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(3) Set of observed effect mutations: We collected 36,317 mutants in 3,790 proteins with experimentally observed effect.
(1) Set of disease-related + observed effect mutations: We collected 1,105 human nsSNPs (from 217 proteins) that were annotated to be both disease-causing and functionally non-neutral.
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To improve the chances of detecting a mosaic mutation, we collected as many tissue types as possible from each individual and analysed these by a number of different techniques (DHPLC, MPS and MLPA) to increase sensitivity above dideoxy sequencing.
To identify the gene affected by the swd mutation, we collected 2500 swd p75fm mutants and isolated genomic DNA for bulked segregant analysis and high-resolution meiotic mapping as described (Yee et al., 2007).
From the COSMIC data, we collected mutations and their corresponding mutated genes and chromosomes to represent the genetic characteristics of each patient.
To study the association between the number of shared mutations and tumor characteristics we collected relevant data from the histopathology reports, including data on tumor type (lobular or ductal), size, grade (according to Elston-Ellis), lymph node status, estrogen and progesterone receptor (ER and PR) status, presence of HER2 amplification and proliferation (Ki-67/MIB1).
We collected 94,755 transition mutations that occurred in ancestral CpG or GpC dinucleotides.
To compare the mutation rates between different chromosomes, we collect orthologous sequence alignments of intronic regions from macro-chromosomes and Z chromosomes.
Information on adherence to therapy and viral resistance mutations was not collected, and thus we were unable to adjust for these potential confounders.
A total of 51 buccal swabs from patients probably with deafness-related mutations were collected and analyzed.
As soon as more information about warnings and mutations are collected, the incremental strategy can be updated aiming at improving its capability, contributing to reduce the cost of static analysis/mutation testing and guiding the reviewer to firstly analyze warnings more probably to lead to fault detection and quality improvement before to conduct mutation testing.
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