acronym.tex

% tex file for Glossaries and Acronyms
% Glossaries and Acronyms won't apear in the list until used
% Maintained by Xing Zhao@CUHKSZ



% Common Molecular Biology Acronyms
\newacronym{dna}{DNA}{Deoxyribonucleic Acid}
\newacronym{rna}{RNA}{Ribonucleic Acid}
\newacronym{lncrna}{lncRNA}{long non-coding RNA}
\newacronym{polya}{poly(A)}{Polyadenylation}
\newacronym{gdna}{gDNA}{Genomic DNA}
\newacronym{cpg}{CpG}{Cytosine-guanine}
\newacronym{mirna}{miRNA}{microRNA}
\newacronym{rrna}{rRNA}{Ribosomal RNA}
\newacronym{mtrna}{mt-RNA}{Mitochondrial RNA}
\newacronym{mtmRNA}{mt-mRNA}{Mitochondrial messenger RNA}
\newacronym{cdna}{cDNA}{Complementary DNA}



% General Sequencing Acronyms
\newacronym{wgs}{WGS}{Whole Genome Sequencing}
\newacronym{rrbs}{RRBS}{Reduced Representation Bisulfite Sequencing}
\newacronym{wgbs}{WGBS}{Whole Genome Bisulfite Sequencing}
\newacronym{ngs}{NGS}{Next-Generation Sequencing}
\newacronym{rnaseq}{RNA-Seq}{RNA Sequencing}
\newacronym{scrnaseq}{scRNA-Seq}{single cell RNA Sequencing}



% Third Generation Sequencing (3GS)
\newacronym{3gs}{3GS}{Third Generation Sequencing}
\newacronym{pacbio}{PacBio}{Pacific Biosciences}
\newacronym{smrt}{SMRT}{Single Molecule Real-Time}
\newacronym{clr}{CLR}{Continuous Long Reads}
\newacronym{ccs}{CCS}{Circular Consensus Sequencing}
\newacronym{hgap}{HGAP}{Hierarchical Genome Assembly Process}
\newacronym{zmw}{ZMW}{Zero Mode Waveguide}
\newacronym{lrs}{LRS}{Long Read Sequencing}
\newacronym{np}{NS}{Nanopore Sequencing}
\newacronym{np.ss}{SS}{Selective Sequencing}
\newacronym{ont}{ONT}{Oxford Nanopore Technology}
\newacronym{nanopore.drs}{DRS}{Direct RNA sequencing}
\newacronym{nanopore.ru}{RU}{Read Until}



% PCR Techniques
\newacronym{pcr}{PCR}{Polymerase Chain Reaction}
\newacronym{rt-pcr}{RT-PCR}{Real-time Polymerase Chain Reaction}
\newacronym{bsp}{BSP}{Bisulfite PCR}
\newacronym{msp}{MSP}{Methylation-Specific PCR}
\newacronym{qpcr}{qPCR}{quantitative Polymerase Chain Reaction}
\newacronym{ptds}{PTDS}{PCR-based two-step DNA synthesis}



% Bioinformatics Tools and Concepts
\newacronym{blat}{BLAT}{BLAST-Like Alignment Tool}
\newacronym{blast}{BLAST}{Basic Local Alignment Search Tool}
\newacronym{pca}{PCA}{Principal Component Analysis}
\newacronym{tsne}{t-SNE}{t-distributed Stochastic Neighbor Embedding}
\newacronym{tsne-kl}{KL}{Kullback-Leibler}
\newacronym{hmm}{HMM}{Hidden Markov Model}
\newacronym{cnv}{CNV}{Copy Number Variation}
\newacronym{snv}{SNV}{Single Nucleotide Variant}
\newacronym{snp}{SNP}{Single Nucleotide Polymorphism}
\newacronym{indel}{Indel}{Insertion-Deletion}



% Cancer Genes and Markers
\newacronym{brca}{BRCA}{Breast Cancer}
\newacronym{brca1}{BRCA1}{BReast CAncer gene 1}
\newacronym{tp53}{TP53}{Tumor Protein 53}
\newacronym{znf709}{ZNF709}{Zinc Finger Protein 709}
\newacronym{rassf1}{RASSF1}{Ras association domain family 1}
\newacronym{dmr}{DMR}{Differential Methylated Region}
\newacronym{5mc}{5mc}{5-methylcytosine}
\newacronym{5hmc}{5hmC}{5-hydroxymethylcytosine}
\newacronym{6ma}{6ma}{6-methyladenine}



% Types of Cancer
\newacronym{gbm}{GBM}{Glioblastoma}
\newacronym{lusc}{LUSC}{Lung Squamous Cell Carcinoma}
\newacronym{ucec}{UCEC}{Uterine Corpus Endometrial Carcinoma}
\newacronym{hnc}{HNC}{Head and Neck Cancer}



% Cancer Detection and Treatment
\newacronym{ctdna}{ctDNA}{circulating tumor DNA}
\newacronym{cfdna}{cfDNA}{cell-free DNA}
\newacronym{ctvalue}{Ct.}{Cycle Threshold}



% Metagenomics and Microbiome Research
\newacronym{fmt}{FMT}{Fecal Microbiota Transplantation}
\newacronym{naats}{NAATs}{Nucleic Acid Amplification Tests}
\newacronym{maldi-tof}{MALDI-TOF MS}{Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry}
\newacronym{amr}{AMR}{Anti-Microbial Resistance}
\newacronym{lca}{LCA}{Lowest Common Ancestor}
\newacronym{sars}{SARS-CoV-2}{Severe Acute Respiratory Syndrome Coronavirus 2}
\newacronym{covid19}{COVID-19}{Coronavirus Disease 2019}
\newacronym{ards}{ARDS}{Acute Respiratory Distress Syndrome}
\newacronym{card}{CARD}{Comprehensive Antibiotic Resistance Database}



% Neural Networks and Machine Learning
\newacronym{ai}{AI}{Artificial Intelligence}
\newacronym{cnn}{CNN}{Convolutional Neural Network}
\newacronym{rnn}{RNN}{Recurrent Neural Network}
\newacronym{gru}{GRU}{Gated Recurrent Unit}
\newacronym{crnn}{CRNN}{Convolutional Recurrent Neural Network}
\newacronym{tcn}{TCN}{Temporal Convolutional Network}
\newacronym{lstm}{LSTM}{Long Short-Term Memory}
\newacronym{svm}{SVM}{Support Vector Machine}
\newacronym{bo}{BO}{Bayesian Optimization}
\newacronym{fc}{FC}{Fully Connected}
\newacronym{co}{CO}{CNN Occlusion}



% Computing and Technical Terms
\newacronym{cpu}{CPU}{Central Processing Unit}
\newacronym{gpu}{GPU}{Graphics Processing Unit}
\newacronym{ram}{RAM}{Random Access Memory}
\newacronym{saas}{SaaS}{Software as a Service}
\newacronym{api}{API}{Application Programming Interface}
\newacronym{asic}{ASIC}{Application Specific Integrated Circuit}
\newacronym{tcp}{TCP}{Transmission Control Protocol}
\newacronym{udp}{UDP}{User Datagram Protocol}
\newacronym{kcp}{KCP}{Kuai Control Protocol}



% CRISPR/Cas Systems
\newacronym{crispr}{CRISPR}{Clustered Regularly Interspaced Short Palindromic Repeats}
\newacronym{grna}{gRNA}{Guide RNA}
\newacronym{tracrna}{tracrRNA}{Trans-activating CRISPR RNA}
\newacronym{crna}{crRNA}{CRISPR RNA}
\newacronym{pam}{PAM}{Protospacer Adjacent Motif}
\newacronym{cas9}{Cas9}{CRISPR-associated protein 9}



% Others
\newacronym{roi}{ROI}{Regions of Interest}
\newacronym{so}{SO}{Symmetrical Occlusion}
\newacronym{nrc}{NRC}{Normalized Read Counts}
\newacronym{tpm}{TPM}{Transcripts Per Million}
\newacronym{rpkm}{RPKM}{Reads Per Kilobase of transcript per million reads Mapped}
\newacronym{deg}{DEG}{Differentially Expressed Genes}
\newacronym{musc}{MuSC}{Muscle Stem Cells}
\newacronym{gcn}{GCN}{Gene Co-expression Networks}
\newacronym{bh}{BH}{Benjamini & Hochberg}