DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles.

Transcription regulation in multicellular species is mediated by modular transcription factor (TF) binding site combinations termed cis-regulatory modules (CRMs). Such CRM-mediated transcription regulation determines the gene expression patterns during development. Biologists frequently investigate CRM transcription regulation on gene expressions.

YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers.

Cells adapt to environmental stresses mainly via transcription reprogramming. Correct transcription control is mediated by the interactions between transcription factors (TF) and their target genes. These TF-gene associations can be probed by chromatin immunoprecipitation techniques and knockout experiments, revealing TF binding (TFB) and regulatory (TFR) evidence, respectively.

Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans.

It is now known that cap-independent translation initiation facilitated by internal ribosome entry sites (IRESs) is vital in selective cellular protein synthesis under stress and different physiological conditions. However, three problems make it hard to understand transcriptome-wide cellular IRES-mediated translation initiation mechanisms: (i) complex interplay between IRESs and other translation initiation-related information, (ii) reliability issue of in silico cellular IRES investigation and (iii) labor-intensive in vivo IRES identification. In this research, we constructed the Human IRES Atlas database for a comprehensive understanding of cellular IRESs in humans.