Frank Eisenhaber, MD, PhD, Bioinformatic Institute, Singapore
Nash Rochman, PhD, City University of New York, United States of America
Submission Status: Open | Submission Deadline: 30 April 2025
Image credit: © metamorworks / Getty Images / iStock
Biology Direct invites researchers to contribute to a new Collection of bioinformatics articles with impact for life science data analysis, biological theory, and biotechnological/medical application.
Roughly 75 years into the "information age", we find ourselves entering into a new era of "big data" where dramatically growing data acquisition is not yet accompanied by adequate means to transform this data into insightful information and scientific discovery. Nowhere has this had a greater impact than within the realm of biology and medicine where recent technological innovations have permitted more robust and entirely new modes of data collection at every scale of organizational complexity from genomics to cell biology and ecology. Advances in bioinformatics can support the development of novel bioengineering applications which require understanding emergent phenomena among new data types previously unseen. This, in turn, can support the development of improved data-analytic methodology. Lastly, but of fundamental importance, this process reveals highly-conserved patterns across disparate experimental systems, proving the raw materials for new theory.
This transformation of data into scientific discovery is not an automatic process and the growth of biological datasets is far outstripping the pace of interpretation as insufficiently analyzed datasets from past decades and many still unknown genome functions certify. This Collection aims to highlight recent advances and ongoing efforts to narrow this gap.
We welcome interdisciplinary research and perspectives that demonstrate innovative approaches to address biological and medical challenges using computational techniques that support new engineering applications, analytic-method development, or mathematical foundations of biological systems.
Topics of interest include but are not limited to:
• Genomic Data Analysis
• Protein Structure Prediction
• Mathematical Modeling
• Drug Discovery and Development
• Disease Biomarker Identification
• Personalized Medicine
Neutrophils play a key role in the tumor microenvironment (TME); however, their functions in glioblastoma (GBM) are overlooked and insufficiently studied. A detailed analysis of GBM-associated neutrophil (GBMA...
Laryngotracheal stenosis (LTS), a pathological narrowing of the upper airway caused by excessive extracellular matrix (ECM) deposition, often leads to dyspnea and even respiratory failure. However, systematic ...
Acute kidney injury (AKI) remains a critical condition with limited therapeutic options, predominantly managed by renal replacement therapy. The challenge of developing targeted treatments persists.
In the quest to elucidate novel therapeutic strategies for myocardial injury, recent investigations have underscored the pivotal roles played by circulating extracellular vesicles (EVs) in intercellular commun...
Protein kinases are essential cellular signal modulators involved in tumorigenesis, metastasis, immune response, and drug resistance. However, the comprehensive features and clinical significance of protein ki...
Diabetic foot ulcers (DFU) are a common and severe complication among diabetic patients, posing a significant burden on patients’ quality of life and healthcare systems due to their high incidence, amputation ...
Doxorubicin (DOXO) is a well-known chemotherapy drug, which is widely used in the treatment of Multiple Myeloma (MM), a treatable but not curable type of blood cancer. Here, we propose a pharmacokinetics and p...
Carotid atherosclerotic plaque is the primary cause of cardiovascular and cerebrovascular diseases. It is closely related to oxidative stress and immune inflammation. This bioinformatic study was conducted to ...
Advances in sequencing technologies are reshaping clinical diagnostics, prompting the development of new software tools to decipher big data. To this end, we developed functional genomic imaging (FGI), a visua...
Diabetic nephropathy (DN) is a common diabetes-related complication with unclear underlying pathological mechanisms. Although recent studies have linked glycolysis to various pathological states, its role in D...
Tumor microenvironment (TME) takes an essential part in the bladder cancer progression, which is associated with intercellular cross-talk between stroma cells and cancer. We aimed use bioinformatics tools to a...
Despite the increasing body of evidence that mitochondrial activities implicate in chronic obstructive pulmonary disease (COPD), we are still far from a causal-logical and mechanistic understanding of the mito...
Endothelial cells are integral components of the tumor microenvironment and play a multifaceted role in tumor immunotherapy. Targeting endothelial cells and related signaling pathways can improve the effective...
Integrating multi-layered information can enhance the accuracy of genomic prediction for complex traits. However, the improvement and application of effective strategies for genomic prediction (GP) using multi...
Intrauterine adhesion (IUA) is a common cause of clinically refractory infertility, and there exists significant heterogeneity in the treatment outcomes among IUA patients with the similar severity after trans...
Clinically, phosphodiesterase type 5 inhibitors (PDE5-Is) remain the first-line therapy for erectile dysfunction (ED) patients; however, approximately 35% of these patients are still failing to respond to the ...
The Correction to this article has been published in Biology Direct 2025 20:12
Precision oncology’s implementation in clinical practice faces significant constraints due to the inadequacies in tools for detailed patient stratification and personalized treatment methodologies. Dysregulate...
Peroxisome proliferator-activated receptor-γ (PPARγ) is a critical regulator of adipogenesis and bone metabolism, playing complex roles in osteoporosis. This study investigates the effects of taurine and homoc...
UCHL5 was initially recognized as a multifunctional molecule. While recent research has highlighted its involvement in tumor malignant biological behaviors, its specific role in promoting tumor cell apoptosis ...
No authoritative books or guidelines are currently available for revealing the interrelationships of prostatitis, benign prostatic hyperplasia (BPH), and prostate cancer (PCa). Moreover, no consensus on this i...
Disulfidptosis, identified as an innovative form of cellular death subsequent to cuproptosis, is currently under investigation for its mechanisms in oncological contexts. In-depth analyses exploring the relati...
MicroRNAs (miRNAs) have shown potential as diagnostic biomarkers for myocardial infarction (MI) due to their early dysregulation and stability in circulation after MI. Moreover, they play a crucial role in reg...
Extrachromosomal circular DNAs (eccDNAs) are commonly found in various tumors and play a critical role in promoting oncogenesis. However, little is known about the characteristics and nature of eccDNAs in huma...
Preeclampsia (PE) is a severe pregnancy complication characterized by complex molecular interactions. Understanding these interactions is crucial for developing effective therapeutic strategies.
Shelterin proteins (TERF1, TERF2, TPP1, TINF2, POT1) protect telomeres, prevent unwarranted repair activation, and regulate telomerase activity. Alterations in these proteins can lead to cancer progression. Th...
Hepatocellular carcinoma (HCC) ranks among the most lethal malignancies around the world. However, the current management strategies for predicting prognosis in HCC patients remain unreliable. Our study develo...
Tumor Mutational Burden (TMB) have emerged as pivotal predictive biomarkers in determining prognosis and response to immunotherapy in colorectal cancer (CRC) patients. While Whole Exome Sequencing (WES) stands...
Gliomas represent a highly aggressive class of tumors located in the brain. Despite the availability of multiple treatment modalities, the prognosis for patients diagnosed with glioma remains unfavorable. Ther...
Accurately identifying effective biomarkers and translating them into clinical practice have significant implications for improving clinical outcomes in hepatocellular carcinoma (HCC). In this study, our objec...
Identifying therapeutic inhibitors of crucial enzymes involved in the peptidoglycan biosynthesis pathway is pivotal for developing new treatments against multidrug-resistant Enterococcus faecalis V583. MurM, an e...
Disulfidptosis refers to cell death caused by the accumulation and bonding of disulfide in the cytoskeleton protein of SLC7A11-high level cells under glucose deprivation. However, the role of disulfidptosis-re...
Limited supply of certain nutrients and deregulation of nucleus pulposus (NP) plays a key role in the pathogenesis of intervertebral disc degeneration (IVDD). However, whether nutrient deprivation-induced cell...
Esophageal squamous cell carcinoma (ESCC) is often diagnosed at advanced stages due to the inherent limitations of current screening methodologies. Central to evaluating tumor invasion and prognostic assessmen...
The recombination landscape and subsequent natural selection have vast consequences forevolution and speciation. However, most of the crossover and recombination hotspots are yet to be discovered. We previousl...
Retinal vascular endothelial cell (RVECs) injury is a major cause of morbidity and mortality among the patients with diabetes. RVECs dysfunction is the predominant pathological manifestation of vascular compli...
Esophageal carcinoma (EC) and gastric cardiac adenocarcinoma (GCA) have high incidence rates in the Chaoshan region of South China. Multifocal esophageal and cardiac cancer (MECC) is commonly observed in this ...
Prostate cancer (PCa) is the second leading cause of tumor-related mortality in men. Metastasis from advanced tumors is the primary cause of death among patients. Identifying novel and effective biomarkers is ...
This Collection welcomes submissions of original research and review articles. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal.
Articles for this Collection should be submitted via our submission system, Snapp. Please, select the appropriate Collection title “Bioinformatics Theory and Methods for Biological Discovery" under the Details tab during the submission stage.
Articles will undergo the journal’s standard peer-review process and are subject to all the journal’s standard policies. Articles will be added to the Collection as they are published.
The Editors have no competing interests with the submissions which they handle through the peer-review process. The peer-review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.