Lior Pachter

According to our database1, Lior Pachter authored at least 57 papers between 1997 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of two.



In proceedings 
PhD thesis 


Online presence:



Interpretable factor models of single-cell RNA-seq via variational autoencoders.
Bioinform., 2020

A curated database reveals trends in single-cell transcriptomics.
Database J. Biol. Databases Curation, 2020

Barcode identification for single cell genomics.
BMC Bioinform., 2019

The barcode, UMI, set format and BUStools.
Bioinform., 2019

Transcript Abundance Estimation and the Laminar Packing Problem.
Proceedings of the Algorithms for Computational Biology - 6th International Conference, 2019

Pseudoalignment for metagenomic read assignment.
Bioinform., 2017

The Lair: a resource for exploratory analysis of published RNA-Seq data.
BMC Bioinform., 2016

The NIH BD2K center for big data in translational genomics.
J. Am. Medical Informatics Assoc., 2015

Near-optimal RNA-Seq quantification.
CoRR, 2015

Fragment assignment in the cloud with eXpress-D.
BMC Bioinform., 2013

Updating RNA-Seq analyses after re-annotation.
Bioinform., 2013

Quantifying uniformity of mapped reads.
Bioinform., 2012

Tracing the Most Parsimonious Indel History.
J. Comput. Biol., 2011

Identification and correction of systematic error in high-throughput sequence data.
BMC Bioinform., 2011

Shape-based peak identification for ChIP-Seq.
BMC Bioinform., 2011

Identification of novel transcripts in annotated genomes using RNA-Seq.
Bioinform., 2011

The neighbor-net algorithm.
Adv. Appl. Math., 2011

RNA structure characterization from chemical mapping experiments.
Proceedings of the 49th Annual Allerton Conference on Communication, 2011

MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.
PLoS Comput. Biol., 2010

Coverage statistics for sequence census methods.
BMC Bioinform., 2010

Convex Rank Tests and Semigraphoids.
SIAM J. Discret. Math., 2009

Fast Statistical Alignment.
PLoS Comput. Biol., 2009

TopHat: discovering splice junctions with RNA-Seq.
Bioinform., 2009

Why Neighbor-Joining Works.
Algorithmica, 2009

Viral Population Estimation Using Pyrosequencing.
PLoS Comput. Biol., 2008

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.
Bioinform., 2008

Specific alignment of structured RNA: stochastic grammars and sequence annealing.
Bioinform., 2008

On the optimality of the neighbor-joining algorithm.
Algorithms Mol. Biol., 2008

The Mathematics of Phylogenomics.
SIAM Rev., 2007

Multiple alignment by sequence annealing.
Bioinform., 2007

Parametric Alignment of <i>Drosophila</i> Genomes.
PLoS Comput. Biol., 2006

Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes.
Proceedings of the Research in Computational Molecular Biology, 2006

Geometry of rank tests.
Proceedings of the Third European Workshop on Probabilistic Graphical Models, 2006

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities.
PLoS Comput. Biol., 2005

Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling.
J. Comput. Biol., 2005

VISTA: computational tools for comparative genomics.
Nucleic Acids Res., 2004

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.
Bioinform., 2004

Reconstructing trees from subtree weights.
Appl. Math. Lett., 2004

Multiple organism gene finding by collapsed gibbs sampling.
Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

Forcing numbers of stop signs.
Theor. Comput. Sci., 2003

SLAM web server for comparative gene finding and alignment.
Nucleic Acids Res., 2003

MAVID multiple alignment server.
Nucleic Acids Res., 2003

Picking Alignments from (Steiner) Trees.
J. Comput. Biol., 2003

Gene Regulation - Session Introduction.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

HMM sampling and applications to gene finding and alternative splicing.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems.
J. Comput. Biol., 2002

The computational challenges of applying comparative-based computational methods to whole genomes.
Briefings Bioinform., 2002

Picking alignments from (steiner) trees.
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

Genome-Wide Analysis and Comparative Genomics - Session Introduction.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

VISTA : visualizing global DNA sequence alignments of arbitrary length.
Bioinform., 2000

Human and mouse gene structure: comparative analysis and application to exon prediction.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

A Dictionary-Based Approach for Gene Annotation.
J. Comput. Biol., 1999

A dictionary based approach for gene annotation.
Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Forcing matchings on square grids.
Discret. Math., 1998

Finding Convex Sets Among Points in the Plane.
Discret. Comput. Geom., 1998

Constructing Status Injective Graphs.
Discret. Appl. Math., 1997

Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes.
Electron. J. Comb., 1997