hui-Min Chen,
- Ming-Yu Yang,
- Chuan-Bao Zhang,
- Kai Yu,
- Wan-Lu Ye,
- Bo-Qiang Hu,
- Wei Yan,
- Wei Zhang,
- Johnny Akers,
- Valya Ramakrishnan,
- Jie Li,
- Bob Carter,
- Yan-Wei Liu,
- Hui-Min Hu,
- Zheng Wang,
- Ming-Yang Li,
- Kun Yao,
- Xiao-Guang Qiu,
- Chun-Sheng Kang,
- Yong-Ping You,
- Xiao-Long Fan,
- Wei Sonya Song,
- Rui-Qiang Li,
- Xiao-Dong Su,
- Clark C. Chen,
- and Tao Jiang
Genome Res. November 2014 24: 1765-1773; Published in Advance August 18, 2014, doi:10.1101/gr.165126.113
...RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas Zhao-Shi Bao 1 , 2 , 3 , 13 , Hui-Min Chen 4 , 13 , Ming-Yu Yang 4 , 13 , Chuan-Bao Zhang 1 , 2 , 3...
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Perspective: Tagmentation-based single-cell genomics
- Andrew C. Adey
Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
...and PCR) can achieve relatively high cell throughput, other strategies have been developed that incorporate additional tiers of indexing to increase throughput to even greater levels using ligation-based index addition, similar to what was developed previously for single-cell RNA-seq (Rosenberg et al...

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