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Biophysical Reviews

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https://read.qxmd.com/read/30783907/a-note-of-appreciation-for-prof-cristobal-dos-remedios-on-behalf-of-biophysical-reviews
#1
EDITORIAL
Damien Hall
Following the initial five-year tenure (2009-2014) of the founding Chief Editor, Dr. Jean Garnier, Prof. Cristobal dos Remedios (University of Sydney) assumed responsibility for Biophysical Reviews as the second Chief Editor (2014-2019). Under his stewardship, Biophysical Reviews has become a six issue per year journal, publishing approximately 100 reviews per year. At the conclusion of his five-year tenure as Chief Editor (and at the age of 78), Cris is stepping down, leaving the journal well placed to apply for (and receive) an impact factor in 2020...
February 19, 2019: Biophysical Reviews
https://read.qxmd.com/read/30771157/mathematical-models-applied-to-thyroid-cancer
#2
REVIEW
Jairo Gomes da Silva, Rafael Martins de Morais, Izabel Cristina Rodrigues da Silva, Paulo Fernando de Arruda Mancera
Thyroid cancer is the most prevalent endocrine neoplasia in the world. The use of mathematical models on the development of tumors has yielded numerous results in this field and modeling with differential equations is present in many papers on cancer. In order to know the use of mathematical models with differential equations or similar in the study of thyroid cancer, studies since 2006 to date was reviewed. Systems with ordinary or partial differential equations were the means most frequently adopted by the authors...
February 15, 2019: Biophysical Reviews
https://read.qxmd.com/read/30729409/bayesian-statistical-learning-for-big-data-biology
#3
REVIEW
Christopher Yau, Kieran Campbell
Bayesian statistical learning provides a coherent probabilistic framework for modelling uncertainty in systems. This review describes the theoretical foundations underlying Bayesian statistics and outlines the computational frameworks for implementing Bayesian inference in practice. We then describe the use of Bayesian learning in single-cell biology for the analysis of high-dimensional, large data sets.
February 7, 2019: Biophysical Reviews
https://read.qxmd.com/read/30684132/stems-cells-big-data-and-compendium-based-analyses-for-identifying-cell-types-signalling-pathways-and-gene-regulatory-networks
#4
REVIEW
Md Humayun Kabir, Michael D O'Connor
Identification of new drug and cell therapy targets for disease treatment will be facilitated by a detailed molecular understanding of normal and disease development. Human pluripotent stem cells can provide a large in vitro source of human cell types and, in a growing number of instances, also three-dimensional multicellular tissues called organoids. The application of stem cell technology to discovery and development of new therapies will be aided by detailed molecular characterisation of cell identity, cell signalling pathways and target gene networks...
January 25, 2019: Biophysical Reviews
https://read.qxmd.com/read/30684131/big-data-challenges-in-genome-informatics
#5
LETTER
Ka-Chun Wong
In recent years, we have witnessed a big data explosion in genomics, thanks to the improvement in high-throughput technologies at drastically decreasing costs. We are entering the era of millions of available genomes. Notably, each genome can be composed of billions of nucleotides stored as plain text files in gigabytes (GBs). It is undeniable that those genome data impose unprecedented data challenges for us. In this article, we briefly discuss the big data challenges associated with genomics in recent years...
January 25, 2019: Biophysical Reviews
https://read.qxmd.com/read/30684130/big-data-the-elements-of-good-questions-open-data-and-powerful-software
#6
EDITORIAL
Joshua W K Ho, Eleni Giannoulatou
No abstract text is available yet for this article.
January 25, 2019: Biophysical Reviews
https://read.qxmd.com/read/30666509/cardiacprofiler-an-r-package-for-extraction-and-visualisation-of-heart-rate-profiles-from-wearable-fitness-trackers
#7
LETTER
Djordje Djordjevic, Beni K Cawood, Sabrina K Rispin, Anushi Shah, Leo H H Yim, Christopher S Hayward, Joshua W K Ho
No abstract text is available yet for this article.
January 21, 2019: Biophysical Reviews
https://read.qxmd.com/read/30627872/host-and-microbiome-multi-omics-integration-applications-and-methodologies
#8
REVIEW
Qing Wang, Kaicen Wang, Wenrui Wu, Eleni Giannoulatou, Joshua W K Ho, Lanjuan Li
The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host...
January 9, 2019: Biophysical Reviews
https://read.qxmd.com/read/30627871/a-review-of-big-data-applications-of-physiological-signal-data
#9
REVIEW
Christina Orphanidou
The proliferation of smart physiological signal monitoring sensors, combined with the advancement of telemetry and intelligent communication systems, has led to an explosion in healthcare data in the past few years. Additionally, access to cheaper and more effective power and storage mechanisms has significantly increased the availability of healthcare data for the development of big data applications. Big data applications in healthcare are concerned with the analysis of datasets which are too big, too fast, and too complex for healthcare providers to process and interpret with existing tools...
January 9, 2019: Biophysical Reviews
https://read.qxmd.com/read/30627870/rna-polymerase-ii-chip-seq-a-powerful-and-highly-affordable-method-for-studying-fungal-genomics-and-physiology
#10
LETTER
Kaeling Tan, Koon Ho Wong
No abstract text is available yet for this article.
January 9, 2019: Biophysical Reviews
https://read.qxmd.com/read/30617454/the-rise-of-the-distributions-why-non-normality-is-important-for-understanding-the-transcriptome-and-beyond
#11
REVIEW
Jessica C Mar
The application of statistics has been instrumental in clarifying our understanding of the genome. While insights have been derived for almost all levels of genome function, most importantly, statistics has had the greatest impact on improving our knowledge of transcriptional regulation. But the drive to extract the most meaningful inferences from big data can often force us to overlook the fundamental role that statistics plays, and specifically, the basic assumptions that we make about big data. Normality is a statistical property that is often swept up into an assumption that we may or may not be consciously aware of making...
January 7, 2019: Biophysical Reviews
https://read.qxmd.com/read/30610579/precision-medicine-review-rare-driver-mutations-and-their-biophysical-classification
#12
REVIEW
Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng
How can biophysical principles help precision medicine identify rare driver mutations? A major tenet of pragmatic approaches to precision oncology and pharmacology is that driver mutations are very frequent. However, frequency is a statistical attribute, not a mechanistic one. Rare mutations can also act through the same mechanism, and as we discuss below, "latent driver" mutations may also follow the same route, with "helper" mutations. Here, we review how biophysics provides mechanistic guidelines that extend precision medicine...
January 4, 2019: Biophysical Reviews
https://read.qxmd.com/read/30594974/mining-data-and-metadata-from-the-gene-expression-omnibus
#13
REVIEW
Zichen Wang, Alexander Lachmann, Avi Ma'ayan
Publicly available gene expression datasets deposited in the Gene Expression Omnibus (GEO) are growing at an accelerating rate. Such datasets hold great value for knowledge discovery, particularly when integrated. Although numerous software platforms and tools have been developed to enable reanalysis and integration of individual, or groups, of GEO datasets, large-scale reuse of those datasets is impeded by minimal requirements for standardized metadata both at the study and sample levels as well as uniform processing of the data across studies...
December 29, 2018: Biophysical Reviews
https://read.qxmd.com/read/30570701/hi-c-analysis-from-data-generation-to-integration
#14
REVIEW
Koustav Pal, Mattia Forcato, Francesco Ferrari
In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and complexity have been produced using experimental techniques based on high-throughput sequencing. In particular, the study of the 3D organization of chromatin has raised increasing interest, thanks to the development of advanced experimental techniques. In this context, Hi-C has been widely adopted as a high-throughput method to measure pairwise contacts between virtually any pair of genomic loci, thus yielding unprecedented challenges for analyzing and handling the resulting complex datasets...
December 20, 2018: Biophysical Reviews
https://read.qxmd.com/read/30565204/towards-testing-big-data-analytics-software-the-essential-role-of-metamorphic-testing
#15
REVIEW
Zhiyi Zhang, Xiaoyuan Xie
In the rapidly growing field of big data analysis, scientists from numerous domains such as computer science and biology are constantly challenged by an unprecedented amount of data. While many software programs have been constructed to support processing and analyzing continuous information flow, one under-appreciated challenge in this field is software quality assurance of these big data software platforms. Metamorphic testing, which was proposed to alleviate the oracle problem in the software engineering community, has become an effective approach for software verification and validation...
December 18, 2018: Biophysical Reviews
https://read.qxmd.com/read/30511266/tom-pollard-father-of-life-science-policy-advocacy
#16
REVIEW
Kevin Wilson
Tom Pollard has played an instrumental role in the creation of the life science policy and advocacy programs familiar to life scientists today. This article reviews the creation of that program and the role Tom played. In addition, it briefly discusses advocacy activities now available to life scientists and why they should participate in these activities.
December 3, 2018: Biophysical Reviews
https://read.qxmd.com/read/30488377/opening-remarks-from-the-editors
#17
EDITORIAL
Enrique M De La Cruz, Laurent Blanchoin, E Michael Ostap
No abstract text is available yet for this article.
November 28, 2018: Biophysical Reviews
https://read.qxmd.com/read/30470968/from-solution-to-surface-to-filament-actin-flux-into-branched-networks
#18
REVIEW
R Dyche Mullins, Peter Bieling, Daniel A Fletcher
The actin cytoskeleton comprises a set of filament networks that perform essential functions in eukaryotic cells. The idea that actin filaments incorporate monomers directly from solution forms both the "textbook picture" of filament elongation and a conventional starting point for quantitative modeling of cellular actin dynamics. Recent work, however, reveals that filaments created by two major regulators, the formins and the Arp2/3 complex, incorporate monomers delivered by nearby proteins. Specifically, actin enters Arp2/3-generated networks via binding sites on nucleation-promoting factors clustered on membrane surfaces...
December 2018: Biophysical Reviews
https://read.qxmd.com/read/30430457/multifunctional-roles-of-tropomodulin-3-in-regulating-actin-dynamics
#19
REVIEW
Justin Parreno, Velia M Fowler
Tropomodulins (Tmods) are proteins that cap the slow-growing (pointed) ends of actin filaments (F-actin). The basis for our current understanding of Tmod function comes from studies in cells with relatively stable and highly organized F-actin networks, leading to the view that Tmod capping functions principally to preserve F-actin stability. However, not only is Tmod capping dynamic, but it also can play major roles in regulating diverse cellular processes involving F-actin remodeling. Here, we highlight the multifunctional roles of Tmod with a focus on Tmod3...
December 2018: Biophysical Reviews
https://read.qxmd.com/read/30460458/polymerization-and-depolymerization-of-actin-with-nucleotide-states-at-filament-ends
#20
REVIEW
Ikuko Fujiwara, Shuichi Takeda, Toshiro Oda, Hajime Honda, Akihiro Narita, Yuichiro Maéda
Polymerization induces hydrolysis of ATP bound to actin, followed by γ-phosphate release, which helps advance the disassembly of actin filaments into ADP-G-actin. Mechanical understanding of this correlation between actin assembly and ATP hydrolysis has been an object of intensive studies in biochemistry and structural biology for many decades. Although actin polymerization and depolymerization occur only at either the barbed or pointed ends and the kinetic and equilibrium properties are substantially different from each other, characterizing their properties is difficult to do by bulk assays, as these assays report the average of all actin filaments in solution and are therefore not able to discern the properties of individual actin filaments...
November 20, 2018: Biophysical Reviews
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