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In Print: Apr 8, 2011

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De Morrée A, Mons B, Peters DJ, et al.
In silico discovery and experimental validation of new protein-protein interactions.
Proteomics. 2011 Mar;11(5):843-53.


Hetényi C, van der Spoel D.
Towards prediction of functional protein pockets using blind docking and pocket search algorithms.
Protein Sci. 2011 Mar 16. doi: 10.1002/pro.618. [Epub ahead of print]


Ivanciuc O, Gendel SM, Power TD, Schein CH, Braun W.
AllerML: Markup Language for Allergens.
Regul Toxicol Pharmacol. 2011 Mar 17. [Epub ahead of print]


Dewey CF, Ayyadurai VA.
CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models.
Cell Mol Bioeng. 2011 Mar;4(1):28-45.


Ma'ayan A, Webb RL.
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.
Source Code Biol Med. 2011 Mar 21;6(1):5.


Consiglio A, De Leo F, Licciulli F, et al.
PlantPIs — An Interactive Web Resource on Plant Protease Inhibitors.
Curr Protein Pept Sci. 2011 Mar 22. [Epub ahead of print]


Yadav AK, Dash D, Kumar D.
MassWiz: A novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry.
J Proteome Res. 2011 Mar 18. [Epub ahead of print]


Andronico A, Randall A, Baldi P, Benz RW.
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress.
J Chem Inf Model. 2011 Mar 18. [Epub ahead of print]


Antonescu C, Gusenleitner D, Liu F, White JA, Quackenbush J.
GCOD — GeneChip Oncology Database.
BMC Bioinformatics. 2011 Feb 3;12:46.


Wenger CD, Phanstiel DH, Bailey DJ, Coon JJ, Lee MV.
COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA.
Proteomics. 2011 Mar;11(6):1064-74.


Decouttere F, Rehm HL, Dunnen JT, et al.
MutaDATABASE: a centralized and standardized DNA variation database.
Nat Biotechnol. 2011 Feb;29(2):117-8.

Macken C, Dietrich J, Dimitrijevic M, Green M, Krishnamoorthy M, Patel P.
Tree Pruner: An efficient tool for selecting data from a biased genetic database.
BMC Bioinformatics. 2011 Feb 9;12:51.


Bujnicki JM, Rother K, Rother M, Puton T.
ModeRNA: a tool for comparative modeling of RNA 3D structure.
Nucleic Acids Res. 2011 Feb 7. [Epub ahead of print]


Lum G, Min XJ.
FunSecKB: the Fungal Secretome KnowledgeBase.
Database. 2011 Feb 6;2011:bar001.


Schmidt B, Liu W, Muller-Wittig W.
CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Feb 16. [Epub ahead of print]


The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.