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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Visualization of Any Data with Elastic Map Method

Recommended citation: Gorban AN, Pitenko A, Zinovyev A, Wunsch D. Visualization of Any Data with Elastic Map Method. Proceedings of Artificial Neural Networks in Engineering, St. Louis, MO, November, 2001

Pitenko A.A

Published in , 1900

Recommended citation: Gorban AN, Zinovyev A.Yu. Pitenko A.A. Visualization of data: Method of elastic maps (in Russian). Neurocomputeri, 2002. N4. p.19-30.

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

Published in , 1900

Recommended citation: Chanrion M, Kuperstein I, Barriere C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Bieche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Ne P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A^, Robine S.^. Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. 2014. Nature Communications, 5:5005 https://www.nature.com/articles/ncomms6005

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

Published in , 1900

Recommended citation: Biton A, Bernard-Pierrot I, Lou Y, Krucker C, Chapeaublanc E, Rubio Perez C, Lopez Bigas N, Kamoun A, Neuzillet Y, Gestraud P, Grieco G, Rebouissou S, de Reynies A, Benhamou S, Lebret T, Southgate J, Barillot E, Allory Y, Zinovyev A.^, Radvanyi F^. Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. 2014. Cell Reports 9(4), 1235-1245 https://www.cell.com/cell-reports/fulltext/S2211-1247(14)00904-8

Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of AsiDNA and PARP inhibitors

Published in , 1900

Recommended citation: Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun J.-S, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M. Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of AsiDNA and PARP inhibitors. 2016. Clinical Cancer Research, pii: clincanres.1193.2016. http://clincancerres.aacrjournals.org/content/23/4/1001.long

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

Recommended citation: Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan G-C, Pinello L. STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data. STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data. 2018. Biorxiv preprint 10.1101/302554v2 https://www.biorxiv.org/content/10.1101/302554v2

Fibroblast heterogeneity and immunosuppressive environment in human breast cancer

Published in , 1900

Recommended citation: Costa A, Kieffer Y, Scholer-Dahirel A, Pelon F, Bourachot B, Cardon M, Sirven P, Magagna I, Fuhrmann L, Bernard C, Bonneau C, Kondratova M, Kuperstein I, Zinovyev A, Givel A.-M, Parrini M.-C, Soumelis V, Vincent-Salomon A, Mechta-Grigoriou F. Fibroblast heterogeneity and immunosuppressive environment in human breast cancer. 2018. Cancer Cell 33(3):463-479.e10. https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30011-4

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Published in , 1900

Recommended citation: Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novere N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. 2018. NPJ systems biology and applications 4 (1), 21 https://www.nature.com/articles/s41540-018-0059-y

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Published in , 1900

Recommended citation: Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, Paulevé L. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. 2018. Front Physiol 9:680. https://www.frontiersin.org/articles/10.3389/fphys.2018.00680/full

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Published in , 1900

Recommended citation: Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky992. https://academic.oup.com/nar/article/47/D1/D614/5146204

Posts

Future Blog Post

less than 1 minute read

Published:

This post will show up by default. To disable scheduling of future posts, edit config.yml and set future: false.

Blog Post number 4

less than 1 minute read

Published:

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 3

less than 1 minute read

Published:

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 2

less than 1 minute read

Published:

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

Blog Post number 1

less than 1 minute read

Published:

This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.

portfolio

publications

Published in , 1900

Visualization of Any Data with Elastic Map Method

Published in , 1900

Recommended citation: Gorban AN, Pitenko A, Zinovyev A, Wunsch D. Visualization of Any Data with Elastic Map Method. Proceedings of Artificial Neural Networks in Engineering, St. Louis, MO, November, 2001

Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization

Published in , 1900

Recommended citation: Gorban AN, Zinovyev A. Elastic Maps and Nets for Approximating Principal Manifolds and Their Application to Microarray Data Visualization. In Principal Manifolds for Data Visualization and Dimension Reduction, Lecture Notes in Computational Science and Engineering 58, Springer, Berlin - Heidelberg, 2008, 96-130 https://arxiv.org/abs/0801.0168

Published in , 1900

Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut

Published in , 1900

Recommended citation: Chanrion M, Kuperstein I, Barriere C, El Marjou F, Cohen D, Vignjevic D, Stimmer L, Paul-Gilloteaux P, Bieche I, Tavares Sdos R, Boccia GF, Cacheux W, Meseure D, Fre S, Martignetti L, Legoix-Ne P, Girard E, Fetler L, Barillot E, Louvard D, Zinovyev A^, Robine S.^. Concomitant Notch activation and p53 deletion trigger epithelial-to-mesenchymal transition and metastasis in mouse gut. 2014. Nature Communications, 5:5005 https://www.nature.com/articles/ncomms6005

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

Published in , 1900

Recommended citation: Biton A, Bernard-Pierrot I, Lou Y, Krucker C, Chapeaublanc E, Rubio Perez C, Lopez Bigas N, Kamoun A, Neuzillet Y, Gestraud P, Grieco G, Rebouissou S, de Reynies A, Benhamou S, Lebret T, Southgate J, Barillot E, Allory Y, Zinovyev A.^, Radvanyi F^. Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. 2014. Cell Reports 9(4), 1235-1245 https://www.cell.com/cell-reports/fulltext/S2211-1247(14)00904-8

Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of AsiDNA and PARP inhibitors

Published in , 1900

Recommended citation: Jdey W, Thierry S, Russo C, Devun F, Al Abo M, Noguiez-Hellin P, Sun J.-S, Barillot E, Zinovyev A, Kuperstein I, Pommier Y, Dutreix M. Drug Driven Synthetic Lethality: bypassing tumor cell genetics with a combination of AsiDNA and PARP inhibitors. 2016. Clinical Cancer Research, pii: clincanres.1193.2016. http://clincancerres.aacrjournals.org/content/23/4/1001.long

Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific And Reproducible Immune-related Signals

Published in , 1900

Recommended citation: Czerwinska U, Cantini L, Kairov U, Barillot E, Zinovyev A. Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific And Reproducible Immune-related Signals. Proceedings of International Conference on Latent Variable Analysis and Signal Separation, Surrey, UK, 2-6 July 2018. https://link.springer.com/chapter/10.1007/978-3-319-93764-9_46

Fibroblast heterogeneity and immunosuppressive environment in human breast cancer

Published in , 1900

Recommended citation: Costa A, Kieffer Y, Scholer-Dahirel A, Pelon F, Bourachot B, Cardon M, Sirven P, Magagna I, Fuhrmann L, Bernard C, Bonneau C, Kondratova M, Kuperstein I, Zinovyev A, Givel A.-M, Parrini M.-C, Soumelis V, Vincent-Salomon A, Mechta-Grigoriou F. Fibroblast heterogeneity and immunosuppressive environment in human breast cancer. 2018. Cancer Cell 33(3):463-479.e10. https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30011-4

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Published in , 1900

Recommended citation: Mazein A, Ostaszewski M, Kuperstein I, Watterson S, Le Novere N, Lefaudeux D, De Meulder B, Pellet J, Balaur I, Saqi M, Nogueira MM, He F, Parton A, Lemonnier N, Gawron P, Gebel S, Hainaut P, Ollert M, Dogrusoz U, Barillot E, Zinovyev A, Schneider R, Balling R, Auffray C. Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. 2018. NPJ systems biology and applications 4 (1), 21 https://www.nature.com/articles/s41540-018-0059-y

The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Published in , 1900

Recommended citation: Naldi A, Hernandez C, Levy N, Stoll G, Monteiro PT, Chaouiya C, Helikar T, Zinovyev A, Calzone L, Cohen-Boulakia S, Thieffry D, Paulevé L. The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. 2018. Front Physiol 9:680. https://www.frontiersin.org/articles/10.3389/fphys.2018.00680/full

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

Published in , 1900

Recommended citation: Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. 2019. Nucleic Acids Res. 47(D1):D614-D624. https://academic.oup.com/nar/article/47/D1/D614/5146204

talks

teaching

Basic introduction into Windows and Microsoft Office tools

Open free course, Krasnoyarsk State Technical University, 1900

In 1998-1999 I participated in creation of a free and open to public intensive 2 weeks introductory course on the basic use of Windows operating system and Microsoft Office tools. Various modifications of the course were adapted to students, general public, children (including 8-10 years old).

Data integration and analysis in cancer research

Master 2 course, Ecole normale superieure, 1900

Starting from 2009, each year I participate in the Systems biology, genomics and bioinformatics master 2 module at ENS, with 3 hours mini-course on data integration in cancer research and systems biology of cancer. I introduce types of data analyzed in cancer research, give examples of multi-omics data analysis, explain, based on real projects, application of some machine learning techniques (such as Independent Component Analysis) to omics data.

Computational Systems Biology of Cancer

PhD course, Alma Ata University, 1900

As a part of joint Kazakhstan-France PhD program, I developed and delivered a 40-hours course on Computational Systems Biology of Cancer, covering many aspects of technology, data analysis, machine learning techniques, mathematical modeling of networks in cancer research. The course included approximately 15 hours of intensive hands-on sessions.

Omics Data Analysis and Medical Applications

Professional course, Skoltech University, 1900

In July 2015, I was as principal organizer, developer and lecturer of 7-days intensive course Omics Data Analysis and Medical Applications aimed at professional bioinformaticians and PhD students. The course covered a wide range of topics in application and analysis of omics data in various diseases including cancer. Theoretical lectures were accompanied by hands-on sessions.

Mathematical modeling of biological systems

Pre-doctoral course, Universite Paris, Institute of Technology and Innovation, 1900

In 2016 and 2017 I was a co-organizer and lecturer of 80 hours teaching module “Mathematical Modeling of Biological Systems” as a part of the pre-doctoral training program at PSL-ITI. The course covered a wide range of topics related to application of mathematical modeling (in wide sense) to understand biology. My lectures in the course were devoted to application of machine learning in cancer research. In 2018, I organized a limited edition of this module, with only few lectures.

International Curie Course on Computational Systems Biology of Cancer

PhD students, Institut Curie, 1900

I co-organize and give lectures at yearly International Curie Course on Computational Systems Biology of Cancer. In 2018, I gave a short course on application of machine learning for characterizing tumor microenvironment. The 2019 edition of International Curie course on computational biology will be devoted to single-cell data analysis. The 2020 edition of International Curie course will focus on application of machine learning and artificial intelligence in biology of cancer.

Participation in teaching courses as invited lecturer

---, Various venues, 1900

I constantly participate as invited lecturer in courses and summer schools organized worldwide. For example, I participated in the thematic school Analysis of Cancer genome (2015) and in the Genopole Summer School on Bioinformatic and Biostatistic tools in medical genomics in 2018. My topics are various, including data visualization, some aspects of machine learning for biomedical applications, mathematical modeling in biology and introductory lectures into systems biology and cancer bioinformatics.