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Lior Pachter
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- affiliation: University of California, Berkeley, USA
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2020 – today
- 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)
2010 – 2019
- 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) - [c13]Atif Rahman
, Lior Pachter
:
Transcript Abundance Estimation and the Laminar Packing Problem. AlCoB 2019: 203-211 - 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) - [i2]Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter:
Near-optimal RNA-Seq quantification. CoRR abs/1505.02710 (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) - [c12]Sharon Aviran, Julius B. Lucks, Lior Pachter
:
RNA structure characterization from chemical mapping experiments. Allerton 2011: 1743-1750 - 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)
2000 – 2009
- 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) - [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 - [i1]Radu Mihaescu, Dan Levy, Lior Pachter:
Why neighbor-joining works. CoRR abs/cs/0602041 (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) - [c9]Sourav Chatterji, Lior Pachter
:
Multiple organism gene finding by collapsed gibbs sampling. RECOMB 2004: 187-193 - 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) - [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
- [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) - [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
- [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) - [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
1990 – 1999
- 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) - [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 - 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)
Coauthor Index
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last updated on 2024-07-05 20:14 CEST by the dblp team
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