Carlo Vittorio Cannistraci

Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Psychological and Cognitive Sciences, Center for Complex Network Intelligence (CCNI), Tsinghua University, Beijing, China.; Department of Computer Science and Technology, Tsinghua University, Beijing, China.; School of Biomedical Engineering, Tsinghua University, Beijing, China.

50 publications 2013 – 2025 ORCID

What does Carlo Vittorio Cannistraci research?

Dr. Cannistraci studies the gastric microbiome, which is the community of bacteria that live in our stomach. His research is particularly concerned with how long-term use of certain medications and infections can disrupt this balance. He employs advanced machine learning to uncover hidden patterns in bacterial behavior and their interactions. This work is crucial for developing better treatment approaches for patients experiencing gastric issues due to these factors, helping doctors improve patient care.

Key findings

  • Advanced analysis techniques revealed hidden patterns in bacterial behavior that traditional methods missed, leading to a better understanding of gastric health.
  • The study showed that disturbances in the gastric microbiome can significantly affect treatment outcomes for patients on certain medications.
  • The findings provide insights that can potentially guide better therapeutic strategies for patients suffering from gastric issues related to medication or infections.

Frequently asked questions

Does Dr. Cannistraci study gastric health?
Yes, he studies the gastric microbiome and how it is affected by medications and infections.
What techniques has Dr. Cannistraci used in his research?
He utilizes advanced machine learning techniques for pattern recognition in the gastric microbiome.
How does this research benefit patients?
His work helps in understanding gastric issues better, which can lead to improved treatment strategies for patients.

Publications in plain English

De novo identification of universal cell mechanics gene signatures.

2025

eLife

Urbanska M, Ge Y, Winzi M, Abuhattum S, Ali SS +12 more

Plain English
This study looked at how the mechanical properties of cells affect their functions, such as how they move and develop. Researchers identified five key genes that consistently influence these mechanical properties in both mouse and human cells. This discovery is important because it opens up new opportunities to manipulate cell mechanics, which could have significant effects on health and disease treatments. Who this helps: This helps researchers and doctors working in regenerative medicine and cancer therapy.

PubMed

Frequency-specific intermuscular coherence of synergistic muscles during an isometric force generation task.

2025

Frontiers in neural circuits

Borzelli D, Cacciola A, Cannistraci CV, Alito A, Milardi D +1 more

Plain English
This study looked at how different muscles work together when generating force in the upper limbs. Researchers recorded muscle activity while participants performed a task and found that muscles grouped into the same function (or synergy) showed stronger connections, particularly in three specific frequency ranges (delta, alpha, and low-beta). This matters because it helps us better understand how our muscles are coordinated during movement, which can improve rehabilitation strategies after injuries. Who this helps: This helps patients recovering from muscle injuries and therapists working with them.

PubMed

"Stealing fire or stacking knowledge" by machine intelligence to model link prediction in complex networks.

2023

iScience

Muscoloni A, Cannistraci CV

Plain English
This study examined how well different methods predict connections in complex networks, like social or biological networks. The researchers found that simply combining many good rules for predictions does not improve accuracy as much as previously thought. They concluded that the existing methods may not be the best solutions and future advancements might need new AI that can create and understand complex rules better. Who this helps: This benefits researchers and data scientists working with complex networks.

PubMed

Spatial Reconstruction of Oligo and Single Cells by De Novo Coalescent Embedding of Transcriptomic Networks.

2023

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Zhao Y, Zhang S, Xu J, Yu Y, Peng G +2 more

Plain English
This study focused on developing a new method to visualize and understand the 3D arrangement of individual cells within tissues based on their gene expression. The researchers introduced a new algorithm called D-CE, which outperformed existing techniques, successfully mapping the spatial distribution of cells across 14 different datasets with 497 reconstructions. This is important because it helps scientists better understand how cells interact in their natural environment, which is crucial for advancing research in development and disease. Who this helps: This benefits researchers and medical professionals studying tissue organization and disease mechanisms.

PubMed

Energy-sparing by 2-methyl-2-thiazoline protects heart from ischaemia/reperfusion injury.

2022

ESC heart failure

Nishi M, Ogata T, Kobayakawa K, Kobayakawa R, Matsuo T +10 more

Plain English
This study explored how a drug called 2-methyl-2-thiazoline (2MT) can protect the heart from damage caused by reduced blood flow and then restoring it, known as ischaemia/reperfusion (I/R) injury. The results showed that 2MT improved heart function significantly, increasing heart efficiency from 37.9% to 54.1%, and reduced heart damage, with infarct size decreasing from 48.3% to 25.6% and troponin levels dropping from 8.9 ng/mL to 1.9 ng/mL. These findings are important because they suggest that 2MT might be a safer and faster alternative to cooling therapies for treating heart damage, potentially improving outcomes for patients with severe heart disease. Who this helps: This helps patients with ischaemic heart disease.

PubMed

Medial prefrontal and occipito-temporal activity at encoding determines enhanced recognition of threatening faces after 1.5 years.

2022

Brain structure & function

Liu X, Zhou X, Zeng Y, Li J, Zhao W +7 more

Plain English
This study looked at how well people remember faces with different emotional expressions, specifically focusing on whether we remember threatening faces (like those showing anger or fear) better than non-threatening ones (like happy or neutral faces) even after 1.5 years. The researchers found that participants were better at recognizing threatening faces compared to non-threatening ones after this long delay, mainly because they forgot the non-threatening faces more easily. The study also revealed that certain brain areas were more active when people initially saw these faces, suggesting this activity helps determine who remembers threatening faces better over time. Who this helps: This benefits researchers and psychologists studying memory and facial recognition, as well as patients with anxiety or trauma who may react strongly to threatening faces.

PubMed

Salt-Specific Gene Expression Reveals Elevated Auxin Levels inPlants Grown Under Saline Conditions.

2022

Frontiers in plant science

Cackett L, Cannistraci CV, Meier S, Ferrandi P, Pěnčík A +4 more

Plain English
This study looked at how salt affects plant growth by separating the different types of stress caused by salinity. Researchers found that plants exposed to salt (like those with 100 mM NaCl) showed higher levels of a growth hormone called auxin, which was linked to their ability to survive and grow better in salty conditions. Specifically, plants with increased auxin levels had improved growth and better balance of sodium and potassium, which is crucial for their health. Who this helps: This research benefits farmers and agricultural scientists working to protect crops from salt stress.

PubMed

Prevalence, Characteristics, and Outcomes of COVID-19-Associated Acute Myocarditis.

2022

Circulation

Ammirati E, Lupi L, Palazzini M, Hendren NS, Grodin JL +51 more

Plain English
This study looked at acute myocarditis (AM), a rare heart condition that can happen in people hospitalized with COVID-19. Researchers found that out of nearly 57,000 patients, 112 were suspected of having AM, with 54 confirmed cases. Among these confirmed cases, 20.4% faced severe outcomes like death or needing advanced heart support, and overall, mortality was higher for those with COVID-related pneumonia (15.1%) compared to those without (0%). Who this helps: This helps doctors and healthcare providers understand the risks and treatment options for COVID-19 patients who develop acute myocarditis.

PubMed

Geometrical congruence, greedy navigability and myopic transfer in complex networks and brain connectomes.

2022

Nature communications

Cannistraci CV, Muscoloni A

Plain English
This study looked at how well the structure of networks, like those in the brain, fits certain geometric patterns. Researchers developed a new algorithm that makes it much faster to analyze these networks, cutting analysis time from 26 years to just one week. They found that traditional beliefs about hyperbolic networks were incorrect, as they do not usually show strong connection patterns. This new understanding of network geometry can improve how we differentiate brain structures using MRI scans. Who this helps: This research benefits neurologists and researchers studying brain connectivity.

PubMed

Cell Mechanics Based Computational Classification of Red Blood Cells Via Machine Intelligence Applied to Morpho-Rheological Markers.

2021

IEEE/ACM transactions on computational biology and bioinformatics

Ge Y, Rosendahl P, Duran C, Topfner N, Ciucci S +2 more

Plain English
This study looked at how to classify two types of red blood cells—young reticulocytes and mature red blood cells—without using fluorescent labels that can interfere with cell function. Researchers used a machine learning method that analyzes cell shape and movement, and they found promising results, successfully distinguishing these cell types in a label-free way. This matters because accurately identifying these cells is crucial for diagnosing conditions like anemia and leukemia. Who this helps: This helps patients with blood disorders and their doctors.

PubMed

Age-sex population adjusted analysis of disease severity in epidemics as a tool to devise public health policies for COVID-19.

2021

Scientific reports

Cannistraci CV, Valsecchi MG, Capua I

Plain English
This research examined how different factors like age and sex affect the severity of COVID-19 in order to help shape public health policies. The study found that people aged 0-40 and females under 60 are much less likely to become seriously ill or die from COVID-19, while males over 60 have a greater risk. This information can guide more tailored public policies that protect vulnerable groups while minimizing harsh restrictions on lower-risk populations. Who this helps: This helps policymakers and public health officials.

PubMed

Nonlinear machine learning pattern recognition and bacteria-metabolite multilayer network analysis of perturbed gastric microbiome.

2021

Nature communications

Durán C, Ciucci S, Palladini A, Ijaz UZ, Zippo AG +14 more

Plain English
This study looked at how long-term use of certain drugs and infections change the balance of bacteria in the stomach. Researchers found that using advanced analysis techniques revealed hidden patterns in bacterial behavior that traditional methods missed, helping to uncover how these bacteria and their associated metabolites interact when the stomach environment is disturbed. Understanding these changes is important because it can lead to better insights into gastric health and treatment strategies. Who this helps: This benefits patients with gastric issues related to medication or infections, as well as doctors working to improve treatment outcomes.

PubMed

Modular gateway-ness connectivity and structural core organization in maritime network science.

2020

Nature communications

Xu M, Pan Q, Muscoloni A, Xia H, Cannistraci CV

Plain English
The study looked at the global shipping network used for international trade, revealing that it operates like a small world where it balances efficient transportation with lower costs. Researchers identified key types of ports that play vital roles, especially "gateway-hub ports," which contribute significantly to how well the network functions in moving cargo. Understanding these structures is important because it can help improve the efficiency of global trade. Who this helps: This helps businesses and policymakers working in international trade and logistics.

PubMed

Publisher Correction: Cortical-like mini-columns of neuronal cells on zinc oxide nanowire surfaces.

2020

Scientific reports

Onesto V, Villani M, Narducci R, Malara N, Imbrogno A +9 more

Plain English
This study looked at tiny structures in the brain called mini-columns, which are made up of nerve cells, and how they grow on special surfaces made from zinc oxide nanowires. The researchers found that these mini-columns develop well on these surfaces, which could improve future brain cell growth research. This is important because understanding how to better support nerve cells can help in developing treatments for brain-related conditions. Who this helps: Patients with neurological disorders.

PubMed

Functional annotation of human long noncoding RNAs via molecular phenotyping.

2020

Genome research

Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y +111 more

Plain English
This study focused on long noncoding RNAs (lncRNAs), which are important parts of human genes but often don't have clear functions. Researchers tested 285 lncRNAs in skin cells to see how they affect cell growth and shape, finding meaningful links between lncRNAs and gene activity. They gathered extensive data from over 1,000 tests, uncovering new roles for these RNAs that could enhance our understanding of cellular behavior. Who this helps: This helps researchers and doctors understand gene function better, potentially leading to new treatments for various conditions.

PubMed

Three-dimensional facial-image analysis to predict heterogeneity of the human ageing rate and the impact of lifestyle.

2020

Nature metabolism

Xia X, Chen X, Wu G, Li F, Wang Y +23 more

Plain English
This study looked at how people age differently by analyzing 3D images of their faces instead of using more invasive methods like blood tests. Researchers examined about 5,000 people and found that the predicted age based on their facial features was off by only about 2.8 years from their actual age, which is quite accurate. Additionally, they discovered that aging rates are more varied in middle age and that lifestyle factors can impact these rates, providing valuable insights into how we understand aging. Who this helps: Patients and healthcare providers looking to assess biological age and the effects of lifestyle on aging.

PubMed

Use of Steroid Profiling Combined With Machine Learning for Identification and Subtype Classification in Primary Aldosteronism.

2020

JAMA network open

Eisenhofer G, Durán C, Cannistraci CV, Peitzsch M, Williams TA +9 more

Plain English
This study examined how a combination of steroid profiling and machine learning could improve the diagnosis and classification of primary aldosteronism, a condition that causes high blood pressure. Researchers analyzed data from 632 patients and found that their new approach was able to detect primary aldosteronism with 69% accuracy and identify specific types of tumors related to a gene variant with 85% accuracy, while maintaining high specificity rates of 94% and 97%. This matters because it can lead to better identification of patients who might benefit from surgery, improving treatment outcomes. Who this helps: Patients with primary aldosteronism, especially those with specific gene variants.

PubMed

Navigability evaluation of complex networks by greedy routing efficiency.

2019

Proceedings of the National Academy of Sciences of the United States of America

Muscoloni A, Cannistraci CV

PubMed

Functional Brain Network Topology Discriminates between Patients with Minimally Conscious State and Unresponsive Wakefulness Syndrome.

2019

Journal of clinical medicine

Cacciola A, Naro A, Milardi D, Bramanti A, Malatacca L +7 more

Plain English
This study looked at the brain networks of patients with two different disorders of consciousness: minimally conscious state (MCS) and unresponsive wakefulness syndrome (UWS). Researchers found that UWS patients had less effective communication between brain areas, especially the fronto-parietal regions, compared to MCS patients. This matters because understanding these differences can help doctors diagnose and treat these conditions more effectively. Who this helps: Patients with disorders of consciousness and their families.

PubMed

Cortical-like mini-columns of neuronal cells on zinc oxide nanowire surfaces.

2019

Scientific reports

Onesto V, Villani M, Narducci R, Malara N, Imbrogno A +9 more

Plain English
This study explores how tiny structures called minicolumns in the brain form when neurons grow on special surfaces made of zinc oxide nanowires. Researchers found that these neurons grouped into clusters of about 200 cells and that their arrangement depends on the surface's design. Understanding this process is important because it helps uncover how the brain's basic units work, which could lead to better treatments for brain-related conditions. Who this helps: This helps patients with neurological disorders and researchers working on brain health.

PubMed

Controlling distinct signaling states in cultured cancer cells provides a new platform for drug discovery.

2019

FASEB journal : official publication of the Federation of American Societies for Experimental Biology

Poser SW, Otto O, Arps-Forker C, Ge Y, Herbig M +20 more

Plain English
Researchers studied how cancer cells, specifically brain cancer cells, react to different conditions in the lab, focusing on one state that makes them vulnerable to certain drugs. They found that when cancer cells expressed high levels of a specific protein, 37 FDA-approved drugs could effectively kill these cells. This discovery is important because it opens up new possibilities for existing medications to be used in treating brain cancer by targeting this unique signaling state. Who this helps: This helps patients with brain cancer by identifying potential new treatment options.

PubMed

Systems Network Genomic Analysis Reveals Cardioprotective Effect of MURC/Cavin-4 Deletion Against Ischemia/Reperfusion Injury.

2019

Journal of the American Heart Association

Nishi M, Ogata T, Cannistraci CV, Ciucci S, Nakanishi N +5 more

Plain English
This study looked at the role of a protein called MURC in heart injury caused by a lack of blood flow followed by its restoration, known as ischemia/reperfusion (I/R) injury. It found that removing MURC in mice reduced heart damage and preserved heart function during such injuries, with a significant decrease in heart tissue damage and changes in cell survival pathways (in particular, MURC deletion led to less cell death). This research is important because it suggests that targeting MURC could be a new way to protect the heart during episodes of blood flow loss and recovery, which is common in heart disease. Who this helps: This helps patients with heart disease and their doctors looking for better treatment strategies.

PubMed

Machine learning of human plasma lipidomes for obesity estimation in a large population cohort.

2019

PLoS biology

Gerl MJ, Klose C, Surma MA, Fernandez C, Melander O +7 more

Plain English
The study explored how specific fats in the blood, known as lipids, can help predict obesity levels in people. Researchers analyzed blood samples from over 1,000 individuals and found that a particular model using these lipid levels could accurately predict body fat percentage (BFP) with 73% accuracy. This research is important because it shows that looking at individual lipid molecules can provide more detailed insights into obesity than traditional methods. Who this helps: This helps patients and doctors understand obesity better and potentially develop targeted treatments.

PubMed

Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory.

2018

Briefings in bioinformatics

Durán C, Daminelli S, Thomas JM, Haupt VJ, Schroeder M +1 more

Plain English
This study investigated new ways to predict how drugs interact with their targets in the body by using a method inspired by how networks in the brain are organized. The researchers found that their new approach, which uses only the structure of the drug-target interactions, made predictions that were just as accurate as traditional methods that rely on more complicated data. This is important because it suggests that simpler methods can be very effective for discovering how drugs work and finding new uses for them. Who this helps: This benefits researchers, doctors, and pharmaceutical companies looking to develop and repurpose drugs more efficiently.

PubMed

Ceruloplasmin replacement therapy ameliorates neurological symptoms in a preclinical model of aceruloplasminemia.

2018

EMBO molecular medicine

Zanardi A, Conti A, Cremonesi M, D'Adamo P, Gilberti E +5 more

Plain English
Researchers studied a genetic disease called aceruloplasminemia, which occurs when the body can't produce a protein that helps manage iron levels. They found that giving mice a replacement version of this protein improved their movement and reduced brain damage caused by iron buildup. Specifically, treated mice showed better coordination, less loss of important brain cells, and similar brain iron patterns as healthy mice. Who this helps: This therapy benefits patients with aceruloplasminemia and their doctors by providing a potential new treatment option for neurological symptoms.

PubMed

"Summer Shift": A Potential Effect of Sunshine on the Time Onset of ST-Elevation Acute Myocardial Infarction.

2018

Journal of the American Heart Association

Cannistraci CV, Nieminen T, Nishi M, Khachigian LM, Viikilä J +6 more

Plain English
Researchers studied the timing of heart attacks known as ST-elevation acute myocardial infarctions (STEMI) and found that in summer, more of these events occur at night compared to winter months when they mostly happen during the day. Specifically, during the summer, the difference in heart attacks occurring during the day versus at night shrinks significantly, indicating a seasonal influence on when these heart attacks happen, likely linked to increased sunshine and Vitamin D levels. This matters because understanding how seasonal changes affect heart attack timing could help in developing better prevention strategies. Who this helps: This helps patients at risk of heart attacks and their doctors.

PubMed

Reward-enhanced encoding improves relearning of forgotten associations.

2018

Scientific reports

Miendlarzewska EA, Ciucci S, Cannistraci CV, Bavelier D, Schwartz S

Plain English
This study looked at how offering money as a reward when learning something helps people remember that information better, even if they forget it for a while. Researchers found that when participants learned object-location pairs and were rewarded, they were able to relearn those associations faster six weeks later compared to items learned without a reward. This matters because it shows that past incentives can help bring back forgotten memories, which can be useful for improving learning strategies in education. Who this helps: This helps students and educators looking to enhance learning and memory retention.

PubMed

Morphogenetic degeneracies in the actomyosin cortex.

2018

eLife

Naganathan SR, Fürthauer S, Rodriguez J, Fievet BT, Jülicher F +3 more

Plain English
This research looked at how small molecular activities in cells lead to larger movements and shapes during development. The scientists found that different molecular processes can produce similar effects on cell flow patterns, indicating a concept called "morphogenetic degeneracy." For example, they showed that changes in various proteins led to similar behavior of cell movement, which helps cells adapt and maintain their structure during development. Who this helps: This benefits researchers studying cell development and could have implications for understanding developmental disorders.

PubMed

Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes.

2018

Scientific reports

Cannistraci CV

Plain English
This study looked at how proteins interact within networks and developed a new model to better understand these interactions. Researchers found that the reliability of protein connections is higher when proteins are part of isolated communities that don't interact much with other proteins and when they avoid linking with outsiders. This new approach, called C1*, improves reliability of protein interactions significantly compared to earlier models, which is useful for fields like systems biology and network medicine. Who this helps: This helps researchers and doctors improve our understanding of protein functions and diseases.

PubMed

Lipidomics in Major Depressive Disorder.

2018

Frontiers in psychiatry

Walther A, Cannistraci CV, Simons K, Durán C, Gerl MJ +2 more

Plain English
This study looked at how lipids, which are fats in the body, relate to major depressive disorder (MDD). Researchers found that certain patterns of lipid changes in patients could help identify and diagnose MDD more effectively. These findings may lead to better treatments by understanding the biological changes in depression more clearly. Who this helps: This helps patients with depression and their doctors.

PubMed

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies.

2017

Scientific reports

Ciucci S, Ge Y, Durán C, Palladini A, Jiménez-Jiménez V +11 more

Plain English
This study looked at a new method called PC-corr that helps scientists understand how different biological features contribute to sample separation in complex datasets, using a technique known as principal component analysis (PCA). The researchers demonstrated that PC-corr can effectively create a network of important features from various biological data, proving its usefulness across multiple areas such as cancer research and genetics. This matters because it simplifies the interpretation of complex data, allowing for better identification of important biomarkers for diseases. Who this helps: Patients and doctors seeking more precise diagnostics and treatment approaches.

PubMed

Machine learning meets complex networks via coalescent embedding in the hyperbolic space.

2017

Nature communications

Muscoloni A, Thomas JM, Ciucci S, Bianconi G, Cannistraci CV

Plain English
Researchers explored how to analyze complex networks, like social media connections or biological systems, using a new method based on geometry. They developed algorithms that can quickly and accurately map these networks to a unique geometry called the hyperbolic circle, which helps understand the structure of the networks better. This advancement is significant because it can improve how we analyze large datasets in areas like medicine and social science, making it easier to uncover meaningful patterns. Who this helps: This helps researchers and professionals working with big data in medicine, biology, and social sciences.

PubMed

Can local-community-paradigm and epitopological learning enhance our understanding of how local brain connectivity is able to process, learn and memorize chronic pain?

2017

Applied network science

Narula V, Zippo AG, Muscoloni A, Biella GEM, Cannistraci CV

Plain English
This study looked at how the brain changes over time in response to chronic pain using a rat model. Researchers found strong connections between the brain's rewiring patterns and pain behavior, with a correlation higher than 0.9, indicating these changes are closely linked to how pain is perceived and managed. Understanding these brain mechanisms is important because it can lead to better treatments for chronic pain. Who this helps: This helps patients suffering from chronic pain.

PubMed

Image Pretreatment Tools I: Algorithms for Map Denoising and Background Subtraction Methods.

2016

Methods in molecular biology (Clifton, N.J.)

Cannistraci CV, Alessio M

Plain English
This study looked at ways to improve images used in a laboratory technique called two-dimensional electrophoresis (2-DE) by reducing unwanted noise and background clutter. Researchers found that a new filtering method, called the Median Modified Wiener Filter (MMWF), effectively cleaned up images, making spot detection easier and providing consistent results regardless of the type of noise present. Additionally, they introduced a new mathematical technique for estimating and removing background noise before analyzing the images, which helps ensure more accurate measurements. Who this helps: This helps scientists and researchers who analyze protein patterns in biological samples.

PubMed

Nonlinear Dimensionality Reduction by Minimum Curvilinearity for Unsupervised Discovery of Patterns in Multidimensional Proteomic Data.

2016

Methods in molecular biology (Clifton, N.J.)

Alessio M, Cannistraci CV

Plain English
This study looked at ways to simplify complex data from protein studies so researchers can better understand hidden patterns, especially in cases of neuropathic pain. It found that a new technique called minimum curvilinear embedding (MCE) outperformed the traditional method (PCA) in revealing important insights from the data. Specifically, MCE is more effective when there are many protein details compared to the number of samples, which is often a challenge in these types of studies. Who this helps: This benefits researchers looking to develop better treatments for patients with neuropathic pain.

PubMed

Gender, Contraceptives and Individual Metabolic Predisposition Shape a Healthy Plasma Lipidome.

2016

Scientific reports

Sales S, Graessler J, Ciucci S, Al-Atrib R, Vihervaara T +8 more

Plain English
This study looked at the types of fats (lipids) found in the blood of 71 healthy young Caucasian men and women to understand how these change based on gender and hormone use. It found that gender significantly influences lipid levels, especially for women using hormonal contraceptives, and about 25% of healthy young men showed early signs that could lead to metabolic syndrome. These findings help to create a better understanding of blood fat profiles, which is important for spotting health risks early on. Who this helps: This helps doctors and healthcare providers who are working to identify early signs of metabolic issues in patients.

PubMed

Serological immune response against ADAM10 pro-domain is associated with favourable prognosis in stage III colorectal cancer patients.

2016

Oncotarget

Álvarez-Fernández SM, Barbariga M, Cannizzaro L, Cannistraci CV, Hurley L +7 more

Plain English
Researchers studied the immune response to a protein called ADAM10 in patients with stage III colorectal cancer. They found that 74% of these patients produced specific antibodies against ADAM10, and those with these antibodies had a significantly longer time without cancer recurrence—from 23 months to 55 months. This is important because it suggests that measuring anti-ADAM10 antibodies can help predict better outcomes for patients with this type of cancer. Who this helps: This helps colorectal cancer patients and their doctors.

PubMed

Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients.

2016

Applied and environmental microbiology

Paroni Sterbini F, Palladini A, Masucci L, Cannistraci CV, Pastorino R +8 more

Plain English
This study looked at how proton pump inhibitors (PPIs), a common treatment for stomach problems, affect the types of bacteria in the stomach of patients with dyspepsia. Researchers analyzed samples from 24 patients and found that while H. pylori infection influenced the bacterial community, the use of the PPI omeprazole led to a significant increase in a type of bacteria called Streptococcus. This is important because it may change how doctors approach treating dyspeptic patients and identify who truly needs PPIs. Who this helps: This helps patients dealing with dyspepsia and their doctors by improving treatment strategies.

PubMed

The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions.

2015

Cellular microbiology

Mavromatis CH, Bokil NJ, Totsika M, Kakkanat A, Schaale K +7 more

Plain English
This study looked at how a specific type of bacteria, uropathogenic Escherichia coli (UPEC), interacts with immune cells in the body during urinary tract infections (UTIs). Researchers found that one strain of UPEC, called UTI89, can survive inside these immune cells for a longer time compared to another strain, 83972, which gets killed. They identified a gene called pspA that is important for UTI89's survival inside the immune cells, indicating new ways that the bacteria can evade the immune response. Who this helps: This research benefits patients with urinary tract infections by improving understanding of how infections occur and may lead to new treatment options.

PubMed

Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra.

2015

Scientific reports

Cannistraci CV, Abbas A, Gao X

Plain English
The researchers studied methods for cleaning up noisy multidimensional NMR spectra, which are important for determining protein structures. They introduced a new filter called the median-modified Wiener filter (MMWF) and its improved version (MMWF*) and found that these filters performed better than traditional wavelet-denoising and other methods. The new MMWF* showed stable high performance across different settings, making it easier to analyze protein structures consistently. Who this helps: This benefits scientists and researchers working on protein structure analysis.

PubMed

Highlighting nonlinear patterns in population genetics datasets.

2015

Scientific reports

Alanis-Lobato G, Cannistraci CV, Eriksson A, Manica A, Ravasi T

Plain English
This study explored ways to better understand population genetics by comparing two methods: Principal Component Analysis (PCA) and a new approach called non-centred Minimum Curvilinear Embedding (ncMCE). The researchers found that ncMCE can do a better job of identifying specific ethnic groups, successfully separating them when PCA fails—showing improved results even with messy data. This matters because it provides a more reliable method to analyze genetic data, helping scientists uncover important patterns that can influence research on diseases and heredity. Who this helps: This helps researchers and scientists studying genetics and population health.

PubMed

Erratum: From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks.

2015

Scientific reports

Cannistraci CV, Alanis-Lobato G, Ravasi T

PubMed

Drug target prioritization by perturbed gene expression and network information.

2015

Scientific reports

Isik Z, Baldow C, Cannistraci CV, Schroeder M

Plain English
This study looked at how changes in gene activity caused by drugs can help identify the proteins they target in cancer cells. Researchers analyzed over 500 drugs and found that just looking at these changes isn't enough to pinpoint drug targets effectively. Instead, they developed a new way called "local radiality" to better prioritize these targets, which could lead to discovering more diverse drug targets with fewer side effects. Who this helps: Patients with cancer who need more effective treatments.

PubMed

Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea.

2014

Molecular ecology

Moitinho-Silva L, Bayer K, Cannistraci CV, Giles EC, Ryu T +3 more

Plain English
This study examined the types and activity of microbes found in two different kinds of sea sponges from the Red Sea: one with a lot of microbes (high microbial abundance, or HMA) and one with fewer microbes (low microbial abundance, or LMA). Researchers gathered and analyzed over 800,000 sequences of microbial DNA, finding that the low microbial abundance sponge shared more similarities with the surrounding seawater compared to the high microbial abundance sponge. This is important because it shows that each sponge type has its own unique community of microbes, which may help scientists understand the role of these organisms in marine ecosystems. Who this helps: This helps marine researchers and conservationists studying ecosystem health.

PubMed

Increased expression of Myosin binding protein H in the skeletal muscle of amyotrophic lateral sclerosis patients.

2014

Biochimica et biophysica acta

Conti A, Riva N, Pesca M, Iannaccone S, Cannistraci CV +4 more

Plain English
This study looked at muscle samples from people with amyotrophic lateral sclerosis (ALS) and found that a protein called Myosin binding protein H (MyBP-H) was much more present in those samples compared to healthy individuals and other muscle disorders. Specifically, MyBP-H levels were linked to abnormal levels of other proteins that could disrupt muscle function. These findings suggest that measuring MyBP-H could help doctors distinguish ALS from other muscle diseases, which is important for diagnosis and understanding the disease’s development. Who this helps: This helps patients with ALS and their doctors.

PubMed

A promoter-level mammalian expression atlas.

2014

Nature

, Forrest AR, Kawaji H, Rehli M, Baillie JK +257 more

Plain English
This study examined how genes are activated in different types of cells throughout the human body and mice. Researchers found that while some genes are commonly active in many cell types, many have unique activation patterns depending on the cell type. Specifically, they discovered that only about 20% of genes are truly 'housekeeping' genes, while the majority have specific roles that vary across cell types. This knowledge helps researchers understand how cells function and can lead to new medical insights. Who this helps: This benefits researchers and medical professionals working on gene-related diseases and therapies.

PubMed

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater.

2014

FEMS microbiology ecology

Bayer K, Moitinho-Silva L, Brümmer F, Cannistraci CV, Ravasi T +1 more

Plain English
This study examined the types of genes found in the microbes living in marine sponges and nearby seawater in the Red Sea and the Mediterranean. Researchers discovered a total of 627 functional genes related to microbial activities, highlighting that while there are some differences in gene abundance, overall, the gene profiles of sponges and seawater are quite similar. This is important because it suggests that the functional roles of these microbes are consistent across different environments, promoting better understanding of marine ecosystems. Who this helps: This helps researchers and marine biologists studying marine life and ecosystems.

PubMed

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding.

2013

Bioinformatics (Oxford, England)

Cannistraci CV, Alanis-Lobato G, Ravasi T

Plain English
This study looked at how to better predict interactions between proteins, which are crucial for many cellular functions, using a method that reduces noise in the data. The researchers developed a new technique called non-centred minimum curvilinear embedding (ncMCE) and found that it outperformed existing methods by improving prediction accuracy. Specifically, their method showed significant advantages in predicting protein interactions, which means it can help researchers identify new protein links more effectively. Who this helps: This benefits scientists and researchers working in cell biology and drug development.

PubMed

Exploitation of genetic interaction network topology for the prediction of epistatic behavior.

2013

Genomics

Alanis-Lobato G, Cannistraci CV, Ravasi T

Plain English
This study looked at a new way to predict how genes interact with each other, which is important for understanding diseases and creating personalized treatments. The researchers developed a method that accurately predicts genetic interactions based on the structure of genetic networks, improving the prediction process and potentially allowing them to reduce the number of interactions that need to be tested in experiments by using a special index. This matters because it can streamline the research process and lead to faster advancements in disease treatment. Who this helps: This helps researchers and doctors working on genetic diseases and personalized medicine.

PubMed

Still need for compelling evidence to support the circadian dependence of infarct size after ST-elevation myocardial infarction.

2013

Circulation research

Ammirati E, Maseri A, Cannistraci CV

PubMed

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