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ORCIDLior Pachter
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- affiliation: University of California, Berkeley, USA
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Journal Articles
- 2024
[j52]Delaney K. Sullivan
, Lior Pachter:
Flexible parsing, interpretation, and editing of technical sequences with splitcode. Bioinform. 40(6) (2024)- 2023
- [j51]Ángel Gálvez-Merchán, Kyung Hoi (Joseph) Min, Lior Pachter, A. Sina Booeshaghi:
Metadata retrieval from sequence databases with ffq. Bioinform. 39(1) (2023) - [j50]Laura Luebbert, Lior Pachter:
Efficient querying of genomic reference databases with gget. Bioinform. 39(1) (2023) - [j49]Tara Chari, Lior Pachter:
The specious art of single-cell genomics. PLoS Comput. Biol. 19(8) (2023) - 2022
- [j48]Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter:
RNA velocity unraveled. PLoS Comput. Biol. 18(9): 1010492 (2022) - 2021
- [j47]A. Sina Booeshaghi, Lior Pachter:
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x). Bioinform. 37(15): 2223-2224 (2021) - 2020
- [j46]Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter:
A curated database reveals trends in single-cell transcriptomics. Database J. Biol. Databases Curation 2020 (2020) - [j45]Valentine Svensson, Adam Gayoso, Nir Yosef, Lior Pachter:
Interpretable factor models of single-cell RNA-seq via variational autoencoders. Bioinform. 36(11): 3418-3421 (2020) - 2019
- [j44]Páll Melsted, Vasilis Ntranos, Lior Pachter:
The barcode, UMI, set format and BUStools. Bioinform. 35(21): 4472-4473 (2019) - [j43]Akshay Tambe, Lior Pachter:
Barcode identification for single cell genomics. BMC Bioinform. 20(1): 32:1-32:9 (2019) - 2017
- [j42]Lorian Schaeffer, Harold Pimentel, Nicolas Bray, Páll Melsted, Lior Pachter:
Pseudoalignment for metagenomic read assignment. Bioinform. 33(14): 2082-2088 (2017) - 2016
- [j41]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: 490:1-490:6 (2016) - 2015
- [j40]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): 1143-1147 (2015) - 2013
- [j39]Adam Roberts, Lorian Schaeffer, Lior Pachter:
Updating RNA-Seq analyses after re-annotation. Bioinform. 29(13): 1631-1637 (2013) - [j38]Adam Roberts, Harvey Feng, Lior Pachter:
Fragment assignment in the cloud with eXpress-D. BMC Bioinform. 14: 358 (2013) - 2012
- [j37]Valerie Hower, Richard Starfield, Adam Roberts, Lior Pachter:
Quantifying uniformity of mapped reads. Bioinform. 28(20): 2680-2682 (2012) - 2011
- [j36]Dan Levy, Lior Pachter:
The neighbor-net algorithm. Adv. Appl. Math. 47(2): 240-258 (2011) - [j35]Adam Roberts, Harold Pimentel, Cole Trapnell, Lior Pachter:
Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinform. 27(17): 2325-2329 (2011) - [j34]Valerie Hower, Steven N. Evans, Lior Pachter:
Shape-based peak identification for ChIP-Seq. BMC Bioinform. 12: 15 (2011) - [j33]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: 451 (2011) - [j32]Sagi Snir, Lior Pachter:
Tracing the Most Parsimonious Indel History. J. Comput. Biol. 18(8): 967-986 (2011) - 2010
- [j31]Steven N. Evans, Valerie Hower, Lior Pachter:
Coverage statistics for sequence census methods. BMC Bioinform. 11: 430 (2010) - [j30]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) - 2009
- [j29]Radu Mihaescu, Dan Levy, Lior Pachter:
Why Neighbor-Joining Works. Algorithmica 54(1): 1-24 (2009) - [j28]Cole Trapnell, Lior Pachter, Steven L. Salzberg:
TopHat: discovering splice junctions with RNA-Seq. Bioinform. 25(9): 1105-1111 (2009) - [j27]Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter:
Fast Statistical Alignment. PLoS Comput. Biol. 5(5) (2009) - [j26]Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand:
Convex Rank Tests and Semigraphoids. SIAM J. Discret. Math. 23(3): 1117-1134 (2009) - 2008
- [j25]Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida:
On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol. 3 (2008) - [j24]Rahul Satija, Lior Pachter, Jotun Hein:
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinform. 24(10): 1236-1242 (2008) - [j23]Robert K. Bradley, Lior Pachter, Ian H. Holmes:
Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinform. 24(23): 2677-2683 (2008) - [j22]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) - 2007
- [j21]Ariel S. Schwartz, Lior Pachter:
Multiple alignment by sequence annealing. Bioinform. 23(2): 24-29 (2007) - [j20]Corey J. Schumacher, Phillip R. Chandler, Meir Pachter, Lior S. Pachter:
Optimization of air vehicles operations using mixed-integer linear programming. J. Oper. Res. Soc. 58(4): 516-527 (2007) - [j19]Lior Pachter, Bernd Sturmfels:
The Mathematics of Phylogenomics. SIAM Rev. 49(1): 3-31 (2007) - 2006
- [j18]Colin N. Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter:
Parametric Alignment of Drosophila Genomes. PLoS Comput. Biol. 2(6) (2006) - 2005
- [j17]Sourav Chatterji, Lior Pachter:
Large Multiple Organism Gene Finding by Collapsed Gibbs Sampling. J. Comput. Biol. 12(6): 599-608 (2005) - [j16]Kevin C. Chen, Lior Pachter:
Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Comput. Biol. 1(2) (2005) - 2004
- [j15]Lior Pachter, David E Speyer:
Reconstructing trees from subtree weights. Appl. Math. Lett. 17(6): 615-621 (2004) - [j14]Jon D. McAuliffe, Lior Pachter, Michael I. Jordan:
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinform. 20(12): 1850-1860 (2004) - [j13]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): 273-279 (2004) - 2003
- [j12]Fumei Lam, Marina Alexandersson, Lior Pachter:
Picking Alignments from (Steiner) Trees. J. Comput. Biol. 10(3/4): 509-520 (2003) - [j11]Simon Cawley, Lior Pachter, Marina Alexandersson:
SLAM web server for comparative gene finding and alignment. Nucleic Acids Res. 31(13): 3507-3509 (2003) - [j10]Nicolas Bray, Lior Pachter:
MAVID multiple alignment server. Nucleic Acids Res. 31(13): 3525-3526 (2003) - [j9]Fumei Lam, Lior Pachter:
Forcing numbers of stop signs. Theor. Comput. Sci. 303(2-3): 409-416 (2003) - 2002
- [j8]Inna Dubchak, Lior Pachter:
The computational challenges of applying comparative-based computational methods to whole genomes. Briefings Bioinform. 3(1): 18-22 (2002) - [j7]Lior Pachter, Marina Alexandersson, Simon Cawley:
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems. J. Comput. Biol. 9(2): 389-399 (2002) - 2000
- [j6]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): 1046-1047 (2000) - 1999
- [j5]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): 419-430 (1999) - 1998
- [j4]Daniel J. Kleitman, Lior Pachter:
Finding Convex Sets Among Points in the Plane. Discret. Comput. Geom. 19(3): 405-410 (1998) - [j3]Lior Pachter, Peter Kim:
Forcing matchings on square grids. Discret. Math. 190(1-3): 287-294 (1998) - 1997
- [j2]Lior Pachter:
Combinatorial Approaches and Conjectures for 2-Divisibility Problems Concerning Domino Tilings of Polyominoes. Electron. J. Comb. 4(1) (1997) - [j1]Lior Pachter:
Constructing Status Injective Graphs. Discret. Appl. Math. 80(1): 107-113 (1997)
Conference and Workshop Papers
- 2019
- [c13]Atif Rahman, Lior Pachter:
Transcript Abundance Estimation and the Laminar Packing Problem. AlCoB 2019: 203-211 - 2011
- [c12]Sharon Aviran, Julius B. Lucks, Lior Pachter:
RNA structure characterization from chemical mapping experiments. Allerton 2011: 1743-1750 - 2006
- [c11]Jason Morton, Lior Pachter, Anne Shiu, Bernd Sturmfels, Oliver Wienand:
Geometry of rank tests. Probabilistic Graphical Models 2006: 207-214 - [c10]Sagi Snir, Lior Pachter:
Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. RECOMB 2006: 265-280 - 2004
- [c9]Sourav Chatterji, Lior Pachter:
Multiple organism gene finding by collapsed gibbs sampling. RECOMB 2004: 187-193 - 2003
- [c8]Simon Cawley, Lior Pachter:
HMM sampling and applications to gene finding and alternative splicing. ECCB 2003: 36-41 - [c7]Serafim Batzoglou, Lior Pachter:
Gene Regulation - Session Introduction. Pacific Symposium on Biocomputing 2003: 3-4 - 2002
- [c6]Inna Dubchak, Lior Pachter, Liping Wei:
Genome-Wide Analysis and Comparative Genomics - Session Introduction. Pacific Symposium on Biocomputing 2002: 112-114 - [c5]Lior Pachter, Fumei Lam:
Picking alignments from (steiner) trees. RECOMB 2002: 246-253 - 2001
- [c4]Lior S. Pachter, Meir Pachter:
Optimal paths for avoiding a radiating source. CDC 2001: 3581-3586 - [c3]Lior Pachter, Marina Alexandersson, Simon Cawley:
Applications of generalized pair hidden Markov models to alignment and gene finding problems. RECOMB 2001: 241-248 - 2000
- [c2]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: 46-53 - 1999
- [c1]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: 285-294
Informal and Other Publications
- 2015
- [i2]Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter:
Near-optimal RNA-Seq quantification. CoRR abs/1505.02710 (2015) - 2006
- [i1]Radu Mihaescu, Dan Levy, Lior Pachter:
Why neighbor-joining works. CoRR abs/cs/0602041 (2006)
Coauthor Index
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