Machine learning for integrating data in biology and medicine: Principles, practice, and opportunities

M Zitnik, F Nguyen, B Wang, J Leskovec… - Information …, 2019 - Elsevier
New technologies have enabled the investigation of biology and human health at an
unprecedented scale and in multiple dimensions. These dimensions include a myriad of …

Identification of non-coding silencer elements and their regulation of gene expression

B Pang, JH van Weerd, FL Hamoen… - … Reviews Molecular Cell …, 2023 - nature.com
Cell type-and differentiation-specific gene expression is precisely controlled by genomic non-
coding regulatory elements (NCREs), which include promoters, enhancers, silencers and …

[HTML][HTML] CRISPR/Cas9-based engineering of the epigenome

J Pulecio, N Verma, E Mejía-Ramírez, D Huangfu… - Cell stem cell, 2017 - cell.com
Determining causal relationships between distinct chromatin features and gene expression,
and ultimately cell behavior, remains a major challenge. Recent developments in targetable …

Genetic circuit design automation for yeast

Y Chen, S Zhang, EM Young, TS Jones… - Nature …, 2020 - nature.com
Cells can be programmed to monitor and react to their environment using genetic circuits.
Design automation software maps a desired circuit function to a DNA sequence, a process …

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

B Lenhard, A Sandelin, P Carninci - Nature Reviews Genetics, 2012 - nature.com
Promoters are crucial for gene regulation. They vary greatly in terms of associated regulatory
elements, sequence motifs, the choice of transcription start sites and other features. Several …

Regulation of Pichia pastoris promoters and its consequences for protein production

T Vogl, A Glieder - New biotechnology, 2013 - Elsevier
The methylotrophic yeast Pichia pastoris is a widely used host for heterologous protein
production. Along with favorable properties such as growth to high cell density and high …

Enhancers as information integration hubs in development: lessons from genomics

C Buecker, J Wysocka - Trends in Genetics, 2012 - cell.com
Transcriptional enhancers are the primary determinants of tissue-specific gene expression.
Although the majority of our current knowledge of enhancer elements comes from detailed …

Gene regulatory elements, major drivers of human disease

S Chatterjee, N Ahituv - Annual review of genomics and human …, 2017 - annualreviews.org
Gene expression changes, the driving forces for cellular diversity in multicellular organisms,
are regulated by a diverse set of gene regulatory elements that direct transcription in specific …

Plant promoters: an approach of structure and function

MS Porto, MPN Pinheiro, VGL Batista… - Molecular …, 2014 - Springer
With current advances in genomics, several technological processes have been generated,
resulting in improvement in different segments of molecular research involving prokaryotic …

Challenges and advances towards the rational design of microalgal synthetic promoters in Chlamydomonas reinhardtii

A Milito, M Aschern, JL McQuillan… - Journal of Experimental …, 2023 - academic.oup.com
Microalgae hold enormous potential to provide a safe and sustainable source of high-value
compounds, acting as carbon-fixing biofactories that could help to mitigate rapidly …