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Method: Automated interpretable artificial intelligence genomic prediction with AlGP
- Lei Wei,
- Ziqin Jiang,
- Baoliang Fan,
- Yidan Yan,
- Zhenqiang Xu,
- Xiaoxiang Hu,
- and Yuzhe Wang
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
...DNA variants to phenotypes, spans the entire central dogma of molecular biology; incorporates various nongenetic factors, such as environmental influences (Yao et al. 2025); and is one of the most challenging tasks in biological prediction. Genomic selection (GS) is the most advanced methodology...
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Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
- Leszek P. Pryszcz,
- Gregor Diensthuber,
- Laia Llovera,
- Rebeca Medina,
- Anna Delgado-Tejedor,
- Luca Cozzuto,
- Julia Ponomarenko,
- and Eva Maria Novoa
Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
...for polymerase chain reaction (PCR) amplification and cDNA synthesis steps, thus preserving the native state of RNA molecules and providing a less biased and comprehensive view of the transcriptome (Workman et al. 2020).However, key challenges persist, such as the lack of commercial barcoding kits...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...Manual workflowPCR amplification. The PCR mastermix (Ultra II Q5 mastermix, and 1 µM sequencing platform-compatible forward and reverse primers [Solexa 1GA and Solexa 1 GB]) was added to each library sample. A PCR program (initial denaturation for 30 sec at 98°C; 12 cycles of denaturation for 10 sec at 98°C...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...Biosciences). After clonal expansion, genomic DNA was extracted from each clone using the SimplePrep reagent for DNA (Takara, #9180) and screened for mutations by quantitative PCR (qPCR). Candidate clones were further verified for mutations by Sanger sequencing.RNA interferenceSmall interfering RNA (si...
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Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
- Hongke Peng,
- Jafar S. Jabbari,
- Luyi Tian,
- Changqing Wang,
- Yupei You,
- Chong Chyn Chua,
- Natasha S. Anstee,
- Noorul Amin,
- Andrew H. Wei,
- Nadia M. Davidson,
- Andrew W. Roberts,
- David C.S. Huang,
- Matthew E. Ritchie,
- and Rachel Thijssen
Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
...expression and 10x Genomics multiome combines transcriptome with chromatin accessibility data (Stoeckius et al. 2017). Our single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method enables the capture of multiple transcripts from preindexed and stored cDNA independent of the 10x Genomics kit...
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Method: 3′-end ligation sequencing is a sensitive method to detect DNA nicks at potential sites of off-target activity induced by prime editors
- Jacob Stewart-Ornstein,
- Matthew J. Irby,
- Marina K. Lilieholm,
- Dylan Laprise,
- Maria D. Collier,
- Thomas Aunins,
- Dewi Harjanto,
- Aaron N. Chang,
- Deepak Reyon,
- and Jeremy S. Duffield
Genome Res. September 2025 35: 2064-2075; Published in Advance August 5, 2025, doi:10.1101/gr.280164.124
...ng of genomic DNA as input for the initial amplification. The first PCR consisted of 15 cycles using a target-specific primer and the Illumina P5 primer, followed by a 1.0× SPRIselect bead cleanup. The second PCR used a nested target-specific forward primer incorporating a 5′ Illumina Read 2 sequence...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...before (DAP-seq) and after PCR amplification (ampDAP-seq), where the amplification depletes the library of DNA methylation. MBD5 and MBD6 showed sequence enrichment, but only for DAP-seq, where DNA methylation was present, and with binding site profiles that closely match those identified by Ch...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
....Here, we present -wide Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), a high-accuracy, PCR-free, -wide cfDNA sequencing method based on a combination of RCA, and consensus calling of long-read nanopore sequences. The concatemeric RCA products ensure the physical...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...were prepared with a starting amount of 300 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay kit, in a Qubit 2.0 Fluorometer (Life Technologies). All libraries from the two...
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Method: An optimized toolkit for high-molecular-weight DNA extraction and ultra-long-read nanopore sequencing using glass beads and hexamminecobalt(III) chloride
- Inswasti Cahyani,
- John Tyson,
- Nadine Holmes,
- Josh Quick,
- Chris Moore,
- Nick Loman,
- and Matthew Loose
Genome Res. May 2025 35: 1154-1166; Published in Advance March 24, 2025, doi:10.1101/gr.279943.124
...process and during the extraction methods to maintain UHMW DNA. Early experiments pioneering UL sequencing used the transposase-based rapid kit (ONT, e.g., RAD004) to obtain reads with an N50 > 100 kb (Jain et al. 2018a). This method eliminated the need for DNA shearing before library preparation. However...
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