Lior Pachter

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 15

Top Topics

High Throughput

Top Venues

PLoS Comput. Biol.

Publications

Delaney K. Sullivan, Lior Pachter
. Bioinform. 40 (6) (2024)
Tara Chari, Lior Pachter
The specious art of single-cell genomics. PLoS Comput. Biol. 19 (8) (2023)
Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi
. Bioinform. 39 (1) (2023)
Laura Luebbert, Lior Pachter
. Bioinform. 39 (1) (2023)
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
RNA velocity unraveled. PLoS Comput. Biol. 18 (9) (2022)
A. Sina Booeshaghi, Lior Pachter
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x). Bioinform. 37 (15) (2021)
Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter
A curated database reveals trends in single-cell transcriptomics. Database J. Biol. Databases Curation 2020 (2020)
Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter
Interpretable factor models of single-cell RNA-seq via variational autoencoders. Bioinform. 36 (11) (2020)
Atif Rahman, Lior Pachter
Transcript Abundance Estimation and the Laminar Packing Problem. AlCoB (2019)
Akshay Tambe, Lior Pachter
Barcode identification for single cell genomics. BMC Bioinform. 20 (1) (2019)
Páll Melsted, Vasilis Ntranos, Lior Pachter
The barcode, UMI, set format and BUStools. Bioinform. 35 (21) (2019)
Lorian Schaeffer, Harold Pimentel, Nicolas Bray, Páll Melsted, Lior Pachter
Pseudoalignment for metagenomic read assignment. Bioinform. 33 (14) (2017)
Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted, Lior Pachter
The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC Bioinform. 17 (2016)
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
The NIH BD2K center for big data in translational genomics. J. Am. Medical Informatics Assoc. 22 (6) (2015)
Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter
Near-optimal RNA-Seq quantification. CoRR (2015)
Adam Roberts, Harvey Feng, Lior Pachter
Fragment assignment in the cloud with eXpress-D. BMC Bioinform. 14 (2013)
Adam Roberts, Lorian Schaeffer, Lior Pachter
Updating RNA-Seq analyses after re-annotation. Bioinform. 29 (13) (2013)
Valerie Hower, Richard Starfield, Adam Roberts, Lior Pachter
Quantifying uniformity of mapped reads. Bioinform. 28 (20) (2012)
Sagi Snir, Lior Pachter
Tracing the Most Parsimonious Indel History. J. Comput. Biol. 18 (8) (2011)
Sharon Aviran, Julius B. Lucks, Lior Pachter
RNA structure characterization from chemical mapping experiments. Allerton (2011)
Dan Levy, Lior Pachter
The neighbor-net algorithm. Adv. Appl. Math. 47 (2) (2011)
Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I. K. Martin, Meromit Singer, Lior Pachter
Identification and correction of systematic error in high-throughput sequence data. BMC Bioinform. 12 (2011)
Valerie Hower, Steven N. Evans, Lior Pachter
Shape-based peak identification for ChIP-Seq. BMC Bioinform. 12 (2011)
Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter
Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinform. 27 (17) (2011)
Steven N. Evans, Valerie Hower, Lior Pachter
Coverage statistics for sequence census methods. BMC Bioinform. 11 (2010)
Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schönhuth, Gary P. Schroth, David I. K. Martin, Lior Pachter
MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations. PLoS Comput. Biol. 6 (8) (2010)
Cole Trapnell, Lior Pachter, Steven L. Salzberg
TopHat: discovering splice junctions with RNA-Seq. Bioinform. 25 (9) (2009)
Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand
Convex Rank Tests and Semigraphoids. SIAM J. Discret. Math. 23 (3) (2009)
Robert K. Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter
Fast Statistical Alignment. PLoS Comput. Biol. 5 (5) (2009)
Radu Mihaescu, Dan Levy, Lior Pachter
Why Neighbor-Joining Works. Algorithmica 54 (1) (2009)
Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida
On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol. 3 (2008)
Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel
Viral Population Estimation Using Pyrosequencing. PLoS Comput. Biol. 4 (5) (2008)
Robert K. Bradley, Lior Pachter, Ian H. Holmes
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinform. 24 (23) (2008)
Rahul Satija, Lior Pachter, Jotun Hein
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinform. 24 (10) (2008)
Lior Pachter, Bernd Sturmfels
The Mathematics of Phylogenomics. SIAM Rev. 49 (1) (2007)
Ariel S. Schwartz, Lior Pachter
Multiple alignment by sequence annealing. Bioinform. 23 (2) (2007)
Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter
Genomes. PLoS Comput. Biol. 2 (6) (2006)
Sagi Snir, Lior Pachter
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. RECOMB (2006)
Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand
Geometry of rank tests. Probabilistic Graphical Models (2006)
Radu Mihaescu, Dan Levy, Lior Pachter
Why neighbor-joining works CoRR (2006)
Kevin C. Chen, Lior Pachter
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Comput. Biol. 1 (2) (2005)
Sourav Chatterji, Lior Pachter
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling. J. Comput. Biol. 12 (6) (2005)
Sourav Chatterji, Lior Pachter
Multiple organism gene finding by collapsed gibbs sampling. RECOMB (2004)
Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak
VISTA: computational tools for comparative genomics. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Lior Pachter, David E Speyer
Reconstructing trees from subtree weights. Appl. Math. Lett. 17 (6) (2004)
Jon D. McAuliffe, Lior Pachter, Michael I. Jordan
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinform. 20 (12) (2004)
Simon Cawley, Lior Pachter
HMM sampling and applications to gene finding and alternative splicing. ECCB (2003)
Nicolas Bray, Lior Pachter
MAVID multiple alignment server. Nucleic Acids Res. 31 (13) (2003)
Serafim Batzoglou, Lior Pachter
Gene Regulation - Session Introduction. Pacific Symposium on Biocomputing (2003)
Fumei Lam, Lior Pachter
Forcing numbers of stop signs. Theor. Comput. Sci. 303 (2-3) (2003)
Fumei Lam, Marina Alexandersson, Lior Pachter
Picking Alignments from (Steiner) Trees. J. Comput. Biol. 10 (3/4) (2003)
Simon Cawley, Lior Pachter, Marina Alexandersson
SLAM web server for comparative gene finding and alignment. Nucleic Acids Res. 31 (13) (2003)
Lior Pachter, Marina Alexandersson, Simon Cawley
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. J. Comput. Biol. 9 (2) (2002)
Inna Dubchak, Lior Pachter, Liping Wei
Genome-Wide Analysis and Comparative Genomics - Session Introduction. Pacific Symposium on Biocomputing (2002)
Inna Dubchak, Lior Pachter
The computational challenges of applying comparative-based computational methods to whole genomes. Briefings Bioinform. 3 (1) (2002)
Lior Pachter, Fumei Lam
Picking alignments from (steiner) trees. RECOMB (2002)
Lior Pachter, Marina Alexandersson, Simon Cawley
Applications of generalized pair hidden Markov models to alignment and gene finding problems. RECOMB (2001)
Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. Lander
Human and mouse gene structure: comparative analysis and application to exon prediction. RECOMB (2000)
Chris Mayor, Michael Brudno, Jody R. Schwartz, Alexander Poliakov, Edward M. Rubin, Kelly A. Frazer, Lior Pachter, Inna Dubchak
VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinform. 16 (11) (2000)
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, Eric Banks, Eric S. Lander, Daniel J. Kleitman, Bonnie Berger
A Dictionary-Based Approach for Gene Annotation. J. Comput. Biol. 6 (3/4) (1999)
Lior Pachter, Serafim Batzoglou, Valentin I. Spitkovsky, William S. Beebee, Eric S. Lander, Bonnie Berger, Daniel J. Kleitman
A dictionary based approach for gene annotation. RECOMB (1999)
Daniel J. Kleitman, Lior Pachter
Finding Convex Sets Among Points in the Plane. Discret. Comput. Geom. 19 (3) (1998)
Lior Pachter, Peter Kim
Forcing matchings on square grids. Discret. Math. 190 (1-3) (1998)
Lior Pachter
Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes. Electron. J. Comb. 4 (1) (1997)
Lior Pachter
Constructing Status Injective Graphs. Discret. Appl. Math. 80 (1) (1997)