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  1. Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
    • Merel Stemerdink,
    • Tabea Riepe,
    • Nick Zomer,
    • Renee Salz,
    • Michael Kwint,
    • Jaap Oostrik,
    • Raoul Timmermans,
    • Barbara Ferrari,
    • Stefano Ferrari,
    • Alfredo Dueñas Rey,
    • Emma Delanote,
    • Suzanne E. de Bruijn,
    • Hannie Kremer,
    • Susanne Roosing,
    • Frauke Coppieters,
    • Alexander Hoischen,
    • Frans P.M. Cremers,
    • Peter A.C. ‘t Hoen,
    • Erwin van Wijk,
    • and Erik de Vrieze
    Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
    ...demonstrated the utility of this approach to capture cDNA as well. By using three detection sequences targeting either 5′—middle and 3′ sites of the longest known transcript encoding usherin isoform B, we were able to enrich for USH2A transcripts, as evidenced by the qPCR results (Supplemental Table S4...
  2. Method: Accurate and efficient detection of gene fusions from RNA sequencing data
    • Sebastian Uhrig,
    • Julia Ellermann,
    • Tatjana Walther,
    • Pauline Burkhardt,
    • Martina Fröhlich,
    • Barbara Hutter,
    • Umut H. Toprak,
    • Olaf Neumann,
    • Albrecht Stenzinger,
    • Claudia Scholl,
    • Stefan Fröhling,
    • and Benedikt Brors
    Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
    ...denaturation of 5 min; 35 cycles or denaturation of 1 min at 95°C, annealing of 1 min at 60°C, and elongation of 1 min at 72°C; and final elongation of 2 min. The PCR products were separated electrophoretically in 2% agarose gels and visualized. Bands at the expected height were cut out and purified...
    OPEN ACCESS ARTICLE
  3. Method: SvABA: genome-wide detection of structural variants and indels by local assembly
    • Jeremiah A. Wala,
    • Pratiti Bandopadhayay,
    • Noah F. Greenwald,
    • Ryan O'Rourke,
    • Ted Sharpe,
    • Chip Stewart,
    • Steve Schumacher,
    • Yilong Li,
    • Joachim Weischenfeldt,
    • Xiaotong Yao,
    • Chad Nusbaum,
    • Peter Campbell,
    • Gad Getz,
    • Matthew Meyerson,
    • Cheng-Zhong Zhang,
    • Marcin Imielinski,
    • and Rameen Beroukhim
    Genome Res. April 2018 28: 581-591; Published in Advance March 13, 2018, doi:10.1101/gr.221028.117
    ....8% of variants being rediscovered in the 250-base reads. When comparing SvABA and DISCOVAR calls from the same data set (250-base PCR-free reads), SvABA detected 69.9% of DISCOVAR variants; conversely, 76.3% of SvABA variants were present in the DISCOVAR results. Relaxing the read-support threshold...
  4. Method: GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
    • Daniel L. Cameron,
    • Jan Schröder,
    • Jocelyn Sietsma Penington,
    • Hongdo Do,
    • Ramyar Molania,
    • Alexander Dobrovic,
    • Terence P. Speed,
    • and Anthony T. Papenfuss
    Genome Res. December 2017 27: 2050-2060; Published in Advance November 2, 2017, doi:10.1101/gr.222109.117
    ...a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient -wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler...
    OPEN ACCESS ARTICLE
  5. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...within that droplet. The absolute number of target molecules is calculated using Poisson statistics, bypassing the need for standard curves and making ddPCR advantageous for low-abundance targets or small fold-changes that may fall below the detection limits of qRT-PCR. Because each amplification occurs...
    OPEN ACCESS ARTICLE
  6. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ...-Vec does not induce demethylation of the target site without the presence of site-specific gRNA. In contrast, cells transfected with Dem6A-Vec expressing the gRNA targeting the m6A:2886 site of EEF2 exhibited a notable upregulation of the produced PCR product, highlighting a successful demethylation...
  7. Resource: Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Brian J. Haas,
    • Dirk Gevers,
    • Ashlee M. Earl,
    • Mike Feldgarden,
    • Doyle V. Ward,
    • Georgia Giannoukos,
    • Dawn Ciulla,
    • Diana Tabbaa,
    • Sarah K. Highlander,
    • Erica Sodergren,
    • Barbara Methé,
    • Todd Z. DeSantis,
    • The Human Microbiome Consortium,
    • Joseph F. Petrosino,
    • Rob Knight,
    • and Bruce W. Birren
    Genome Res. March 2011 21: 494-504; Published in Advance January 6, 2011, doi:10.1101/gr.112730.110
    ...PCR cycle. If this aborted extension product anneals to and primes DNA synthesis from an improper template, a chimeric molecule is formed. Genome Research 495 www..org Chimeric 16S rRNA detection using chimera slayer divergence to flag at least 50% of the chimeric sequences as chimeras...
    OPEN ACCESS ARTICLE
  8. Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
    • Judith Arres,
    • Santosh Elavalli,
    • Shalini Behl,
    • Daniel Matias Sanchez,
    • Ayesha Al Ali,
    • Abdelrahman Ahmed Yehia Abdelaziz Saad,
    • Azza Attia,
    • Cyla Minas,
    • Sharika Pariyachery,
    • Shariq Ahmed,
    • Fatmah Aldhuhoori,
    • Nitu Thulasidharan,
    • Gurunath Katagi,
    • Omar Soliman,
    • Shilp Purohit,
    • Vinay Kusuma,
    • Raony Cardenas,
    • Thyago Cardoso,
    • Luis F. Paulin,
    • Philippe Sanio,
    • Joseph Mafofo,
    • Haiguo Wu,
    • Val Zvereff,
    • Albarah El-Khani,
    • Fahed Al Marzooqi,
    • Tiago R. Magalhães,
    • Fritz J. Sedlazeck,
    • and Javier Quilez
    Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
    ...-characterized reference samples with 11 clinical variants representing nine different genetic diseases. To enable this, we have implemented a production-ready pipeline including SNV, indel, STR, SV, and CNV detection, alongside reporting key summary metrics to ensure high-quality data at the production sequencing level...
  9. Method: Application of microdroplet PCR for large-scale targeted bisulfite sequencing
    • H. Kiyomi Komori,
    • Sarah A. LaMere,
    • Ali Torkamani,
    • G. Traver Hart,
    • Steve Kotsopoulos,
    • Jason Warner,
    • Michael L. Samuels,
    • Jeff Olson,
    • Steven R. Head,
    • Phillip Ordoukhanian,
    • Pauline L. Lee,
    • Darren R. Link,
    • and Daniel R. Salomon
    Genome Res. October 2011 21: 1738-1745; Published in Advance July 14, 2011, doi:10.1101/gr.116863.110
    ...of the ampliconswas observed (Supplemental Fig. S3). This is likely due to the nature of the shearing protocol employed prior to sequencing adapter ligation. To resolve the uneven distribution of sequencing reads across the amplicons, the microdroplet PCR-amplified product was concatenated prior to shearing (see...
  10. Method: Restoring the potency of neutralizing antibody via guided hypermutation with hyper-antibody editor
    • Yuhong Wang,
    • Yuefeng Guo,
    • Qiuyu Lu,
    • Xinyi Liu,
    • Haoqi Xu,
    • Jiayi Chen,
    • Ruiqi Pi,
    • Shaopeng Yuan,
    • Ziting Yang,
    • Rusen Lu,
    • Fei-Long Meng,
    • Tingting Gan,
    • and Jiazhi Hu
    Genome Res. March 19, 2026 gr.281396.125; Published in Advance March 19, 2026, doi:10.1101/gr.281396.125
    ...cycles was performed with TranStart Fastpfu high-335 fidelity DNA polymerase, and a second round of 15 cycles was used to add sequencing adaptor and 336 barcodes. The final PCR products were gel-purified, quantified by DeNovix, and sequenced by PE150 337 on the NovaSeq 6000 platform (GENEWIZ). 338 DNA...
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