About

I work at the intersection of scientific computing, bioinformatics, and open science.

Check out my Github Profile!

Projects

OpenEM

OpenEM is an open research data infrastructure for Swiss electron microscopy facilities. It uses the PSI Data Catalog to catalog image datasets, and is built on the SciCat data catalog.

TRAL

The Tandem Repeat Annotation Library (TRAL) is a method for detecting repeats in protein sequences.

TRAL 2.0: Tandem Repeat Detection with Circular Profile Hidden Markov Models and Evolutionary Aligner.
Delucchi, M., Näf, P., Bliven, S., & Anisimova, M. Frontiers in Bioinformatics (2021) 1:691865.

EPPIC

The Evolutionary Protein Protein Interface Classifier (EPPIC) is a software package for the analysis of interfaces in protein crystal structures and for quaternary structure prediction. github

Automated evaluation of quaternary structures from protein crystals.
Bliven S, Lafita A, Parker A, Capitani G, Duarte JM
PLoS Comput Biol (2018) 14(4): e1006104.

Protein structural alignment algorithms

These algorithms are discussed in my PhD thesis from UC San Diego under Prof. Philip Bourne.

Structure-Preserving Rearrangements: Algorithms for Structural Comparison and Protein Analysis

CE-Symm is a tool for finding structural repeats in protein structures, including pseudosymmetry, translational repeats, and hierarchical combinations of symmetric relationships. These can lead to important insights on the function and evolution of proteins.

Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm
Spencer E Bliven, Aleix Lafita, Peter W Rose, Guido Capitani, Andreas Prlić, & Philip E Bourne
PLOS Computational Biology (2019) 15 (4):e1006842.

Systematic detection of internal symmetry in proteins using CE-Symm
Douglas Myers-Turnbull, Spencer E Bliven, Peter W Rose, Zaid K Aziz, Philippe Youkharibache, Philip E Bourne, & Andreas Prlić
J Mol Biol (2013) 426 (11): 2255–2268.

The QuatSymm tool identifies symmetries in protein complexes. It was used to assess protein assembly predictions at the CASP12 challenge.

Detection of circular permutations within protein structures using CE-CP
Spencer E Bliven, Philip E Bourne, Andreas Prlić
Bioinformatics (2014) 31(8):1316–1318

All algorithms are included in the BioJava library.

BioJava 5: A community driven open-source bioinformatics library
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte
PLOS Computational Biology 15(2): e1006791

Structure of VEGFR-1 with VEGF-A

PDB ID 5T89

Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A
Sandra Markovic-Mueller, Edward Stuttfeld, Mayanka Asthana, Tobias Weinert, Spencer Bliven, Kenneth N. Goldie, Kaisa Kisko, Guido Capitani, Kurt Ballmer-Hofer
Structure (2017) 25: 2, 341-352