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In press
M. Singer and L. Pachter, Bayesian networks in the study of genomewide DNA methylation, in press.

2014
R. Forster, K. Chiba, L. Schaeffer, S.G. Regaldo, C.S. Lai, Q. Gao, S. Kiani, H.F. Farin, H. Clevers, G.J. Cost, A. Chan, E.J. Rebar, F.D. Urnov, P.D. Gregory, L. Pachter, R. Jaenisch and D. Hockemeyer, Human Intestinal Tissue with Adult Stem Cell Properties Derived from Pluripotent Stem Cells, Stem Cell Reports, 2 (2014), p 838--852.

Sachiko Takayama, Joseph Dhahbi, Adam Roberts, Guanxiong Mao, Seok-Jin Heo, Lior Pachter, David I.K. Martin and Dario Boffelli, Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity, Genome Research, (2014), advance access.

H. Pimentel, M. Parra, S. Gee, D. Ghanem, X. An, J. Li, N. Mohandas, L. Pachter and J. Conboy, A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis, Nucleic Acids Research, (2014), advance access.

2013
A. Roberts, H. Feng and L. Pachter, Fragment assignment in the cloud with eXpress-D, BMC Bioinformatics, (2013), advance access.

A. Roberts, L. Schaeffer and L. Pachter, Updating RNA-Seq analyses after re-annotation, Bioinformatics, (2013) published online.

A. Rahman and L. Pachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14 (2013), R8.

2012
C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, advance online publication (2012).

S.A. Mortimer, C. Trapnell, S. Aviran, L. Pachter and J.B. Lucks, SHAPE-Seq: High throughput RNA structure analysis, Current Protocols in Chemical Biology, advance online publication.

A. Kleinman, M. Harel and L. Pachter, Affine and projective tree metric theorems, Annals of Combinatorics, advance online publication (2012).

A. Roberts and L. Pachter, Streaming fragment assignment for real-time analysis of sequencing experiments, Nature Methods, advance online publication (2012).

V. Hower, R. Starfield, A. Roberts, and L. Pachter, Quantifying uniformity in mapped reads, Bioinformatics, 28 (2012), 2680--2682.

L. Pachter, A closer look at RNA editing, Nature Biotechnology, 30 (2012), 246--247.

C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn and L. Pachter, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, 7 (2012), 562--578.

2011
S. Aviran, J. Lucks and L. Pachter, RNA structure characterization from chemical mapping experiments, Proceedings of the 49th Allerton Conference on Communication, Control and Computing, p 1743--1750, 2012.

A. Roberts and L. Pachter, RNA-Seq and find: entering the RNA deep field, Genome Medicine, 3 (2011), 74 [PDF].

F. Meacham, D. Boffelli, J. Dhahbi, D.I.K. Martin, M. Singer and L. Pachter, Identification and correction of systematic error in high-throughput sequence data, BMC Bioinformatics, in press.

M. Singer, A. Engstrom, A. Schoenhuth and L. Pachter, Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains, Statistical Applications in Genetics and Molecular Biology, 10 (2011), Article 43.

D. Martin, M. Singer, J. Dhahbi, G. Mao, L. Zhang, G. Schroth, L. Pachter and D. Boffelli, Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states, Genome Research (2011), Advance publication.

A. Roberts, H. Pimentel, C. Trapnell and L. Pachter, Identification of novel transcripts in annotated genomes using RNA-Seq, Bioinformatics, 27 (2011), p 2325--2329.

S. Snir and L. Pachter, Tracing the most parsimonious indel history, Journal of Computational Biology, 8 (2011), p 1--20.

S. Aviran, C. Trapnell, J.B. Lucks, S.A. Mortimer, S. Luo, G.P. Schroth, J.A. Doudna, A.P. Arkin and L. Pachter,Modeling and automation of sequencing-based characterization of RNA structure, Proceedings of the National Academy of Sciences, (2011), early online.

J.B. Lucks, S.A. Mortimer, C. Trapnell, S. Luo, S. Aviran, G.P. Schroth, L. Pachter, J.A. Doudna and A.P. Arkin, Multiplexed RNA Secondary and Tertiary Structure Characterization with SHAPE-Seq, Proceedings of the National Academy of Sciences, (2011), early online.

A. Roberts, C. Trapnell, J. Donaghey, J.L. Rinn and L. Pachter, Improving RNA-Seq expression estimates by correcting for fragment bias, Genome Biology, 12 (2011), R22.

V. Hower, S.N. Evans and L. Pachter, Shape-based peak identification for ChIP-Seq, BMC Bioinformatics, 12 (2011), 15.

2010
D. Levy and L. Pachter, The neighbor-net algorithm, Advances in Applied Mathematics, doi:10.1016/j.aam.2010.09.002.

S.M. Willerth, H.A. Pedro, L. Pachter, L.M. Humeau, A.P. Arkin and D.V. Shaffer, Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology, PLoS One, 5 (2010), e13564.

M. Singer, D. Boffelli, J. Dhahbi, A. Schoenhuth, G.P. Schroth, D.I.K. Martin and L. Pachter, MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations, PLoS Computational Biology, 6 (2010), e1000888.

S.N. Evans, V. Hower and L. Pachter, Coverage statistics for sequences census methods, BMC Bioinformatics, 11 (2010), 430.

T.C. Levin, A.M. Glazer, L. Pachter, R.B. Brem and M.B. Eisen, Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study, PLoS One, 5 (201), e11645.

A. Lapuk, H. Marr, L. Jakkula, H. Pedro, S. Bhattacharya, E. Purdom, Z. Hu, K. Simpson, L. Pachter, S. Durinck et al., Exon-level microarray analyses identify alternative splicing programs in breast cancer, Molecular Cancer Research, (2010), online first.

C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold and L. Pachter, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology 28, (2010), p 511--515. News and Views report by B.J. Haas and M.C. Zody, Cufflinks highlighted as breakthrough of the year in computational biology.

R. Bradley, X.Y. Li, C. Trapnell, S. Davidson, L. Pachter, H.C. Chu, L.A. Tonkin, M.D. Biggin and M.B. Eisen, Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species, PloS Biology 8, (2010) e1000343.

M. Hilty, C. Burke, H. Pedro, P. Cardenas, A. Bush, C. Bossley, J. Davies, A. Ervine, L. Poulter, L. Pachter, M.F. Moffatt and W.O. Cookson, Disordered microbial communities in asthmatic airways, PLoS One 5, (2010) e8578.

2009
J. Morton, L. Pachter, A. Shiu, B. Sturmfels and O. Wienand, Convex rank tests and semigraphoids, SIAM Journal on Discrete Mathematics 23, (2009) p 1117--1134.

R. Bradley, A. Roberts, M. Smoot, S. Juvekar, J. Do, C. Dewey, I. Holmes and L. Pachter,Fast statistical alignment, PLoS Computational Biology 5, (2009) e1000392.

C. Trapnell, L. Pachter and S. Salzberg, TopHat: discovering splice junctions with RNA-seq, Bioinformatics 25, (2009) 1105--1111. Selected best next-gen sequencing paper published in Bioinformatics.

2008
R. Bradley, L. Pachter and I. Holmes, Specific alignment of structured RNA: stochastic grammars and sequence annealing, Bioinformatics 24, (2008) 2677--2683.

R. Mihaescu and L. Pachter, Combinatorics of least squares trees, Proceedings of the National Academy of Sciences, 105(36), 13206--13211.

M-L. Dequéant et al., Comparison of pattern detection methods in microarray time series of the segmentation clock, PLoS ONE 3(8), (2008): e2856.

K. Eickmeyer, P. Huggins, L. Pachter and R. Yoshida, On the optimality of the neighbor-joining algorithm, Algorithms for Molecular Biology 3, (2008).

N. Eriksson, L. Pachter, Y. Mitsuya, S.Y. Rhee, C. Wang, B. Gharizadeh, M. Ronaghi, R.W. Shafer and N. Beerenwinkel, Viral population estimation using pyrosequencing, PLoS Computational Biology 4, (2008), e1000074.

R. Satija, L. Pachter and J. Hein, Combining statistical alignment and phylogenetic footprinting to detect regulatory elements, Bioinformatics, (2008), advanced access.

R. Mihaescu, D. Levy and L. Pachter, Why neighbor-joining works, Algorithmica, (2008), online first.

2007
A. Stark et al., Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures, Nature 450, (2007), p 219--232.

Drosophila Comparative Genome Sequencing and Analysis Consortium, Evolution of genes and genomes in the context of the Drosophila phylogeny, Nature 450, (2007), p 203--218.

D. J. Begun, A.K. Holloway, K. Stevens, L.W. Hillier, Y-P. Poh, M.W. Hahn, P.N. Nista, C.D. Jones, A.D. Kern, C.N. Dewey, L. Pachter, E. Myers and C.H. Langley, Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans, PLoS Biology 5(11): e310.

P. Huggins, L. Pachter and B. Sturmfels, Towards the human genotope, Bulletin of Mathematical Biology, Volume 69, Number 8, (2007), p 2723--2725.

N. Beerenwinkel, L. Pachter and B. Sturmfels, Epistasis and shapes of fitness landscapes, Statistica Sinica, Volume 17, Number 4, (2007), p 1317--1342.

L. Pachter, An introduction to reconstructing ancestral genomes, Proceedings of Symposia in Applied Mathematics, AMS Short Course Subseries, Volume 64, (2007), p 1--20.

J. Morton, L. Pachter, A. Shiu and B. Sturmfels, The cyclohedron test for finding periodic genes in time course expression studies, Statistical Applications in Genetics and Molecular Biology, Volume 6 Issue 1, (2007).

The ENCODE Project Consortium, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature 447, (2007), p 799--816.

E.H. Margulies et al., Analysis of deep mammalian sequence alignments and constraint predictions for 1% of the human genome, Genome Research 17 (2007), p 760--774.

S. Chatterji and L. Pachter, Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor, Genomics 90 (2007), p 44--48.

L. Pachter, Interpreting the unculturable majority, Nature Methods vol. 4, (2007), p 479--480.

N. Beerenwinkel, L. Pachter, B. Sturmfels, S. Elena and R. Lenski, Analysis of epistatic interactions and fitness landscapes using a new geometric approach, BMC Evolutionary Biology 7:60 (2007).

L. Pachter and B. Sturmfels, The mathematics of phylogenomics, SIAM review, Volume 49, Issue 1 (2007) 3--31. Introduction by F. Santosa.

A.S. Schwartz and L. Pachter, Multiple alignment by sequence annealing, Bioinformatics 23 (2007), e24--e29. Best paper award ECCB 2006.

2006
J. Morton, L. Pachter, A. Shiu, B. Sturmfels and O. Wienand, Geometry of rank tests, Proceedings of the Third European Workshop on Probabilistic Graphical Models (PGM 3), Prague, Czech Republic, September 2006.

C. Dewey, P. Huggins, K, Woods, B. Sturmfels and L. Pachter, Parametric alignment of Drosophila genomes, PLoS Computational Biology, Volume 2, Number 6 (2006) p e73.

C. Dewey and L. Pachter, Evolution at the Nucleotide Level: The Problem of Multiple Whole Genome Alignment, Human Molecular Genetics 15 (2006), R51--R56.

S. Chatterji and L. Pachter, Reference based annotation with GeneMapper, Genome Biology 7 (2006), R29.

S. Snir and L. Pachter, Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes, Lecture Notes in Computer Science, Proceedings of the Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), (2006) p 265--280.

D. Levy, R. Yoshida and L. Pachter, Beyond pairwise distances: neighbor joining with phylogenetic diversity estimates, Molecular Biology and Evolution, 23 (2006), p 491--498.

S. Lall, D. Grün, A. Krek, K. Chen, Y. Wang, C. Dewey, P. Sood, T. Colombo, N. Bray, P. MacMenamin, H. Kao, K.C. Gunsalus, L. Pachter, F. Piano and N. Rajewsky, A genome-wide map of conserved microRNA targets in C. elegans, Current Biology 16 (2006), p 460--471.

A. Caspi and L. Pachter, Identification of transposable elements using multiple alignments of related genomes, Genome Research 16 (2006), p 260--270.

2005
  L. Pachter and B. Sturmfels, Algebraic Statistics for Computational Biology, Cambridge University Press, 2005.  

Reviewed at Amazon.com, Computing Reviews and in the journal Briefings in Bioinformatics.

M. Alexandersson, N. Bray and L. Pachter, Pair hidden Markov models, special review in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (L. B. Jorde, P. Little, M. Dunn and S. Subramanian, editors), October 2005.

K. Chen and L. Pachter, Bioinformatics for whole-genome shotgun sequencing of microbial communities, PLoS Computational Biology, Volume 1, Number 2 (2005) p e24.

S. Chatterji and L. Pachter, Multiple organism gene finding by collapsed Gibbs sampling, Journal of Computational Biology, 12 (2005), p 599--608.

J. D. McAuliffe, M. I. Jordan and L. Pachter, Subtree power analysis finds optimal species for comparative genomics, Proceedings of the National Academy of Sciences, Volume 102, Number 22 (2005), p 7900--7905.

2004
International Chicken Genome Sequencing Consortium, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, vol. 432, (2004), p 695--716.

D. Boffelli, C. V. Weer, L. Weng, K. D. Lewis, M. I. Shoukry, L. Pachter, D. N. Keys and E. M. Rubin, Intraspecies sequence comparisons for annotating genomes, Genome Research 14 (2004), p 2406--2411.

L. Pachter and B. Sturmfels, Parametric inference for biological sequence analysis, Proceedings of the National Academy of Sciences, Volume 101, Number 46 (2004), p 16138--16143.

L. Pachter and B. Sturmfels, Tropical geometry of statistical models, Proceedings of the National Academy of Sciences, Volume 101, Number 46 (2004), p 16132--16137.

The ENCODE Project Consortium, The ENCODE (ENCyclopedia Of DNA Elements) project, Science, Volume 306, Number 5696 (2004), p 636--640.

L. Pachter and D. Speyer, Reconstructing trees from subtree weights, Applied Mathematics Letters 17 (2004), p 615 -- 621.

J. D. McAuliffe, L. Pachter and M. I. Jordan, Multiple-sequence functional annotation and the generalized hidden Markov phylogeny, Bioinformatics 20 (2004) p 1850 -- 1860.

K. A. Frazer, L. Pachter, A. Poliakov, E. M. Rubin and I. Dubchak, VISTA: computational tools for comparative genomics, Nucleic Acids Research 32 (2004) p 273 -- 279.

S. Chatterji and L. Pachter, Multiple organism gene finding by collapsed Gibbs sampling , Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), (2004) p 187--193.

K. Chakrabarti and L. Pachter, Visualization of multiple genome annotations and alignments with the K-BROWSER , Genome Research 14 (2004), p 716--720.

N. Bray and L. Pachter, MAVID: Constrained ancestral alignment of multiple sequences, Genome Research 14 (2004), p 693--699.

C. Dewey, J.Q. Wu, S. Cawley, M. Alexandersson, R. Gibbs and L. Pachter, Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat, Genome Research 14 (2004), p 661--664.

V.B. Yap and L. Pachter, Identification of evolutionary hotspots in the rodent genomes, Genome Research 14 (2004), p 574--579.

Rat Genome Sequencing Consortium, Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol. 428, (2004), p 493--521 [PDF].

2003
S. Cawley and L. Pachter, HMM sampling and applications to gene finding and alternative splicing, Bioinformatics, 19 Supplement 2, (2003) p 36--41.

F. Lam and L. Pachter, Forcing numbers of stop signs, Theoretical Computer Science, 303 (2003) p 409--416.

N. Bray and L. Pachter, MAVID multiple alignment server, Nucleic Acids Research, 31 (2003) p 3525--3526.

S. Cawley, L. Pachter and M. Alexandersson, SLAM web server for comparative gene finding and alignment, Nucleic Acids Research, 13 (2003) p 3507--3509.

F. Lam, M. Alexandersson, L. Pachter, Picking alignments from (Steiner) trees, Journal of Computational Biology, 10 (2003) p 509--520.

M. Alexandersson, S. Cawley, L. Pachter, SLAM- Cross-species gene finding and alignment with a generalized pair hidden Markov model, Genome Research, 13 (2003) p 496--502.

D. Boffelli, J. McAuliffe, D. Ovcharenko, K. D. Lewis, I. Ovcharenko, L. Pachter, E. M. Rubin, Phylogenetic shadowing of primate sequences to find functional regions of the human genome, Science, Volume 299, Number 5611 (2003), p 1391--1394. Introduction by R. A. Gibbs and D. L. Nelson.

N. Bray, I. Dubchak, L. Pachter, AVID: A global alignment program, Genome Research, 13 (2003) p 97--102.

O. Couronne, A. Poliakov, N. Bray, T. Ishkhanov, D.V. Ryaboy, E. M. Rubin, L. Pachter, I. Dubchak, Strategies and tools for whole genome alignments, Genome Research, 13 (2003) p 73--80.
2002
R. H. Waterston et al., Initial sequencing and comparative analysis of the mouse genome, Nature, vol. 420, (2002), p 520--562.

L. Pachter, M. Alexandersson, S. Cawley, Applications of generalized pair hidden Markov models to alignment and gene finding problems, Journal of Computational Biology, Volume 9, Number 2, 2002, p 389--400.

G. Loots, I. Ovcharenko, L. Pachter, I. Dubchak and E. M. Rubin, Comparative sequence-based approach to high-throughput discovery of functional regulatory elements, Genome Research 12, (2002), p 832--839.

I. Dubchak and L. Pachter, The computational challenges of applying comparative-based computational methods to whole genomes, Briefings in Bioinformatics, March 2002, vol. 3, no. 1, p 18--22.

L. Pachter, F. Lam, M. Alexandersson, Picking alignments from (Steiner) trees, Proceedings of the Sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2002) (2002).

A. Peter et al., Mapping and identification of essential gene functions on the X chromosome of Drosophila , EMBO reports, vol. 3 number 1, (2002), p 34--38.
2001
P. V. Benos et al., From First Base: The sequence of the tip of the X Chromosome of D. melanogaster, a comparison of two sequencing strategies, Genome Research 11, (2001), p 710--730.

L. Pachter and M. Pachter, Avoiding points in the plane, Proceedings of the 40th IEEE Conference on Decision and Control (2001).

L. Pachter, M. Alexandersson, S. Cawley, Applications of generalized pair hidden Markov models to alignment and gene finding problems, Proceedings of the Fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2001) (2001).
2000
C. Mayor, M. Brudno, J.R. Schwartz, A. Poliakov, E. M. Rubin, K. A. Frazer, L. Pachter and I. Dubchak, VISTA: Visualizing global DNA sequence alignments of arbitrary length, Bioinformatics, 16 (2000), p 1046--1047.

S. Batzoglou, L. Pachter, J. P. Mesirov, B. Berger, E. S. Lander, Human and mouse gene structure: comparative analysis and application to exon prediction, Genome Research 10, (2000), p 950--958.

I. Dubchak, C. Mayor, M. Brudno, L. Pachter, E. M. Rubin and K. A. Frazer, Active conservation of noncoding sequences revealed by 3-way species comparisons, Genome Research 10 (2000), p 1304--1306.

S. Batzoglou, L. Pachter, J. P. Mesirov, B. Berger, E. S. Lander, Human and mouse gene structure: comparative analysis and application to exon prediction, Proceedings of the Fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2000) (2000).
1999
L. Pachter, S. Batzoglou, V. I. Spitkovsky, E. Banks, E. S. Lander, D. J. Kleitman and B. Berger, A dictionary based approach for gene annotation, Journal of Computational Biology (1999) Fall-Winter; (6)3-4:419--430.

L. Pachter, S. Batzoglou, V. I. Spitkovsky, W. Beebee, E. S. Lander, B. Berger and D. J. Kleitman, A dictionary based approach for gene annotation, Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology (RECOMB 1999) (1999) p 285--294.
1998
D. J. Kleitman and L. Pachter, Finding convex sets among points in the plane, Discrete and Computational Geometry, 19 (3) (1998) p 405--410.

L. Pachter and P. Kim, Forcing Matchings on Square Grids, Discrete Mathematics, 190 (1998) p 287--294.

S. Batzoglou, B. Berger, D. J. Kleitman, E. S. Lander and L. Pachter, Recent developments in computational gene recognition, Documenta Mathematica, Extra Volume ICM 1998 I (1998).
1997
L. Pachter, Constructing status injective graphs, Discrete Applied Mathematics, 80 (1) (1997) p 107--113.

L. Pachter, Combinatorial approaches and conjectures for 2-Divisibility problems concerning domino tilings of polyominoes, Electronic Journal of Combinatorics, 4 (1), R29 (1997).
1995
L. Pachter, H. Snevily and B. Voxman, On pebbling graphs, Proceedings of the Twenty-sixth Southeastern International Conference on Combinatorics, Graph Theory and Computing. Congressus Numerantium, 107 (1995) p 65--80.
Other manuscripts
N. Bray and L. Pachter, Comment on "Evidence of Abundant and Purifying Selection in Humans for Recently Acquired Regulatory Functions" (2012).

L. Pachter, Models for transcript quantification from RNA-Seq (2011).

P. Huggins and L. Pachter, Selecting universities: personal preference and rankings (2008).

R. Mihaescu, D. Levy and L. Pachter, Erratum to "On the edge l radius of Saitou and Nei's method for phylogenetic reconstruction" [Theoret. Comput. Sci. 369(1-3) (2006) 448-455] (2007).

A.S. Schwartz, E.W. Myers and L. Pachter, Alignment metric accuracy (2005).

L. Pachter, A Nobel Prize in mathematical biology?, Department of Mathematics Newsletter, UC Berkeley (2006).

R. Guigo, E. Birney, M. Brent, E. Dermitzakis, L. Pachter, H. Roest Crollius, V. Solovyev and M. Q. Zhang Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models, arXiv q-bio.GN/0410008 (2004).

N. Kitchloo and L. Pachter, An interesting result about subset sums (1993).

R. Dawson, B. McDonald, J. Mycielski and L. Pachter, Light traps (1992).