All molecular biology (MB) tool can be employed in functional genomics (FG), as the aim of MB is to identify the function of a certain gene, transcript or protein in a certain organism and / or condition. However, nowadays the majority of the FG studies have been focused on high-throughput tools, such as:

• Microarray to evaluate mutations and (earlier) gene expression.
• Next Generation Sequencing to sequence genomes, transcriptomes, metagenomEs and many other sets of nucleotide libraries.
• Mass Espectrometry to analyze proteins in a sample.

All these techniques depends on complex bioinformatics analysis, and require accuracy statistical validations in most cases.

thanks for your answer.

what about molecular cloning, plasmid-mediated gene transfer, silencing and gene knock-out ?

Molecular Biology exclusively refers to wet lab work, functional genomics uses almost all of the molecular biology tools but adds bioinformatics to it since it usually deals with large datasets.