Literature DB >> 28448070

How to deduplicate PCR.

Vivien Marx1.   

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Year:  2017        PMID： 28448070     DOI： 10.1038/nmeth.4268

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  7 in total

1.  Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation.

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2.  Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR.

Authors:  Brooks E Miner; Reinhard J Stöger; Alice F Burden; Charles D Laird; R Scott Hansen
Journal:  Nucleic Acids Res       Date:  2004-09-30       Impact factor: 16.971

3.  Counting absolute numbers of molecules using unique molecular identifiers.

Authors:  Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Martin Enge; Sten Linnarsson; Jussi Taipale
Journal:  Nat Methods       Date:  2011-11-20       Impact factor: 28.547

4.  Detection and quantification of rare mutations with massively parallel sequencing.

Authors:  Isaac Kinde; Jian Wu; Nick Papadopoulos; Kenneth W Kinzler; Bert Vogelstein
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-17       Impact factor: 11.205

5.  Towards error-free profiling of immune repertoires.

Authors:  Mikhail Shugay; Olga V Britanova; Ekaterina M Merzlyak; Maria A Turchaninova; Ilgar Z Mamedov; Timur R Tuganbaev; Dmitriy A Bolotin; Dmitry B Staroverov; Ekaterina V Putintseva; Karla Plevova; Carsten Linnemann; Dmitriy Shagin; Sarka Pospisilova; Sergey Lukyanov; Ton N Schumacher; Dmitriy M Chudakov
Journal:  Nat Methods       Date:  2014-05-04       Impact factor: 28.547

6.  UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.

Authors:  Tom Smith; Andreas Heger; Ian Sudbery
Journal:  Genome Res       Date:  2017-01-18       Impact factor: 9.043

7.  Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches.

Authors:  Mark T W Ebbert; Mark E Wadsworth; Lyndsay A Staley; Kaitlyn L Hoyt; Brandon Pickett; Justin Miller; John Duce; John S K Kauwe; Perry G Ridge
Journal:  BMC Bioinformatics       Date:  2016-07-25       Impact factor: 3.169
  7 in total
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1.  Accurate Prediction of Protein Sequences for Proteogenomics Data Integration.

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Journal:  Methods Mol Biol       Date:  2022

Review 2.  Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.

Authors:  Daniel B Sloan; Amanda K Broz; Joel Sharbrough; Zhiqiang Wu
Journal:  Trends Biotechnol       Date:  2018-03-14       Impact factor: 19.536

3.  The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules.

Authors:  Taisaku Ogawa; Kirill Kryukov; Tadashi Imanishi; Katsuyuki Shiroguchi
Journal:  Sci Rep       Date:  2017-10-19       Impact factor: 4.379

4.  Systematic comparison of somatic variant calling performance among different sequencing depth and mutation frequency.

Authors:  Zixi Chen; Yuchen Yuan; Xiaoshi Chen; Jiayun Chen; Shudai Lin; Xingsong Li; Hongli Du
Journal:  Sci Rep       Date:  2020-02-26       Impact factor: 4.379

5.  Corrigendum: Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.

Authors: 
Journal:  Nat Methods       Date:  2018-02-28       Impact factor: 28.547

6.  Replicate sequencing libraries are important for quantification of allelic imbalance.

Authors:  Asia Mendelevich; Svetlana Vinogradova; Saumya Gupta; Andrey A Mironov; Shamil R Sunyaev; Alexander A Gimelbrant
Journal:  Nat Commun       Date:  2021-06-07       Impact factor: 14.919

7.  A novel virtual barcode strategy for accurate panel-wide variant calling in circulating tumor DNA.

Authors:  Leilei Wu; Qinfang Deng; Ze Xu; Songwen Zhou; Chao Li; Yi-Xue Li
Journal:  BMC Bioinformatics       Date:  2020-04-03       Impact factor: 3.169

8.  Eomes broadens the scope of CD8 T-cell memory by inhibiting apoptosis in cells of low affinity.

Authors:  Inga Kavazović; Hongya Han; Giulia Balzaretti; Erik Slinger; Niels A W Lemmermann; Anja Ten Brinke; Doron Merkler; Jan Koster; Yenan T Bryceson; Niek de Vries; Stipan Jonjić; Paul L Klarenbeek; Bojan Polić; Eric Eldering; Felix M Wensveen
Journal:  PLoS Biol       Date:  2020-03-17       Impact factor: 8.029

9.  Spatio-temporal dynamics of intra-host variability in SARS-CoV-2 genomes.

Authors:  Ankit K Pathak; Gyan Prakash Mishra; Bharathram Uppili; Safal Walia; Saman Fatihi; Tahseen Abbas; Sofia Banu; Arup Ghosh; Amol Kanampalliwar; Atimukta Jha; Sana Fatma; Shifu Aggarwal; Mahesh Shanker Dhar; Robin Marwal; Venkatraman Srinivasan Radhakrishnan; Kalaiarasan Ponnusamy; Sandhya Kabra; Partha Rakshit; Rahul C Bhoyar; Abhinav Jain; Mohit Kumar Divakar; Mohamed Imran; Mohammed Faruq; Divya Tej Sowpati; Lipi Thukral; Sunil K Raghav; Mitali Mukerji
Journal:  Nucleic Acids Res       Date:  2022-02-22       Impact factor: 16.971
  9 in total

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