23 papers · ranked by Valyu relevance
Gizem Damla Yalcin, Nurseda Danisik, Rana Can Baygin, Ahmet Acar
Over the past decade, we have witnessed an increasing number of large-scale studies that have provided multi-omics data by high-throughput sequencing approaches. This has particularly helped with identifying key (epi)genetic alterations in cancers. Importantly, aberrations that lead to the activation of signaling…
Isa Mambetsariev, Jeremy Fricke, Stephen B. Gruber, Tingting Tan + 7 more
In recent decades, cancer biology and medicine have ushered in a new age of precision medicine through high-throughput approaches that led to the development of novel targeted therapies and immunotherapies for different cancers. The availability of multifaceted high-throughput omics data has revealed that cancer…
Hehuan Zhu, Xi Zhang, Ehsan Nazemalhosseini-Mojarad, Jessica Roelands + 10 more
Traditionally, scientists tend to approach cancer research in a reductionistic way: aiming at uncovering underlying, separate components in malignant processes. And indeed, great progress has been made by reducing the development of a tumor to single, specific genes and mutations. For instance, familial adenomatous…
Yongjun Wei, Cheng Zhang, Adil Mardinoglu, Peng Zhang
Cancer is the leading death cause worldwide, and it is one of the biggest contributors for premature mortality ([1]). According to the global cancer statistics in 2020, 19.3 million new cancer cases were identified, and 10 million cancer patients were died ([7]). Normally, due to the heterogeneity in individual tumor…
Mahnoor Naseer Gondal, Safee Ullah Chaudhary
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built on top of this data have the potential to provide specific insights…
Krastan B. Blagoev, David T. Ting, Herbert Levine, Yvonne Saenger + 2 more
'Thea D. Tlsty' 'Bo Sun'] One of the most remarkable expansions in complexity of life on Earth was the transition from single cell to multicellular organisms. This transition lead to cellular specialization and cooperation among cell types, including the ability to reproduce the entire organism from highly specialized…
Edwin Wang, Jinfeng Zou, Naif Zaman, Lenore K. Beitel + 2 more
'Miltiadis Paliouras'] A tumor often consists of multiple cell subpopulations (clones). Current chemotreatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and computational analysis allows to computational dissection of…
Edwin Wang, Jinfeng Zou, Naif Zaman, Lenore K. Beitel + 2 more
'Miltiadis Paliouras'] Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional…
Mahnoor N Gondal, Muhammad U Sultan, Ammar Arif, Abdul Rehman + 33 more
Multi-scale models integrating biomolecular data from genetic, transcriptional, and translational levels, coupled with extracellular microenvironments can assist in decoding the complex mechanisms underlying system-level diseases such as cancer. To investigate the emergent properties and clinical translation of such…
Anders Bredberg
The two outlined general observations indicate that cancer has much in common with how complexity is viewed within some branches of the physical sciences (31-39). A complicated system or problem like a human-made machine typically contains many components, with well-known properties and interactions. Stimulating or…
Abhijeet Das, Ramray Bhat, Mohit Kumar Jolly
Breast cancer (BC) is the most widespread cancer globally, yet current diagnostic and prognostic methods inadequately capture its biological complexity, despite the benefits of early detection. Cancer systems biology (SB) has advanced over the past two decades as a multiscale approach, but often neglects morphological…
Edwin Wang, Naif Zaman, Shauna R. McGee, Jean‐Sébastien Milanese + 2 more
'Ali Masoudi‐Nejad' "Maureen D. O'Connor‐McCourt"] Tumor genome sequencing leads to documenting thousands of DNA mutations and other genomic alterations. At present, these data cannot be analyzed adequately to aid in the understanding tumorigenesis and its evolution. Moreover, we have little insight into how to use…
Jonathan Ozik, Nicholson Collier, Justin Wozniak, Charles Macal + 6 more
Cancer is a complex, multiscale dynamical system, with interactions between tumor cells and non-cancerous systems. Therapies act on this cancer-host system, sometimes with unexpected results. Systematic investigation of mechanistic models could help identify the factors driving a treatment’s success or failure, but…
Abicumaran Uthamacumaran, Héctor Zenil
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires the integration of information dynamics across multidimensional spatiotemporal…
Edwin Wang
In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storms), and their implications for cancer are discussed. Genomic…
Ting Jin, Flaminia Talos, Daifeng Wang
Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. The increasing amount of genomics data gathered from patients allows for better understanding of gene regulatory mechanisms that occur during disease development at a system level.…
Joao B. Xavier, William K. Chang
We present a type of agent-based model that uses off-lattice spheres to represent individual cells in a solid tumor. The model calculates chemical gradients and determines the dynamics of the tumor as emergent properties of the interactions between the cells. As an example, we present an investigation of cooperation…
Inna Kuperstein
| ABSTRACT | | 3 | | --- | --- | --- | | PREFACE | | 5 | | INTRODUCTION | | 6 | | ALZHEIMER'S DISEASE: A DISORDER OF PROTEIN MISFOLDING AND SYNAPTIC FAILURE | | 7 | | CANCER: A SYSTEMS BIOLOGY DISORDER | | 7 | | 1. MOLECULAR MECHANISMS OF NEURODEGENERATION | | 12 | | CHAPTER | AT GLANCE | 12 | | 1.1 | PHOSPHORYLATION…
Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi + 4 more
A tumor is thought to result from successive accumulation of genetic alterations – each resulting population manifesting itself with a novel ‘cancer phenotype.’ In each such population, clones of higher fitness, contributing to the selection of the cancer phenotype, enjoy a Darwinian selective advantage, thus driving…
Rumiana Tenchov, Aparna Sapra, Janet Sasso, Krittika Ralhan + 3 more
Cancer is one of the leading causes of death worldwide. Early cancer detection is critical because it can significantly improve treatment outcome thus saving lives, reducing suffering, and lessening psychological and economic burdens. Cancer biomarkers provide varied information about cancer, from early detection of…
Authors not listed
Immuno-oncology, a rapidly evolving field at the forefront of cancer research, leverages the body’s immune system to fight cancer. In this follow up report, we extend our natural language processing (NLP)-based analysis to pinpoint the context of emergence of the previously identified emerging concepts. To achieve this…
Juerg Straubhaar, Alexandria D’Souza, Zachary Niziolek, Bogdan Budnik
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling…
Authors not listed
Despite $100 billion in investment and more than 100,000 publications, nanomedicine translation fails primarily at biological validation, not at synthesis or characterization. We present the first systematic technology readiness assessment across autonomous nanomedicine components, revealing a critical finding: while…