Efficient approximations for learning phylogenetic HMM models from data. - Vladimir Jojic; Nebojsa Jojic; Christopher Meek; Dan Geiger; Adam C. Siepel; David Haussler; David Heckerman (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Joint Discovery of Haplotype Blocks and Complex Trait Associations from SNP Sequences. - Nebojsa Jojic; Vladimir Jojic; David Heckerman (UAI, 2004)

Using epitomes to model genetic diversity: Rational design of HIV vaccines. - Nebojsa Jojic; Vladimir Jojic; Brendan J. Frey; Christopher Meek; David Heckerman (NIPS, 2005)

Algorithms for rational vaccine design. - Vladimir Jojic (2007)

Population Sequencing Using Short Reads: HIV as a Case Study. - Vladimir Jojic; Tomer Hertz; Nebojsa Jojic (Pacific Symposium on Biocomputing, 2008)

Constructing Treatment Portfolios Using Affinity Propagation. - Delbert Dueck; Brendan J. Frey; Nebojsa Jojic; Vladimir Jojic; Guri Giaever; Andrew Emili; Gabe Musso; Robert Hegele (RECOMB, 2008)

Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al. - David C. Nickle; Nebojsa Jojic; David Heckerman; Vladimir Jojic; Darko Kirovski; Morgane Rolland; Sergei L. Kosakovsky Pond; James I. Mullins (PLoS Comput. Biol., 2008)

Accelerated dual decomposition for MAP inference. - Vladimir Jojic; Stephen Gould; Daphne Koller (ICML, 2010)

Genovo: De Novo Assembly for Metagenomes. - Jonathan Laserson; Vladimir Jojic; Daphne Koller (J. Comput. Biol., 2011)

Convex envelopes of complexity controlling penalties: the case against premature envelopment. - Vladimir Jojic; Suchi Saria; Daphne Koller (AISTATS, 2011)

Metric Learning from Relative Comparisons by Minimizing Squared Residual. - Eric Yi Liu; Zhishan Guo; Xiang Zhang 001; Vladimir Jojic; Wei Wang 010 (ICDM, 2012)

Robust Multimodal Dictionary Learning. - Tian Cao 001; Vladimir Jojic; Shannon Modla; Debbie Powell; Kirk Czymmek; Marc Niethammer (MICCAI (1), 2013)

AMP: Assembly Matching Pursuit. - Surojit Biswas; Vladimir Jojic (Pacific Symposium on Biocomputing, 2013)

PatchMatch Based Joint View Selection and Depthmap Estimation. - Enliang Zheng; Enrique Dunn; Vladimir Jojic; Jan-Michael Frahm (CVPR, 2014)

An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data. - Chen-Ping Fu; Vladimir Jojic; Leonard McMillan (RECOMB, 2014)

A deep framework for bacterial image segmentation and classification. - Dong Nie; Elizabeth A. Shank; Vladimir Jojic (BCB, 2015)

Semi-coupled dictionary learning for deformation prediction. - Tian Cao 001; Nikhil Singh 002; Vladimir Jojic; Marc Niethammer (ISBI, 2015)

Drug-induced mRNA Signatures Are Enriched for the Minority of Genes that Are Highly Heritable. - Tianxiang Gao; Petter Brodin; Mark M. Davis; Vladimir Jojic (Pacific Symposium on Biocomputing, 2015)

Deconvolving molecular signatures of interactions between microbial colonies. - Yeu-Chern Harn; M. J. Powers; Elizabeth A. Shank; Vladimir Jojic (Bioinform., 2015)

Classification of Prostate Cancer Grades and T-Stages Based on Tissue Elasticity Using Medical Image Analysis. - Shan Yang; Vladimir Jojic; Jun Lian; Ronald C. Chen; Hongtu Zhu; Ming C. Lin (MICCAI (1), 2016)

Degrees of Freedom in Deep Neural Networks. - Tianxiang Gao; Vladimir Jojic (UAI, 2016)

Learning Microbial Interaction Networks from Metagenomic Count Data. - Surojit Biswas; Meredith McDonald; Derek S. Lundberg; Jeffery L. Dangl; Vladimir Jojic (J. Comput. Biol., 2016)

Composition and decomposition of GANs. - Yeu-Chern Harn; Zhenghao Chen; Vladimir Jojic (CoRR, 2019)

Modeling Multiplexed Images with Spatial-LDA Reveals Novel Tissue Microenvironments. - Zhenghao Chen; Ilya Soifer; Hugo Hilton; Leeat Keren; Vladimir Jojic (J. Comput. Biol., 2020)