netphorest.science

NetPhorest 2.0

Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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NetPhorest 2.0 | netphorest.science Reviews

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Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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NetPhorest 2.0 | netphorest.science Reviews

https://netphorest.science

Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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netphorest.science

1

NetPhorest 2.0

http://www.netphorest.science/help.shtml

Both algorithms work on the same input data, and you can switch at any point of the workflow between the different algorithms. Using KinomeXplorer on mouse. KinomeXplorer was trained on human and yeast data, and it is possible to use KinomeXplorer on their neighbour species, such as mouse. There are many studies that employed NetworKIN in species other than human and yeast, from which you can get some idea. For the analysis of high-throughput experiments (more than 100 sites), please refer to the high-th...

2

NetPhorest 2.0

http://www.netphorest.science/download.shtml

Here you can download the precomputed data for all available kinase predictors against ENSEMBL version 59 on known phosphorylation sites from the KinomeXplorer-DB. Version 59 of Ensembl protein sequences for human. Version 74 of Ensembl protein sequences for yeast. If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4. NetworKIN3.0 release.zip.

3

NetPhorest 2.0

http://www.netphorest.science/index_ht.shtml

Select the sequence database:. Human - Ensembl 74. Human - Ensembl 73. Human - Ensembl 72. Human - Ensembl 71. Human - Ensembl 70. Human - Ensembl 69. Human - Ensembl 68. Human - STRING 9.0. Human - Uniprot 2013/12. Human - Uniprot 2013/01 (Maxquant). Human - NCBI 62. Yeast - Ensembl 74. Yeast - Ensembl 73. Yeast - Ensembl 72. Yeast - Ensembl 71. Yeast - Ensembl 70. Yeast - Ensembl 69. Yeast - Ensembl 68. Yeast - Uniprot 2013/12. Yeast - NCBI 62. Put modified sites below in the format:.

4

NetPhorest 2.0

http://www.netphorest.science/index.shtml

Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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lindinglab.science

Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells — Rune Linding : Research Group

http://www.lindinglab.science/news

Only in current section. Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells. Scientists have discovered how genetic cancer mutations systematically attack the networks controlling human cells, knowledge critical for the future development of personalized precision cancer treatments. Lori Waters, Waters Biomedical, 2015. Computational Rosetta Stone decodes Mutations Rewiring Cancer Signaling. Lead researcher on the projects, Prof Dr Rune Linding from the Biotech Research and Innovation Cen...

lindinglab.org

Tony Pawson (1952 - 2013) — Rune Linding : Research Group

http://www.lindinglab.org/news/tony-pawson-1952-2013

Only in current section. Tony Pawson (1952 - 2013). Tony Pawson (1952 - 2013). The entire world-wide research community mourns the passing of Dr Tony Pawson. It is with great sadness that we learned that we have lost our great hero, close friend, fantastic mentor, superb colleague, wonderful human being and maverick of a scientist Tony Pawson. Across biology and life-sciences this will be felt deep and long. There is no field we can imagine that will not be touched by this massive loss. Take care and sta...

lindinglab.org

Links — Rune Linding : Research Group

http://www.lindinglab.org/links

Only in current section. Links to other laboratories, useful tools and databases, institutional units. Doug Lauffenburger : Research Group. Department of Biological Engineering Massachusetts Institute of Technology (MIT). Laboratory of Norbert Perrimon, Ph.D. Department of Genetics Harvard Medical School Howard Hughes Medical Institute. Institute of Molecular Life Sciences University of Zurich. Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital. Simple Modular Architecture Research Tool.

lindinglab.org

Publications — Rune Linding : Research Group

http://www.lindinglab.org/Publications

Only in current section. Here, we provide all our research publications and related information, including web-services and supplements. Linding Lab, BRIC [2014-present]. Publications from our group at the Biotech Research and Innovation Center (BRIC), University of Copenhagen (UCPH). Linding Lab, DTU [work from 2011-2014]. Publications of the Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU).

lindinglab.org

Press — Rune Linding : Research Group

http://www.lindinglab.org/press

Only in current section. Press releases related to our research. KU-forskere slår igennem med banebrydende kræftforskning. GENNEMBRUD - Det anerkendte tidskrift CELL hylder KU-forskning i spritny publikation. Resultaterne kan ændre måden vi undersøger og behandler kræftpatienter på, siger laboratorieleder. Using Proteomics to Understand How Genetic Mutations Rewire Cancer Cells. University of Copenhagen (UCPH) and Beckman Coulter Genomics (BCG) Collaborate to Unravel How Mutations Rewire Cancer Cells.

lindinglab.org

Rune Linding : Research Group

http://www.lindinglab.org/accessibility-info

Only in current section. This site uses the Open Source Content Management System Plone. And has been designed to be completely accessible and usable, working in accordance with the Web Content Accessibility Guidelines (. V10) If there is anything on this site — accessibility or validation related — that is not according to the standard, please contact the Site Administration. And not the Plone Team. Access keys are a navigation device enabling you to get around this web site using your keyboard. Are sub...

lindinglab.org

Funding — Rune Linding : Research Group

http://www.lindinglab.org/funding

Only in current section. We gratefully acknowledge support from the following agencies. Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells. Sep 17, 2015. Enzyme paves the way for the spread of cancer cells to bones. May 27, 2015. Linding Lab moves to BRIC@UCPH. Jul 31, 2014. Tony Pawson (1952 - 2013). Aug 11, 2013. Navigating cancer network attractors for tumor-specific therapy. Sep 16, 2012. August 2016 ». Powered by Plone and Python.

lindinglab.org

Photos — Rune Linding : Research Group

http://www.lindinglab.org/photos

Only in current section. Fish Creek Falls, Steamboat Springs, CO, USA. From left to right (top to bottom): Rune Linding, James Longden, Franziska Völlmy, Xavier Robin, Jinho Kim, Jesper Ferkinghoff-Borg, Craig Simpson and Mathias Engel. Summer 2013 - Enroute to Volcano Hekla, Selfoss, Iceland. Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells. Sep 17, 2015. Enzyme paves the way for the spread of cancer cells to bones. May 27, 2015. Linding Lab moves to BRIC@UCPH. Jul 31, 2014.

lindinglab.org

Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells — Rune Linding : Research Group

http://www.lindinglab.org/news

Only in current section. Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells. Scientists have discovered how genetic cancer mutations systematically attack the networks controlling human cells, knowledge critical for the future development of personalized precision cancer treatments. Lori Waters, Waters Biomedical, 2015. Computational Rosetta Stone decodes Mutations Rewiring Cancer Signaling. Lead researcher on the projects, Prof Dr Rune Linding from the Biotech Research and Innovation Cen...

lindinglab.org

Navigating cancer network attractors for tumor-specific therapy — Rune Linding : Research Group

http://www.lindinglab.org/news/navigating-cancer-network-attractors-for-tumor-specific-therapy

Only in current section. Navigating cancer network attractors for tumor-specific therapy. Navigating cancer network attractors for tumor-specific therapy. Perspective in Nature Biotechnology - Creixell et al. 2012. Digital ‘Rosetta Stone’ Decrypts How Mutations Rewire Cancer Cells. Sep 17, 2015. Enzyme paves the way for the spread of cancer cells to bones. May 27, 2015. Linding Lab moves to BRIC@UCPH. Jul 31, 2014. Tony Pawson (1952 - 2013). Aug 11, 2013. Sep 16, 2012. Linding Lab moves to BRIC@UCPH.

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netphorest.info

NetPhorest 2.1

NetPhorest 2.1 Update. We are happy to announce the release of NetPhorest 2.1, which fixes two major bugs that resulted in arbitrary scores from neural network predictors on SH2 domain, and partially arbitrary scores from neural networks on other domains. PSSM/scansite predictors remain unchanged. Both web and command line versions were affected. We recommend repeating any analysis performed before May XX, 2017. Learn more and download the updated binaries on the download page.

netphorest.science

NetPhorest 2.0

Paste sequences (FASTA format) or protein names (one per line) below. Example: #1. For protein names, HGNC symbol is recommended.). In case you have more than 100 sequences, please consider using the high throughput workflow. If you use any of the data from this web site please cite this article: Horn et al., KinomeXplorer: an integrated platform for kinome biology studies. Nature Methods 2014 Jun;11(6):603–4. C) 2005-2013 Rune Linding and Lars Juhl Jensen.

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