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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...protein (PICALM) LAP. (B) Split ends protein spen. (C) Ly-6 protein qvr. Note that 12 CV and 12 GF samples were subjected to PCR, but only nine CV and six GF samples were successfully sequenced. (D) Voltage-gated potassium channel protein Shab and leukocyte receptor member 8. Duan et al. 8 Genome Research...
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Research: SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
- Nicolae Sapoval,
- Medhat Mahmoud,
- Michael D. Jochum,
- Yunxi Liu,
- R.A. Leo Elworth,
- Qi Wang,
- Dreycey Albin,
- Huw A. Ogilvie,
- Michael D. Lee,
- Sonia Villapol,
- Kyle M. Hernandez,
- Irina Maljkovic Berry,
- Jonathan Foox,
- Afshin Beheshti,
- Krista Ternus,
- Kjersti M. Aagaard,
- David Posada,
- Christopher E. Mason,
- Fritz J. Sedlazeck,
- and Todd J. Treangen
Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
...-CoV-2. In this setting, sensitivity determines how well the detection tests can capture the diversity of all SARS-CoV-2 variants. Lack of sensitivity leads to an increase in false-negative qRT-PCR results, because two or more mismatches can result in increases in CT values and degradation in accuracy...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...Determining the impact of uncharacterized inversions in the human by droplet digital PCR Marta Puig1, Jon Lerga-Jaso1, Carla Giner-Delgado1, Sarai Pacheco1, David Izquierdo1, Alejandra Delprat1, Magdalena Gayà-Vidal2, Jack F. Regan3, George Karlin-Neumann3 and Mario Cáceres1,4 1Institut de...
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Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
- Ryan O'Hara,
- Enzo Tedone,
- Andrew Ludlow,
- Ejun Huang,
- Beatrice Arosio,
- Daniela Mari,
- and Jerry W. Shay
Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
...and therefore might be considered as a biomarker that mirrors alterations within the human body. Here, we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method, droplet digital mitochondrial DNA measurement (ddMDM), to measure mtDNA copy number not only from cell populations but also...
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Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
- Egor Dolzhenko,
- Joke J.F.A. van Vugt,
- Richard J. Shaw,
- Mitchell A. Bekritsky,
- Marka van Blitterswijk,
- Giuseppe Narzisi,
- Subramanian S. Ajay,
- Vani Rajan,
- Bryan R. Lajoie,
- Nathan H. Johnson,
- Zoya Kingsbury,
- Sean J. Humphray,
- Raymond D. Schellevis,
- William J. Brands,
- Matt Baker,
- Rosa Rademakers,
- Maarten Kooyman,
- Gijs H.P. Tazelaar,
- Michael A. van Es,
- Russell McLaughlin,
- William Sproviero,
- Aleksey Shatunov,
- Ashley Jones,
- Ahmad Al Khleifat,
- Alan Pittman,
- Sarah Morgan,
- Orla Hardiman,
- Ammar Al-Chalabi,
- Chris Shaw,
- Bradley Smith,
- Edmund J. Neo,
- Karen Morrison,
- Pamela J. Shaw,
- Catherine Reeves,
- Lara Winterkorn,
- Nancy S. Wexler,
- The US–Venezuela Collaborative Research Group,
- David E. Housman,
- Christopher W. Ng,
- Alina L. Li,
- Ryan J. Taft,
- Leonard H. van den Berg,
- David R. Bentley,
- Jan H. Veldink,
- and Michael A. Eberle
Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
...Detection of long repeat expansions from PCR-free whole- sequence data Egor Dolzhenko,1,18 Joke J.F.A. van Vugt,2,18 Richard J. Shaw,3,4 Mitchell A. Bekritsky,3 Marka van Blitterswijk,5 Giuseppe Narzisi,6 Subramanian S. Ajay,1 Vani Rajan,1 Bryan R. Lajoie,1 Nathan H. Johnson,1 Zoya Kingsbury,3 Sean...
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ARTICLE: A comparison of methods for RNA extraction from lymphocytes for RT-PCR.
- W Liedtke,
- L Battistini,
- C F Brosnan,
- and C S Raine
Genome Res. December 1994 4: 185-187
....T. Bolander, M.E. and Sarkar. G. 1993 . Stimulatory effect of potassium glutamate in PCR. PCR Methods Applic. 3 : 73 – 74 Genome Res Genome Research Genome Res. 1088-9051 Cold Spring Harbor Laboratory Press 7580904 ;4/3/185 7580904 185 4/3/185 ARTICLES ARTICLE ARTICLES A comparison of methods for RNA...
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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
...Application of microdroplet PCR for large-scale targeted bisulfite sequencing H. Kiyomi Komori 1 , Sarah A. LaMere 1 , Ali Torkamani 1 , G. Traver Hart 1 , Steve Kotsopoulos 2 , Jason Warner 2 , Michael L. Samuels 2...
ARTICLE: Rapid PCR site-directed mutagenesis.
- M P Weiner and
- G L Costa
Genome Res. December 1994 4: S131-S136
...134 PCR Methods and Applications ll|llllManual Supplement TABLE 2 The Genetic Code Abbreviation (letters) Amino acid 1 3 Codon a Alanine A Ala (GCN) Arginine R Arg (CGN) or (AGR) Asparagine N Asn (AAY) Aspartic acid D Asp (GAY) Cysteine C Cys (TGY) Glutamine Q Gln (CAR) Glutamic acid E Glu (GAR...
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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
...techniques including error-prone PCR and saturated mutations to construct and display antibody 56 libraries in phage or yeast (Hawkins et al. 1992; Chao et al. 2006). In contrast, continuous evolution 57 4 requires a hypermutation system that induces mutagenesis autonomously in growing cells (Molina et 58 al...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
..., and rotifers. We downloaded homologous genes from selected plants and insects and used Escherichia coli glutamate-5-semialdehyde dehydrogenase (PorA) as outgroups to construct a phylogenetic tree of P5CS (Fig. 5; Supplemental Fig. S20). The phylogenetic tree of P5CS across species indicates that the P5CS genes...
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