Works by Zaikin, Alexey

Results: 48

Time series radiomics for the prediction of prostate cancer progression in patients on active surveillance.

Published in:

European Radiology, 2023, v. 33, n. 6, p. 3792, doi. 10.1007/s00330-023-09438-x

By:

Sushentsev, Nikita;
Rundo, Leonardo;
Abrego, Luis;
Li, Zonglun;
Nazarenko, Tatiana;
Warren, Anne Y.;
Gnanapragasam, Vincent J.;
Sala, Evis;
Zaikin, Alexey;
Barrett, Tristan;
Blyuss, Oleg

Publication type:

Article

Evaluating the Effect of Climate on Viral Respiratory Diseases Among Children Using AI.

Published in:

Journal of Clinical Medicine, 2024, v. 13, n. 23, p. 7474, doi. 10.3390/jcm13237474

By:

Krivonosov, Mikhail I.;
Pazukhina, Ekaterina;
Zaikin, Alexey;
Viozzi, Francesca;
Lazzareschi, Ilaria;
Manca, Lavinia;
Caci, Annamaria;
Santangelo, Rosaria;
Sanguinetti, Maurizio;
Raffaelli, Francesca;
Fiori, Barbara;
Zampino, Giuseppe;
Valentini, Piero;
Munblit, Daniel;
Blyuss, Oleg;
Buonsenso, Danilo

Publication type:

Article

Impact of Astrocytic Coverage of Synapses on the Short-Term Memory of a Computational Neuron-Astrocyte Network.

Published in:

Mathematics (2227-7390), 2022, v. 10, n. 18, p. 3275, doi. 10.3390/math10183275

By:

Li, Zonglun;
Tsybina, Yuliya;
Gordleeva, Susanna;
Zaikin, Alexey

Publication type:

Article

Symmetry in cancer networks identified: Proposal for multicancer biomarkers.

Published in:

Network Science, 2019, v. 7, n. 4, p. 541, doi. 10.1017/nws.2019.55

By:

Shinde, Pramod;
Marrec, Loïc;
Rai, Aparna;
Yadav, Alok;
Kumar, Rajesh;
Ivanchenko, Mikhail;
Zaikin, Alexey;
Jalan, Sarika

Publication type:

Article

Emergent digital bio-computation through spatial diffusion and engineered bacteria.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49264-3

By:

Fedorec, Alex J. H.;
Treloar, Neythen J.;
Wen, Ke Yan;
Dekker, Linda;
Ong, Qing Hsuan;
Jurkeviciute, Gabija;
Lyu, Enbo;
Rutter, Jack W.;
Zhang, Kathleen J. Y.;
Rosa, Luca;
Zaikin, Alexey;
Barnes, Chris P.

Publication type:

Article

A mathematical model of in vitro hepatocellular cholesterol and lipoprotein metabolism for hyperlipidemia therapy.

Published in:

PLoS ONE, 2022, v. 17, n. 6, p. 1, doi. 10.1371/journal.pone.0264903

By:

Efremov, Yuri;
Ermolaeva, Anastasia;
Vladimirov, Georgiy;
Gordleeva, Susanna;
Svistunov, Andrey;
Zaikin, Alexey;
Timashev, Peter

Publication type:

Article

Improved early detection of ovarian cancer using longitudinal multimarker models.

Published in:

2020

By:

Whitwell, Harry J.;
Worthington, Jenny;
Blyuss, Oleg;
Gentry-Maharaj, Aleksandra;
Ryan, Andy;
Gunu, Richard;
Kalsi, Jatinderpal;
Menon, Usha;
Jacobs, Ian;
Zaikin, Alexey;
Timms, John F.

Publication type:

journal article

Development of PancRISK, a urine biomarker-based risk score for stratified screening of pancreatic cancer patients.

Published in:

2020

By:

Blyuss, Oleg;
Zaikin, Alexey;
Cherepanova, Valeriia;
Munblit, Daniel;
Kiseleva, Elena M.;
Prytomanova, Olga M.;
Duffy, Stephen W.;
Crnogorac-Jurcevic, Tatjana

Publication type:

journal article

Integrated Placental Modelling of Histology with Gene Expression to Identify Functional Impact on Fetal Growth.

Published in:

Cells (2073-4409), 2023, v. 12, n. 7, p. 1093, doi. 10.3390/cells12071093

By:

Yong, Hannah Ee Juen;
Maksym, Katarzyna;
Yusoff, Muhammad Ashraf Bin;
Salazar-Petres, Esteban;
Nazarenko, Tatiana;
Zaikin, Alexey;
David, Anna L.;
Hillman, Sara L.;
Sferruzzi-Perri, Amanda N.

Publication type:

Article

Asymmetry in Erythroid-Myeloid differentiation switch and the role of timing in a binary cell fate decision.

Published in:

Frontiers in Immunology, 2013, v. 4, p. 1, doi. 10.3389/fimmu.2013.00426

By:

Alagha, Afnan;
Zaikin, Alexey

Publication type:

Article

Novel efficient reservoir computing methodologies for regular and irregular time series classification: Novel efficient reservoir computing methodologies: Z.Li et al.

Published in:

Nonlinear Dynamics, 2025, v. 113, n. 5, p. 4045, doi. 10.1007/s11071-024-10244-3

By:

Li, Zonglun;
Andreev, Andrey;
Hramov, Alexander;
Blyuss, Oleg;
Zaikin, Alexey

Publication type:

Article

Parenclitic Network Analysis of Methylation Data for Cancer Identification.

Published in:

PLoS ONE, 2017, v. 12, n. 1, p. 1, doi. 10.1371/journal.pone.0169661

By:

Karsakov, Alexander;
Bartlett, Thomas;
Ryblov, Artem;
Meyerov, Iosif;
Ivanchenko, Mikhail;
Zaikin, Alexey

Publication type:

Article

Modeling Working Memory in a Spiking Neuron Network Accompanied by Astrocytes.

Published in:

Frontiers in Cellular Neuroscience, 2021, v. 15, p. N.PAG, doi. 10.3389/fncel.2021.631485

By:

Gordleeva, Susanna Yu.;
Tsybina, Yuliya A.;
Krivonosov, Mikhail I.;
Ivanchenko, Mikhail V.;
Zaikin, Alexey A.;
Kazantsev, Victor B.;
Gorban, Alexander N.

Publication type:

Article

Parenclitic and Synolytic Networks Revisited.

Published in:

Frontiers in Genetics, 2021, v. 12, p. 1, doi. 10.3389/fgene.2021.733783

By:

Nazarenko, Tatiana;
Whitwell, Harry J.;
Blyuss, Oleg;
Zaikin, Alexey

Publication type:

Article

The Human Body as a Super Network: Digital Methods to Analyze the Propagation of Aging.

Published in:

Frontiers in Aging Neuroscience, 2020, v. 12, p. 1, doi. 10.3389/fnagi.2020.00136

By:

Whitwell, Harry J.;
Bacalini, Maria Giulia;
Blyuss, Oleg;
Chen, Shangbin;
Garagnani, Paolo;
Gordleeva, Susan Yu;
Jalan, Sarika;
Ivanchenko, Mikhail;
Kanakov, Oleg;
Kustikova, Valentina;
Mariño, Ines P.;
Meyerov, Iosif;
Ullner, Ekkehard;
Franceschi, Claudio;
Zaikin, Alexey

Publication type:

Article

A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks.

Published in:

PLoS ONE, 2017, v. 12, n. 8, p. 1, doi. 10.1371/journal.pone.0182015

By:

Mariño, Inés P.;
Zaikin, Alexey;
Míguez, Joaquín

Publication type:

Article

Serial Patterns of Ovarian Cancer Biomarkers in a Prediagnosis Longitudinal Dataset.

Published in:

BioMed Research International, 2015, v. 2015, p. 1, doi. 10.1155/2015/681416

By:

Blyuss, Oleg;
Gentry-Maharaj, Alex;
Fourkala, Evangelia-Orania;
Ryan, Andy;
Zaikin, Alexey;
Menon, Usha;
Jacobs, Ian;
Timms, John F.

Publication type:

Article

Variations in the Intragene Methylation Profiles Hallmark Induced Pluripotency.

Published in:

BioMed Research International, 2015, v. 2015, p. 1, doi. 10.1155/2015/976362

By:

Druzhkov, Pavel;
Zolotykh, Nikolay;
Meyerov, Iosif;
Alsaedi, Ahmed;
Shutova, Maria;
Ivanchenko, Mikhail;
Zaikin, Alexey

Publication type:

Article

Multi-Marker Longitudinal Algorithms Incorporating HE4 and CA125 in Ovarian Cancer Screening of Postmenopausal Women.

Published in:

Cancers, 2020, v. 12, n. 7, p. 1931, doi. 10.3390/cancers12071931

By:

Gentry-Maharaj, Aleksandra;
Blyuss, Oleg;
Ryan, Andy;
Burnell, Matthew;
Karpinskyj, Chloe;
Gunu, Richard;
Kalsi, Jatinderpal K.;
Dawnay, Anne;
Marino, Ines P.;
Manchanda, Ranjit;
Lu, Karen;
Yang, Wei-Lei;
Timms, John F.;
Parmar, Mahesh;
Skates, Steven J.;
Bast, Robert C.;
Jacobs, Ian J.;
Zaikin, Alexey;
Menon, Usha

Publication type:

Article

Astrocytes mediate analogous memory in a multi-layer neuron–astrocyte network.

Published in:

Neural Computing & Applications, 2022, v. 34, n. 11, p. 9147, doi. 10.1007/s00521-022-06936-9

By:

Tsybina, Yuliya;
Kastalskiy, Innokentiy;
Krivonosov, Mikhail;
Zaikin, Alexey;
Kazantsev, Victor;
Gorban, Alexander N.;
Gordleeva, Susanna

Publication type:

Article

Bayesian and deep‐learning models applied to the early detection of ovarian cancer using multiple longitudinal biomarkers.

Published in:

Cancer Medicine, 2024, v. 13, n. 7, p. 1, doi. 10.1002/cam4.7163

By:

Abrego, Luis;
Zaikin, Alexey;
Marino, Ines P.;
Krivonosov, Mikhail I.;
Jacobs, Ian;
Menon, Usha;
Gentry‐Maharaj, Aleksandra;
Blyuss, Oleg

Publication type:

Article

Cancer-associated autoantibodies to MUC1 and MUC4-A blinded case-control study of colorectal cancer in UK collaborative trial of ovarian cancer screening.

Published in:

International Journal of Cancer, 2014, v. 134, n. 9, p. 2180, doi. 10.1002/ijc.28538

By:

Pedersen, Johannes W.;
Gentry‐Maharaj, Aleksandra;
Nøstdal, Alexander;
Fourkala, Evangelia‐Ourania;
Dawnay, Anne;
Burnell, Matthew;
Zaikin, Alexey;
Burchell, Joy;
Papadimitriou, Joyce Taylor;
Clausen, Henrik;
Jacobs, Ian;
Menon, Usha;
Wandall, Hans H.

Publication type:

Article

Systems Medicine of Cancer: Bringing Together Clinical Data and Nonlinear Dynamics of Genetic Networks.

Published in:

Computational & Mathematical Methods in Medicine, 2016, p. 1, doi. 10.1155/2016/7904693

By:

Blyuss, Konstantin B.;
Manchanda, Ranjit;
Kurths, Jürgen;
Alsaedi, Ahmed;
Zaikin, Alexey

Publication type:

Article

Network, degeneracy and bow tie integrating paradigms and architectures to grasp the complexity of the immune system.

Published in:

Theoretical Biology & Medical Modelling, 2010, v. 7, p. 32, doi. 10.1186/1742-4682-7-32

By:

Tieri, Paolo;
Grignolio, Andrea;
Zaikin, Alexey;
Mishto, Michele;
Remondini, Daniel;
Castellani, Gastone C.;
Franceschi, Claudio

Publication type:

Article

Integrated Information in the Spiking–Bursting Stochastic Model.

Published in:

Entropy, 2020, v. 22, n. 12, p. 1334, doi. 10.3390/e22121334

By:

Kanakov, Oleg;
Gordleeva, Susanna;
Zaikin, Alexey

Publication type:

Article

Integrated Information as a Measure of Cognitive Processes in Coupled Genetic Repressilators.

Published in:

Entropy, 2019, v. 21, n. 4, p. 382, doi. 10.3390/e21040382

By:

Abrego, Luis;
Zaikin, Alexey

Publication type:

Article

The 20S Proteasome Splicing Activity Discovered by SpliceMet.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000830

By:

Liepe, Juliane;
Mishto, Michele;
Textoris-Taube, Kathrin;
Janek, Katharina;
Keller, Christin;
Henklein, Petra;
Kloetzel, Peter Michael;
Zaikin, Alexey

Publication type:

Article

Analysis of Multidimensional Clinical and Physiological Data with Synolitical Graph Neural Networks.

Published in:

Technologies (2227-7080), 2025, v. 13, n. 1, p. 13, doi. 10.3390/technologies13010013

By:

Krivonosov, Mikhail;
Nazarenko, Tatiana;
Ushakov, Vadim;
Vlasenko, Daniil;
Zakharov, Denis;
Chen, Shangbin;
Blyus, Oleg;
Zaikin, Alexey

Publication type:

Article

Editorial: Multiscale Modeling of Rhythm, Pattern and Information Generation: from Genome to Physiome.

Published in:

2020

By:

Chen, Shangbin;
Zaikin, Alexey

Publication type:

Editorial

Post-COVID-19 Condition Prediction in Hospitalised Cancer Patients: A Machine Learning-Based Approach.

Published in:

Cancers, 2025, v. 17, n. 4, p. 687, doi. 10.3390/cancers17040687

By:

Mahvash Mohammadi, Sara;
Rumyantsev, Mikhail;
Abdeeva, Elina;
Baimukhambetova, Dina;
Bobkova, Polina;
El-Taravi, Yasmin;
Pikuza, Maria;
Trefilova, Anastasia;
Zolotarev, Aleksandr;
Andreeva, Margarita;
Iakovleva, Ekaterina;
Bulanov, Nikolay;
Avdeev, Sergey;
Pazukhina, Ekaterina;
Zaikin, Alexey;
Kapustina, Valentina;
Fomin, Victor;
Svistunov, Andrey A.;
Timashev, Peter;
Avdeenko, Nina

Publication type:

Article

Technical and biological sources of unreliability of Infinium probes on Illumina methylation microarrays.

Published in:

Clinical Epigenetics, 2024, v. 16, n. 1, p. 1, doi. 10.1186/s13148-024-01739-2

By:

Nazarenko, Tatiana;
Vavourakis, Charlotte Dafni;
Jones, Allison;
Evans, Iona;
Schreiberhuber, Lena;
Kastner, Christine;
Ishaq-Parveen, Isma;
Redl, Elisa;
Watson, Anthony W.;
Brandt, Kirsten;
Carter, Clive;
Zaikin, Alexey;
Herzog, Chiara Maria Stella;
Widschwendter, Martin

Publication type:

Article

Leptin induces upregulation of sphingosine kinase 1 in oestrogen receptor-negative breast cancer via Src family kinase-mediated, janus kinase 2-independent pathway.

Published in:

2014

By:

Alshaker, Heba;
Krell, Jonathan;
Frampton, Adam E;
Waxman, Jonathan;
Blyuss, Oleg;
Zaikin, Alexey;
Winkler, Mathias;
Stebbing, Justin;
Yagüe, Ernesto;
Pchejetski, Dmitri

Publication type:

journal article

Complex and unexpected dynamics in simple genetic regulatory networks.

Published in:

International Journal of Modern Physics B: Condensed Matter Physics; Statistical Physics; Applied Physics, 2014, v. 28, n. 14, p. 1, doi. 10.1142/S0217979214300060

By:

Borg, Yanika;
Ullner, Ekkehard;
Alaghat, Afnan;
Alsaedi, Ahmed;
Nesbeth, Darren;
Zaikin, Alexey

Publication type:

Article

Editorial: Closed-loop iterations between neuroscience and artificial intelligence.

Published in:

Frontiers in Systems Neuroscience, 2022, v. 16, p. 1, doi. 10.3389/fnsys.2022.1002095

By:

Jinyu Li;
Zaikin, Alexey;
Xiaochun Zhang;
Shangbin Chen

Publication type:

Article

Effect of Noise in Intelligent Cellular Decision Making.

Published in:

PLoS ONE, 2015, v. 10, n. 5, p. 1, doi. 10.1371/journal.pone.0125079

By:

Bates, Russell;
Blyuss, Oleg;
Alsaedi, Ahmed;
Zaikin, Alexey

Publication type:

Article

Multi-Input Distributed Classifiers for Synthetic Genetic Circuits.

Published in:

PLoS ONE, 2015, v. 10, n. 5, p. 1, doi. 10.1371/journal.pone.0125144

By:

Kanakov, Oleg;
Kotelnikov, Roman;
Alsaedi, Ahmed;
Tsimring, Lev;
Huerta, Ramón;
Zaikin, Alexey;
Ivanchenko, Mikhail

Publication type:

Article

A DNA Methylation Network Interaction Measure, and Detection of Network Oncomarkers.

Published in:

PLoS ONE, 2014, v. 9, n. 1, p. 1, doi. 10.1371/journal.pone.0084573

By:

Bartlett, Thomas E.;
Olhede, Sofia C.;
Zaikin, Alexey

Publication type:

Article

Parameter Estimation Methods for Chaotic Intercellular Networks.

Published in:

PLoS ONE, 2013, v. 8, n. 11, p. 1, doi. 10.1371/journal.pone.0079892

By:

Mariño, Inés P.;
Ullner, Ekkehard;
Zaikin, Alexey

Publication type:

Article

Corruption of the Intra-Gene DNA Methylation Architecture Is a Hallmark of Cancer.

Published in:

PLoS ONE, 2013, v. 8, n. 7, p. 1, doi. 10.1371/journal.pone.0068285

By:

Bartlett, Thomas E.;
Zaikin, Alexey;
Olhede, Sofia C.;
West, James;
Teschendorff, Andrew E.;
Widschwendter, Martin

Publication type:

Article

Interplay between Path and Speed in Decision Making by High-Dimensional Stochastic Gene Regulatory Networks.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0040085

By:

Nené, Nuno R.;
Zaikin, Alexey

Publication type:

Article

Speed-Dependent Cellular Decision Making in Nonequilibrium Genetic Circuits.

Published in:

PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0032779

By:

Nené, Nuno R.;
Garca-Ojalvo, Jordi;
Zaikin, Alexey

Publication type:

Article

Timing Cellular Decision Making Under Noise via Cell- Cell Communication.

Published in:

PLoS ONE, 2009, v. 4, n. 3, p. 1, doi. 10.1371/journal.pone.0004872

By:

Koseska, Aneta;
Zaikin, Alexey;
Kurths, Jürgen;
García-Ojalvo, Jordi

Publication type:

Article

An Account of Models of Molecular Circuits for Associative Learning with Reinforcement Effect and Forced Dissociation.

Published in:

Sensors (14248220), 2022, v. 22, n. 15, p. 5907, doi. 10.3390/s22155907

By:

Li, Zonglun;
Fattah, Alya;
Timashev, Peter;
Zaikin, Alexey

Publication type:

Article

Unraveling Aβ-Mediated Multi-Pathway Calcium Dynamics in Astrocytes: Implications for Alzheimer's Disease Treatment From Simulations.

Published in:

Frontiers in Physiology, 2021, v. 12, p. 1, doi. 10.3389/fphys.2021.767892

By:

Liu, Langzhou;
Gao, Huayi;
Zaikin, Alexey;
Chen, Shangbin

Publication type:

Article

Optimal Length Transportation Hypothesis to Model Proteasome Product Size Distribution.

Published in:

Journal of Biological Physics, 2006, v. 32, n. 3/4, p. 231, doi. 10.1007/s10867-006-9014-z

By:

Zaikin, Alexey;
Kurths, Juergen

Publication type:

Article

Brain aging and garbage cleaning: Modelling the role of sleep, glymphatic system, and microglia senescence in the propagation of inflammaging.

Published in:

Seminars in Immunopathology, 2020, v. 42, n. 5, p. 647, doi. 10.1007/s00281-020-00816-x

By:

Gordleeva, Susanna;
Kanakov, Oleg;
Ivanchenko, Mikhail;
Zaikin, Alexey;
Franceschi, Claudio

Publication type:

Article

Synthetic biology routes to bio-artificial intelligence.

Published in:

Essays in Biochemistry, 2016, v. 60, n. 4, p. 381, doi. 10.1042/EBC20160014

By:

Nesbeth, Darren N.;
Zaikin, Alexey;
Saka, Yasushi;
Romano, M. Carmen;
Giuraniuc, Claudiu V.;
Oleg, Kanakov;
Laptyeva, Tetyana

Publication type:

Article

Identification of a serum proteomic biomarker panel using diagnosis specific ensemble learning and symptoms for early pancreatic cancer detection.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 8, p. 1, doi. 10.1371/journal.pcbi.1012408

By:

Ney, Alexander;
Nené, Nuno R.;
Sedlak, Eva;
Acedo, Pilar;
Blyuss, Oleg;
Whitwell, Harry J.;
Costello, Eithne;
Gentry-Maharaj, Aleksandra;
Williams, Norman R.;
Menon, Usha;
Fusai, Giuseppe K.;
Zaikin, Alexey;
Pereira, Stephen P.

Publication type:

Article