Natoli, Marina Gallon, John Lu, Haonan Amgheib, Ala Pinato, David J Mauri, Francesco A Marafioti, Teresa Akarca, Ayse U Ullmo, Ines Ip, Jacey
...
Published in
Journal for Immunotherapy of Cancer
Background Endogenous retroviruses (ERVs) play a role in a variety of biological processes, including embryogenesis and cancer. DNA methyltransferase inhibitors (DNMTi)-induced ERV expression triggers interferon responses in ovarian cancer cells via the viral sensing machinery. Baseline expression of ERVs also occurs in cancer cells, though this pr...
DuPai, Cory D Davies, Bryan W Wilke, Claus O
Published in
Protein science : a publication of the Protein Society
The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here, we systematically probe all 49,000 unique beta hairpin substructures containe...
Shujaat, Muhammad Wahab, Abdul Tayara, Hilal Chong, Kil To
Published in
Genes
A promoter is a small region within the DNA structure that has an important role in initiating transcription of a specific gene in the genome. Different types of promoters are recognized by their different functions. Due to the importance of promoter functions, computational tools for the prediction and classification of a promoter are highly desir...
Zhu, Lei Kan, Ke-Jia Grün, Johanna L. Hissa, Barbara Yang, Cui Győrffy, Balázs Loges, Sonja Reißfelder, Christoph Schölch, Sebastian
Published in
Cancers
Simple Summary The analysis of circulating tumor cells (CTC) is a mainstay of liquid biopsy of solid malignancies. However, research to date has not yet determined a universal and specific marker for CTCs of pancreatic cancer. Genetically engineered mouse models (GEMMs) of pancreatic cancer, can mimic the human disease very closely. This study aime...
Savino, Aurora Provero, Paolo Poli, Valeria
Published in
International Journal of Molecular Sciences
Biological systems respond to perturbations through the rewiring of molecular interactions, organised in gene regulatory networks (GRNs). Among these, the increasingly high availability of transcriptomic data makes gene co-expression networks the most exploited ones. Differential co-expression networks are useful tools to identify changes in respon...
Kane, Gary A Lopes, Gonçalo Saunders, Jonny L Mathis, Alexander Mathis, Mackenzie W
Published in
eLife
The ability to control a behavioral task or stimulate neural activity based on animal behavior in real-time is an important tool for experimental neuroscientists. Ideally, such tools are noninvasive, low-latency, and provide interfaces to trigger external hardware based on posture. Recent advances in pose estimation with deep learning allows resear...
Hu-Lieskovan, Siwen Bhaumik, Srabani Dhodapkar, Kavita Grivel, Jean-Charles J B Gupta, Sumati Hanks, Brent A Janetzki, Sylvia Kleen, Thomas O Koguchi, Yoshinobu Lund, Amanda W
...
Published in
Journal for Immunotherapy of Cancer
Since the publication of the Society for Immunotherapy of Cancer’s (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor imm...
Khomtchouk, Bohdan B Tran, Diem-Trang Vand, Kasra A Might, Matthew Gozani, Or Assimes, Themistocles L
Published in
Briefings in bioinformatics
Cardiovascular disease (CVD) is the leading cause of death worldwide, causing over 17 million deaths per year, which outpaces global cancer mortality rates. Despite these sobering statistics, most bioinformatics and computational biology research and funding to date has been concentrated predominantly on cancer research, with a relatively modest fo...
Huang, Wenjie Wu, Ke Wu, Ruoyu Chen, Zhiguo Zhai, Wei Zheng, Junhua
Published in
Translational Andrology and Urology
Background Renal cell carcinoma (RCC) is one of the most prevalent malignant tumors of the urinary system. Hypertension can cause hypertensive nephropathy (HN). Meanwhile, Hypertension is considered to be related to kidney cancer. We analyzed co-expressed genes to find out the relationship between hypertension and RCC and show possible biomarkers a...
Wade, James D. Lun, Xiao-Kang Zivanovic, Nevena Voit, Eberhard O. Bodenmiller, Bernd
Published in
Frontiers in Physiology
Intracellular signaling pathways are at the core of cellular information processing. The states of these pathways and their inputs determine signaling dynamics and drive cell function. Within a cancerous tumor, many combinations of cell states and microenvironments can lead to dramatic variations in responses to treatment. Network rewiring has been...
