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

Constructing Status Injective Graphs. - Lior Pachter (Discret. Appl. Math., 1997)

Finding Convex Sets Among Points in the Plane. - Daniel J. Kleitman; Lior Pachter (Discret. Comput. Geom., 1998)

Forcing matchings on square grids. - Lior Pachter; Peter Kim (Discret. Math., 1998)

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 (RECOMB, 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)

Human and mouse gene structure: comparative analysis and application to exon prediction. - Serafim Batzoglou; Lior Pachter; Jill P. Mesirov; Bonnie Berger; Eric S. Lander (RECOMB, 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)

Optimal paths for avoiding a radiating source. - Lior S. Pachter; Meir Pachter (CDC, 2001)

Genome-Wide Analysis and Comparative Genomics - Session Introduction. - Inna Dubchak; Lior Pachter; Liping Wei (Pacific Symposium on Biocomputing, 2002)

Picking alignments from (steiner) trees. - Lior Pachter; Fumei Lam (RECOMB, 2002)

The computational challenges of applying comparative-based computational methods to whole genomes. - Inna Dubchak; Lior Pachter (Briefings Bioinform., 2002)

Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. - Lior Pachter; Marina Alexandersson; Simon Cawley (J. Comput. Biol., 2002)

HMM sampling and applications to gene finding and alternative splicing. - Simon Cawley; Lior Pachter (ECCB, 2003)

Gene Regulation - Session Introduction. - Serafim Batzoglou; Lior Pachter (Pacific Symposium on Biocomputing, 2003)

Picking Alignments from (Steiner) Trees. - Fumei Lam; Marina Alexandersson; Lior Pachter (J. Comput. Biol., 2003)

MAVID multiple alignment server. - Nicolas Bray; Lior Pachter (Nucleic Acids Res., 2003)

SLAM web server for comparative gene finding and alignment. - Simon Cawley; Lior Pachter; Marina Alexandersson (Nucleic Acids Res., 2003)

Forcing numbers of stop signs. - Fumei Lam; Lior Pachter (Theor. Comput. Sci., 2003)

Multiple organism gene finding by collapsed gibbs sampling. - Sourav Chatterji; Lior Pachter (RECOMB, 2004)

Reconstructing trees from subtree weights. - Lior Pachter; David E Speyer (Appl. Math. Lett., 2004)

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. - Jon D. McAuliffe; Lior Pachter; Michael I. Jordan (Bioinform., 2004)

VISTA: computational tools for comparative genomics. - Kelly A. Frazer; Lior Pachter; Alexander Poliakov; Edward M. Rubin; Inna Dubchak (Nucleic Acids Res., 2004)

Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling. - Sourav Chatterji; Lior Pachter (J. Comput. Biol., 2005)

Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. - Kevin C. Chen; Lior Pachter (PLoS Comput. Biol., 2005)

Geometry of rank tests. - Jason Morton; Lior Pachter; Anne Shiu; Bernd Sturmfels; Oliver Wienand (Probabilistic Graphical Models, 2006)

Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. - Sagi Snir; Lior Pachter (RECOMB, 2006)

Parametric Alignment of Drosophila Genomes. - Colin N. Dewey; Peter Huggins; Kevin Woods; Bernd Sturmfels; Lior Pachter (PLoS Comput. Biol., 2006)

Multiple alignment by sequence annealing. - Ariel S. Schwartz; Lior Pachter (Bioinform., 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)

The Mathematics of Phylogenomics. - Lior Pachter; Bernd Sturmfels (SIAM Rev., 2007)

On the optimality of the neighbor-joining algorithm. - Kord Eickmeyer; Peter Huggins; Lior Pachter; Ruriko Yoshida (Algorithms Mol. Biol., 2008)

Specific alignment of structured RNA: stochastic grammars and sequence annealing. - Robert K. Bradley; Lior Pachter; Ian H. Holmes (Bioinform., 2008)

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. - Rahul Satija; Lior Pachter; Jotun Hein (Bioinform., 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)

Why Neighbor-Joining Works. - Radu Mihaescu; Dan Levy; Lior Pachter (Algorithmica, 2009)

TopHat: discovering splice junctions with RNA-Seq. - Cole Trapnell; Lior Pachter; Steven L. Salzberg (Bioinform., 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)

Convex Rank Tests and Semigraphoids. - Jason Morton; Lior Pachter; Anne Shiu; Bernd Sturmfels; Oliver Wienand (SIAM J. Discret. Math., 2009)

Coverage statistics for sequence census methods. - Steven N. Evans; Valerie Hower; Lior Pachter (BMC Bioinform., 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)

RNA structure characterization from chemical mapping experiments. - Sharon Aviran; Julius B. Lucks; Lior Pachter (Allerton, 2011)

The neighbor-net algorithm. - Dan Levy; Lior Pachter (Adv. Appl. Math., 2011)

Identification of novel transcripts in annotated genomes using RNA-Seq. - Adam Roberts; Harold Pimentel; Cole Trapnell; Lior Pachter (Bioinform., 2011)

Shape-based peak identification for ChIP-Seq. - Valerie Hower; Steven N. Evans; Lior Pachter (BMC Bioinform., 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)

Tracing the Most Parsimonious Indel History. - Sagi Snir; Lior Pachter (J. Comput. Biol., 2011)

Quantifying uniformity of mapped reads. - Valerie Hower; Richard Starfield; Adam Roberts; Lior Pachter (Bioinform., 2012)

Updating RNA-Seq analyses after re-annotation. - Adam Roberts; Lorian Schaeffer; Lior Pachter (Bioinform., 2013)

Fragment assignment in the cloud with eXpress-D. - Adam Roberts; Harvey Feng; Lior Pachter (BMC Bioinform., 2013)

Near-optimal RNA-Seq quantification. - Nicolas Bray; Harold Pimentel; Páll Melsted; Lior Pachter (CoRR, 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; et al. (J. Am. Medical Informatics Assoc., 2015)

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)

Pseudoalignment for metagenomic read assignment. - Lorian Schaeffer; Harold Pimentel; Nicolas Bray; Páll Melsted; Lior Pachter (Bioinform., 2017)

Transcript Abundance Estimation and the Laminar Packing Problem. - Atif Rahman 001; Lior Pachter (AlCoB, 2019)

The barcode, UMI, set format and BUStools. - Páll Melsted; Vasilis Ntranos; Lior Pachter (Bioinform., 2019)

Barcode identification for single cell genomics. - Akshay Tambe; Lior Pachter (BMC Bioinform., 2019)

A curated database reveals trends in single-cell transcriptomics. - Valentine Svensson; Eduardo da Veiga Beltrame; Lior Pachter (Database J. Biol. Databases Curation, 2020)

Interpretable factor models of single-cell RNA-seq via variational autoencoders. - Valentine Svensson; Adam Gayoso; Nir Yosef; Lior Pachter (Bioinform., 2020)

Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x). - A. Sina Booeshaghi; Lior Pachter (Bioinform., 2021)

RNA velocity unraveled. - Gennady Gorin; Meichen Fang; Tara Chari; Lior Pachter (PLoS Comput. Biol., 2022)

The specious art of single-cell genomics. - Tara Chari; Lior Pachter (PLoS Comput. Biol., 2023)

Metadata retrieval from sequence databases with ffq. - Ángel Gálvez-Merchán; Kyung Hoi (Joseph) Min; Lior Pachter; A. Sina Booeshaghi (Bioinform., 2023)

Efficient querying of genomic reference databases with gget. - Laura Luebbert; Lior Pachter (Bioinform., 2023)

Flexible parsing, interpretation, and editing of technical sequences with splitcode. - Delaney K. Sullivan; Lior Pachter (Bioinform., 2024)

Biophysically interpretable inference of cell types from multimodal sequencing data. - Tara Chari; Gennady Gorin; Lior Pachter (Nat. Comput. Sci., 2024)

Trajectory inference from single-cell genomics data with a process time model. - Meichen Fang; Gennady Gorin; Lior Pachter (PLoS Comput. Biol., 2025)