Lior Pachter

71 papers B 6C 1Misc 2Journal 59Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Long-read sequencing transcriptome quantification with lr-kallisto.
PLoS Comput. Biol.
Rebekah K. Loving, Delaney K. Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Y. Liang, Ghassan Filimban, Shimako Kawauchi, A. Sina Booeshaghi, Páll Melsted, Conrad Oakes, Diane Trout, Brian A. Williams, Grant R. Macgregor, Barbara J. Wold, Ali Mortazavi, Lior Pachter
2025 J jnl
Optimizing alluvial plots.
CoRR
Joseph Rich, Conrad Oakes, Lior Pachter
2025 J jnl
Trajectory inference from single-cell genomics data with a process time model.
PLoS Comput. Biol.
Meichen Fang, Gennady Gorin, Lior Pachter
2024 J jnl
A machine-readable specification for genomics assays.
Bioinform.
A. Sina Booeshaghi, Xi Chen, Lior Pachter
2024 J jnl
Biophysically interpretable inference of cell types from multimodal sequencing data.
Nat. Comput. Sci.
Tara Chari, Gennady Gorin, Lior Pachter
2024 J jnl
Fast and scalable querying of eukaryotic linear motifs with
Bioinform.
Laura Luebbert, Chi Hoang, Manjeet Kumar, Lior Pachter
2024 J jnl
Flexible parsing, interpretation, and editing of technical sequences with
Bioinform.
Delaney K. Sullivan, Lior Pachter
2023 J jnl
Efficient querying of genomic reference databases with
Bioinform.
Laura Luebbert, Lior Pachter
2023 J jnl
Metadata retrieval from sequence databases with
Bioinform.
Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi
2023 J jnl
The specious art of single-cell genomics.
PLoS Comput. Biol.
Tara Chari, Lior Pachter
2022 J jnl
RNA velocity unraveled.
PLoS Comput. Biol.
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
2021 J jnl
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x).
Bioinform.
A. Sina Booeshaghi, Lior Pachter
2020 J jnl
A curated database reveals trends in single-cell transcriptomics.
Database J. Biol. Databases Curation
Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter
2020 J jnl
Interpretable factor models of single-cell RNA-seq via variational autoencoders.
Bioinform.
Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter
2019 J jnl
Barcode identification for single cell genomics.
BMC Bioinform.
Akshay Tambe, Lior Pachter
2019 J jnl
The barcode, UMI, set format and BUStools.
Bioinform.
Páll Melsted, Vasilis Ntranos, Lior Pachter
2019 — conf
Transcript Abundance Estimation and the Laminar Packing Problem.
AlCoB
Atif Rahman, Lior Pachter
2017 J jnl
Pseudoalignment for metagenomic read assignment.
Bioinform.
Lorian Schaeffer, Harold Pimentel, Nicolas Bray, Páll Melsted, Lior Pachter
2016 J jnl
The Lair: a resource for exploratory analysis of published RNA-Seq data.
BMC Bioinform.
Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
2015 J jnl
Near-optimal RNA-Seq quantification.
CoRR
Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter
2015 J jnl
The NIH BD2K center for big data in translational genomics.
J. Am. Medical Informatics Assoc.
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
2013 J jnl
Fragment assignment in the cloud with eXpress-D.
BMC Bioinform.
Adam Roberts, Harvey Feng, Lior Pachter
2013 J jnl
Updating RNA-Seq analyses after re-annotation.
Bioinform.
Adam Roberts, Lorian Schaeffer, Lior Pachter
2012 J jnl
Quantifying uniformity of mapped reads.
Bioinform.
Valerie Hower, Richard Starfield, Adam Roberts, Lior Pachter
2011 J jnl
Identification and correction of systematic error in high-throughput sequence data.
BMC Bioinform.
Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I. K. Martin, Meromit Singer, Lior Pachter
2011 J jnl
Identification of novel transcripts in annotated genomes using RNA-Seq.
Bioinform.
Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter
2011 — conf
RNA structure characterization from chemical mapping experiments.
Allerton
Sharon Aviran, Julius B. Lucks, Lior Pachter
2011 J jnl
Shape-based peak identification for ChIP-Seq.
BMC Bioinform.
Valerie Hower, Steven N. Evans, Lior Pachter
2011 J jnl
The neighbor-net algorithm.
Adv. Appl. Math.
Dan Levy, Lior Pachter
2011 J jnl
Tracing the Most Parsimonious Indel History.
J. Comput. Biol.
Sagi Snir, Lior Pachter
2010 J jnl
Coverage statistics for sequence census methods.
BMC Bioinform.
Steven N. Evans, Valerie Hower, Lior Pachter
2010 J jnl
MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations.
PLoS Comput. Biol.
Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter
2009 J jnl
Convex Rank Tests and Semigraphoids.
SIAM J. Discret. Math.
Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand
2009 J jnl
Fast Statistical Alignment.
PLoS Comput. Biol.
Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter
2009 J jnl
TopHat: discovering splice junctions with RNA-Seq.
Bioinform.
Cole Trapnell, Lior Pachter, Steven L. Salzberg
2009 J jnl
Why Neighbor-Joining Works.
Algorithmica
Radu Mihaescu, Dan Levy, Lior Pachter
2008 J jnl
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.
Bioinform.
Rahul Satija, Lior Pachter, Jotun Hein
2008 J jnl
On the optimality of the neighbor-joining algorithm.
Algorithms Mol. Biol.
Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida
2008 J jnl
Specific alignment of structured RNA: stochastic grammars and sequence annealing.
Bioinform.
Robert K. Bradley, Lior Pachter, Ian H. Holmes
2008 J jnl
Viral Population Estimation Using Pyrosequencing.
PLoS Comput. Biol.
Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel
2007 J jnl
Multiple alignment by sequence annealing.
Bioinform.
Ariel S. Schwartz, Lior Pachter
2007 J jnl
The Mathematics of Phylogenomics.
SIAM Rev.
Lior Pachter, Bernd Sturmfels
2006 — conf
Geometry of rank tests.
Probabilistic Graphical Models
Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand
2006 J jnl
Parametric Alignment of
PLoS Comput. Biol.
Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
2006 B conf
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes.
RECOMB
Sagi Snir, Lior Pachter
2006 J jnl
Why neighbor-joining works
CoRR
Radu Mihaescu, Dan Levy, Lior Pachter
2005 J jnl
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities.
PLoS Comput. Biol.
Kevin C. Chen, Lior Pachter
2005 J jnl
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling.
J. Comput. Biol.
Sourav Chatterji, Lior Pachter
2004 B conf
Multiple organism gene finding by collapsed gibbs sampling.
RECOMB
Sourav Chatterji, Lior Pachter
2004 J jnl
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.
Bioinform.
Jon D. McAuliffe, Lior Pachter, Michael I. Jordan
2004 J jnl
Reconstructing trees from subtree weights.
Appl. Math. Lett.
Lior Pachter, David E Speyer
2004 J jnl
VISTA: computational tools for comparative genomics.
Nucleic Acids Res.
Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak
2003 J jnl
Forcing numbers of stop signs.
Theor. Comput. Sci.
Fumei Lam, Lior Pachter
2003 Misc conf
Gene Regulation - Session Introduction.
Pacific Symposium on Biocomputing
Serafim Batzoglou, Lior Pachter
2003 C conf
HMM sampling and applications to gene finding and alternative splicing.
ECCB
Simon Cawley, Lior Pachter
2003 J jnl
MAVID multiple alignment server.
Nucleic Acids Res.
Nicolas Bray, Lior Pachter
2003 J jnl
Picking Alignments from (Steiner) Trees.
J. Comput. Biol.
Fumei Lam, Marina Alexandersson, Lior Pachter
2003 J jnl
SLAM web server for comparative gene finding and alignment.
Nucleic Acids Res.
Simon Cawley, Lior Pachter, Marina Alexandersson
2002 J jnl
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems.
J. Comput. Biol.
Lior Pachter, Marina Alexandersson, Simon Cawley
2002 Misc conf
Genome-Wide Analysis and Comparative Genomics - Session Introduction.
Pacific Symposium on Biocomputing
Inna Dubchak, Lior Pachter, Liping Wei
2002 B conf
Picking alignments from (steiner) trees.
RECOMB
Lior Pachter, Fumei Lam
2002 J jnl
The computational challenges of applying comparative-based computational methods to whole genomes.
Briefings Bioinform.
Inna Dubchak, Lior Pachter
2001 B conf
Applications of generalized pair hidden Markov models to alignment and gene finding problems.
RECOMB
Lior Pachter, Marina Alexandersson, Simon Cawley
2000 B conf
Human and mouse gene structure: comparative analysis and application to exon prediction.
RECOMB
Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander
2000 J jnl
VISTA : visualizing global DNA sequence alignments of arbitrary length.
Bioinform.
Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak
1999 J jnl
A Dictionary-Based Approach for Gene Annotation.
J. Comput. Biol.
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger
1999 B conf
A dictionary based approach for gene annotation.
RECOMB
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman
1998 J jnl
Finding Convex Sets Among Points in the Plane.
Discret. Comput. Geom.
Daniel J. Kleitman, Lior Pachter
1998 J jnl
Forcing matchings on square grids.
Discret. Math.
Lior Pachter, Peter Kim
1997 J jnl
Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes.
Electron. J. Comb.
Lior Pachter
1997 J jnl
Constructing Status Injective Graphs.
Discret. Appl. Math.
Lior Pachter