Lior Pachter

According to our database, Lior Pachter authored at least 66 papers between 1997 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of two.

2024

Biophysically interpretable inference of cell types from multimodal sequencing data.

Tara Chari, Gennady Gorin, Lior Pachter

Nat. Comput. Sci., September, 2024

Flexible parsing, interpretation, and editing of technical sequences with <i>splitcode</i>.

Delaney K. Sullivan, Lior Pachter

Bioinform., 2024

2023

Efficient querying of genomic reference databases with <i>gget</i>.

Laura Luebbert, Lior Pachter

Bioinform., January, 2023

Metadata retrieval from sequence databases with <i>ffq</i>.

Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi

Bioinform., January, 2023

The specious art of single-cell genomics.

Tara Chari, Lior Pachter

PLoS Comput. Biol., 2023

2022

RNA velocity unraveled.

Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter

PLoS Comput. Biol., September, 2022

2021

Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x).

A. Sina Booeshaghi, Lior Pachter

Bioinform., 2021

2020

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

Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter

Bioinform., 2020

A curated database reveals trends in single-cell transcriptomics.

Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter

Database J. Biol. Databases Curation, 2020

2019

Barcode identification for single cell genomics.

Akshay Tambe, Lior Pachter

BMC Bioinform., 2019

The barcode, UMI, set format and BUStools.

Páll Melsted, Vasilis Ntranos, Lior Pachter

Bioinform., 2019

Transcript Abundance Estimation and the Laminar Packing Problem.

Atif Rahman, Lior Pachter

Proceedings of the Algorithms for Computational Biology - 6th International Conference, 2019

2017

Pseudoalignment for metagenomic read assignment.

Lorian Schaeffer, Harold Pimentel, Nicolas Bray, Páll Melsted, Lior Pachter

Bioinform., 2017

2016

The Lair: a resource for exploratory analysis of published RNA-Seq data.

Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter

BMC Bioinform., 2016

2015

The NIH BD2K center for big data in translational genomics.

Benedict Paten, Mark Diekhans, Brian J. Druker, Stephen H. Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W. James Kent, Patrick Mantey, Adam A. Margolin, Matt Massie, Adam M. Novak, Frank A. Nothaft, Lior Pachter, David A. Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura J. van't Veer, Barbara J. Wold, David Haussler

J. Am. Medical Informatics Assoc., 2015

Near-optimal RNA-Seq quantification.

Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter

CoRR, 2015

2013

Fragment assignment in the cloud with eXpress-D.

Adam Roberts, Harvey Feng, Lior Pachter

BMC Bioinform., 2013

Updating RNA-Seq analyses after re-annotation.

Adam Roberts, Lorian Schaeffer, Lior Pachter

Bioinform., 2013

2012

Quantifying uniformity of mapped reads.

Valerie Hower, Richard Starfield, Adam Roberts, Lior Pachter

Bioinform., 2012

2011

Tracing the Most Parsimonious Indel History.

Sagi Snir, Lior Pachter

J. Comput. Biol., 2011

Identification and correction of systematic error in high-throughput sequence data.

Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I. K. Martin, Meromit Singer, Lior Pachter

BMC Bioinform., 2011

Shape-based peak identification for ChIP-Seq.

Valerie Hower, Steven N. Evans, Lior Pachter

BMC Bioinform., 2011

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

Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter

Bioinform., 2011

The neighbor-net algorithm.

Dan Levy, Lior Pachter

Adv. Appl. Math., 2011

RNA structure characterization from chemical mapping experiments.

Sharon Aviran, Julius B. Lucks, Lior Pachter

Proceedings of the 49th Annual Allerton Conference on Communication, 2011

2010

MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.

Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter

PLoS Comput. Biol., 2010

Coverage statistics for sequence census methods.

Steven N. Evans, Valerie Hower, Lior Pachter

BMC Bioinform., 2010

2009

Convex Rank Tests and Semigraphoids.

Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand

SIAM J. Discret. Math., 2009

Fast Statistical Alignment.

Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter

PLoS Comput. Biol., 2009

TopHat: discovering splice junctions with RNA-Seq.

Cole Trapnell, Lior Pachter, Steven L. Salzberg

Bioinform., 2009

Why Neighbor-Joining Works.

Radu Mihaescu, Dan Levy, Lior Pachter

Algorithmica, 2009

2008

Viral Population Estimation Using Pyrosequencing.

Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel

PLoS Comput. Biol., 2008

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Rahul Satija, Lior Pachter, Jotun Hein

Bioinform., 2008

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

Robert K. Bradley, Lior Pachter, Ian H. Holmes

Bioinform., 2008

On the optimality of the neighbor-joining algorithm.

Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida

Algorithms Mol. Biol., 2008

2007

The Mathematics of Phylogenomics.

Lior Pachter, Bernd Sturmfels

SIAM Rev., 2007

Optimization of air vehicles operations using mixed-integer linear programming.

Corey J. Schumacher, Phillip R. Chandler, Meir Pachter, Lior S. Pachter

J. Oper. Res. Soc., 2007

Multiple alignment by sequence annealing.

Ariel S. Schwartz, Lior Pachter

Bioinform., 2007

2006

Parametric Alignment of <i>Drosophila</i> Genomes.

Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter

PLoS Comput. Biol., 2006

Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes.

Sagi Snir, Lior Pachter

Proceedings of the Research in Computational Molecular Biology, 2006

Geometry of rank tests.

Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand

Proceedings of the Third European Workshop on Probabilistic Graphical Models, 2006

2005

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities.

Kevin C. Chen, Lior Pachter

PLoS Comput. Biol., 2005

Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling.

Sourav Chatterji, Lior Pachter

J. Comput. Biol., 2005

2004

VISTA: computational tools for comparative genomics.

Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak

Nucleic Acids Res., 2004

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

Jon D. McAuliffe, Lior Pachter, Michael I. Jordan

Bioinform., 2004

Reconstructing trees from subtree weights.

Lior Pachter, David E Speyer

Appl. Math. Lett., 2004

Multiple organism gene finding by collapsed gibbs sampling.

Sourav Chatterji, Lior Pachter

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

2003

Forcing numbers of stop signs.

Fumei Lam, Lior Pachter

Theor. Comput. Sci., 2003

SLAM web server for comparative gene finding and alignment.

Simon Cawley, Lior Pachter, Marina Alexandersson

Nucleic Acids Res., 2003

MAVID multiple alignment server.

Nicolas Bray, Lior Pachter

Nucleic Acids Res., 2003

Picking Alignments from (Steiner) Trees.

Fumei Lam, Marina Alexandersson, Lior Pachter

J. Comput. Biol., 2003

Gene Regulation - Session Introduction.

Serafim Batzoglou, Lior Pachter

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

HMM sampling and applications to gene finding and alternative splicing.

Simon Cawley, Lior Pachter

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003

2002

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems.

Lior Pachter, Marina Alexandersson, Simon Cawley

J. Comput. Biol., 2002

The computational challenges of applying comparative-based computational methods to whole genomes.

Inna Dubchak, Lior Pachter

Briefings Bioinform., 2002

Picking alignments from (steiner) trees.

Lior Pachter, Fumei Lam

Proceedings of the Sixth Annual International Conference on Computational Biology, 2002

Genome-Wide Analysis and Comparative Genomics - Session Introduction.

Inna Dubchak, Lior Pachter, Liping Wei

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001

Optimal paths for avoiding a radiating source.

Lior S. Pachter, Meir Pachter

Proceedings of the 40th IEEE Conference on Decision and Control, 2001

2000

VISTA : visualizing global DNA sequence alignments of arbitrary length.

Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak

Bioinform., 2000

Human and mouse gene structure: comparative analysis and application to exon prediction.

Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander

Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999

A Dictionary-Based Approach for Gene Annotation.

Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger

J. Comput. Biol., 1999

A dictionary based approach for gene annotation.

Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

1998

Forcing matchings on square grids.

Lior Pachter, Peter Kim

Discret. Math., 1998

Finding Convex Sets Among Points in the Plane.

Daniel J. Kleitman, Lior Pachter

Discret. Comput. Geom., 1998

1997

Constructing Status Injective Graphs.

Lior Pachter

Discret. Appl. Math., 1997

Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes.

Lior Pachter

Electron. J. Comb., 1997