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Debora S. Marks Lab

The Raymond and Beverley Sackler Laboratory for Computational Biology at Harvard Medical School. What will we do when there are a million genomes? We develop computational approaches to make sense of genetic variation. Learn more about our Research ». MicroRNA.org ». EVfold.org ». 945-Helical Transmembrane Protein 3D Structure Predictions ». Debora S. Marks. Anna G. Green.

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Debora S. Marks Lab | marks.hms.harvard.edu Reviews
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The Raymond and Beverley Sackler Laboratory for Computational Biology at Harvard Medical School. What will we do when there are a million genomes? We develop computational approaches to make sense of genetic variation. Learn more about our Research ». MicroRNA.org ». EVfold.org ». 945-Helical Transmembrane Protein 3D Structure Predictions ». Debora S. Marks. Anna G. Green.
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Debora S. Marks Lab | marks.hms.harvard.edu Reviews

https://marks.hms.harvard.edu

The Raymond and Beverley Sackler Laboratory for Computational Biology at Harvard Medical School. What will we do when there are a million genomes? We develop computational approaches to make sense of genetic variation. Learn more about our Research ». MicroRNA.org ». EVfold.org ». 945-Helical Transmembrane Protein 3D Structure Predictions ». Debora S. Marks. Anna G. Green.

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marks.hms.harvard.edu marks.hms.harvard.edu
1

TMPS - Predicted by ECs

https://marks.hms.harvard.edu/tmproteins/tmp_index.html

Transmembrane Protein 3D Structures - Predicted by Evolutionary Couplings. EVfold Predications for &#945-Helical Transmembrane Proteins. This page links you to our most recent EVfold runs for &#945-helical membrane proteins (EVfold - Membrane 2.0). This includes updated results from all the proteins that were presented in our 2012 paper ( Hopf et al 2012. We will be updating these results regularly. Comparison to known structures:. Predictions for unknown structures:.

2

Debora S. Marks Lab

https://marks.hms.harvard.edu/people.html

Marks Lab Members and Collaborators. Debora S. Marks. Rohan defended his PhD on the evolution of laboratory and natural populations of Escherichia coli at Michigan State University in 2016. His main interest is molecular evolution. Rohan is especially interested in whether coevolution at the molecular scale is sufficient (or not) in driving the evolution of complex cellular lifeforms. Postdoc (joint with Chris Sander). Postdoc (joint with Chris Sander). Charlotta is a Bioinformatics PhD student from the ...

3

Debora S. Marks Lab

https://marks.hms.harvard.edu/resources.html

Marks Lab Resources and Webservers. EVfold.org ». Web server to predict evolutionary couplings and tertiary protein folding. GitHub Repo ». Helical Transmembrane Protein 3D Structure Predictions ». List of predictions for alpha-helical transmembrane proteins of unknown structure. MicroRNA.org ». Predicted microRNA targets and target downregulation scores along with xperimentally observed expression patterns.

4

Publications

https://marks.hms.harvard.edu/publications.html

Marks Lab Selected Publications. Debbie's Google Scholar Page. Structured States of Disordered Proteins from Genomic Sequences. A Toth-Petroczy, P Palmedo, JB Ingraham, TA Hopf, B Berger, C Sander and DS Marks. Volume 167, 158-170. View on Journal Website. Genomic Epidemiology of Gonococcal Resistance to Extended Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the US, 2000-2013. YH Grad, SR Harris, RD Kikcaldy, AG Green, DS Marks, SD Bentley, D Trees and M Lipsitch. J Infect Dis. (2016).

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sysbio.med.harvard.edu sysbio.med.harvard.edu

faculty | Systems Biology – HMS

http://sysbio.med.harvard.edu/faculty/depace

Skip to main content. Marc W. Kirschner Ph.D. The Kirschner lab studies spatial organization and temporal control in several different biological contexts, including the cell cycle, the cytoskeleton, and embryonic development. They also study a number of important signaling pathways, notably the Wnt pathway and various post-translational modification systems. Http:/ kirschner.hms.harvard.edu/. Markus Basan, PhD. Angela DePace Ph.D. Angela DePace@hms.harvard.edu. Http:/ depace.med.harvard.edu. The Fontana...

sysbio.med.harvard.edu sysbio.med.harvard.edu

faculty | Systems Biology – HMS

http://sysbio.med.harvard.edu/faculty

Skip to main content. Marc W. Kirschner Ph.D. The Kirschner lab studies spatial organization and temporal control in several different biological contexts, including the cell cycle, the cytoskeleton, and embryonic development. They also study a number of important signaling pathways, notably the Wnt pathway and various post-translational modification systems. Http:/ kirschner.hms.harvard.edu/. Markus Basan, PhD. Angela DePace Ph.D. Angela DePace@hms.harvard.edu. Http:/ depace.med.harvard.edu. The Fontana...

evfold.org evfold.org

EVcouplings

http://evfold.org/evfold-web/about.do

Computational Biologist. Head of Debora Marks Lab. At Harvard Medical School. Computational Biologist. Head of the Computational Biology Center (cBio). At Memorial Sloan Kettering Cancer Cancer. Thomas A. Hopf. PhD student at Rostlab. TUM Computer Science) and Debora Marks lab (Harvard Medical School). Software Engineer, Debora Marks lab (Harvard Medical School). Software Engineer, Computational Biology Center (cBio), MSKCC. Postdoctoral fellow at MSKCC. V116 [ Back to top ].

sysbio.med.harvard.edu sysbio.med.harvard.edu

faculty | Systems Biology – HMS

http://sysbio.med.harvard.edu/faculty/fontana

Skip to main content. Marc W. Kirschner Ph.D. The Kirschner lab studies spatial organization and temporal control in several different biological contexts, including the cell cycle, the cytoskeleton, and embryonic development. They also study a number of important signaling pathways, notably the Wnt pathway and various post-translational modification systems. Http:/ kirschner.hms.harvard.edu/. Markus Basan, PhD. Angela DePace Ph.D. Angela DePace@hms.harvard.edu. Http:/ depace.med.harvard.edu. The Fontana...

microrna.org microrna.org

microRNA.org

http://www.microrna.org/microrna/getGeneForm.do

MicroRNA.org - Targets and Expression. Predicted microRNA targets and target downregulation scores. Experimentally observed expression patterns. Last Update: 2010-11-01 [ release notes. You are currently searching:. MirSVR predicted target site scoring method:. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Betel D, Koppal A, Agius P, Sander C, Leslie C., Genome Biology. The microRNA.org resource: targets and expression. MicroRNA targets in Drosophila.

microrna.org microrna.org

microRNA.org

http://www.microrna.org/microrna/faq.do

MicroRNA.org - Targets and Expression. Predicted microRNA targets and target downregulation scores. Experimentally observed expression patterns. Last Update: 2010-11-01 [ release notes. You are currently searching:. How can I get a list of all target sites for a gene / all genes targeted for a microRNA / etc. Why is the energy score always 0 for the Sept2008 downloadable tables? What expression data is available? Where can I find it? How do I select multiple tissues for the miRNA expression section?

evfold.org evfold.org

EVcouplings

http://evfold.org/evfold-web

Sign In / Register. Runs your protein of interest. Generates an alignment (if you don‘t have one). Calculates EC scores for all pairs of residues. Maps high ranking ECs onto a contact map. Compares ECs to contacts in 3D structure (if you want). Calculates cumulative EC strength for individual residues. Paints strong ECs onto a 3D structure Read More. Delivers ALL the output as EVCouplings. Folds the protein when unknown structure. Ranks all the models. Allows alternative membrane topology input. Calculat...

microrna.org microrna.org

microRNA.org

http://www.microrna.org/microrna/getExprForm.do

MicroRNA.org - Targets and Expression. Predicted microRNA targets and target downregulation scores. Experimentally observed expression patterns. Last Update: 2010-11-01 [ release notes. You are currently searching:. 172 human, 64 mouse and 16 rat small RNA libraries from major organs and cell types:. A mammalian microRNA expression atlas based on small RNA library sequencing. Landgraf P., et al., Cell. 2007 Jun 29; 129. MirSVR predicted target site scoring method:. 2008 Jan; 36(Database Issue): D149-53.

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Debora S. Marks Lab

The Raymond and Beverley Sackler Laboratory for Computational Biology at Harvard Medical School. What will we do when there are a million genomes? We develop computational approaches to make sense of genetic variation. Learn more about our Research ». MicroRNA.org ». EVfold.org ». 945-Helical Transmembrane Protein 3D Structure Predictions ». Debora S. Marks. Anna G. Green.

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