Personal web page for Jens Lagergren

Nada

Jens Lagergren

<jensl@nada.kth.se>
Telephone: +46 8 55 37 85 70, fax: +46 8 55 37 82 14
Address: KTH, Albanova, SBC, S - 100 44 Stockholm
Visiting address: Albanova, Roslagstullsbacken 21 (see map)
(Denna sida finns ej tillgänglig på svenska.)

Affiliation

I am professor in computer science in the theoretical computer science group at Nada. I also belong to SBC (Stockholm Bioinformatics Center), where my office can be found. SBC is a joint venture between KTH (Kunliga Tekniska Högskolan, i.e. The Royal Institute of Technology), SU (Stockholm University), and KI (Karolinska Institutet). SBC is funded by the Swedish Foundation for Strategic Research.

Ph.D. Students

Samuel Andersson
Isaac Elias
Marcus Hjelm
Örjan Svensson
Ali Tofigh

Former Post-docs

Ann-Charlotte Berglund
Öjvind Johansson

Former Ph.D. Students

Recent Service

Program committee WABI 2005.
Program committee ISMB 2005
Member of the BICI Scientific Advisory Board
Program committee chair Second RECOMB Satellite Workshop on Comparative Genomics, Bertinoro, 16-19 October, 2004).
Co-organizer Second RECOMB Satellite Workshop on Comparative Genomics, Bertinoro, 16-19 October, 2004).
Program committee Bioinformatics 2005
Program committee WABI 2004
Program committee RECOMB 2004
Board member of SocBiN -- Society for Bioinformatics in the Nordic countries.
Co-organizer IMA/RECOMB Satellite Workshop on Comparative Genomics (October 2003).
Program committee Bioinformatics 2003
Co-organizer First Bertinoro Computational Biology Workshop.
Co-organizer Second Annual Barbados Bioinformatics Workshop (November-December 2002).
Co-organizer First Annual Barbados Bioinformatics Workshop.
Program committee WABI 2001
Program committee Bioinformatics 2002
Program committee ICALP'00
Program committee SWAT'98
Co-organizer SWAT'98

Refereed Publications since 1996 (in most cases authors are listed in alphabetic order, i.e. computer science style)

MSCAN: identification of functional clusters of transcription factor binding sites.: W. Alkema, Öjvind Johansson, Jens Lagergren, and Wyeth W. Wasserman; Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W195-8.; PDF
Ancestral Maximum Likelihood of Phylogenetic Trees is Hard: L. Addario-Berry, B. Chor, M. Hallett, J. Lagergren, A. Panconesi, and T. Wareham.; Journal of Bioinformatics and Computational Biology, January 2004, 12:55; doi:10.1142/S0219720004000557
Algorithms for RH Mapping: New Ideas and Improved Analysis: L. Ivansson and J. Lagergren.; SIAM Journal on Computing, accepted for publication 2004.
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution: Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad; RECOMB 2004, 326-335.; PS
Simultaneous Identification of Duplications and Lateral Transfers: M. Hallett, J. Lagergren, and A. Tofigh; RECOMB 2004, 347-356.; PDF, PS
Ancestral Maximum Likelihood of Phylogenetic Trees is Hard: Louigi Addario-Berry, Benny Chor, Mike Hallett, Jens Lagergren, Alessandro Panconesi, and Todd Wareham; WABI 2003: 202-215; PS A4, PS Letter
Fitting Point on the Real Line and its Application to RH Mapping: J. Håstad, L. Ivansson, and J. Lagergren; J. Algorithms 49(1): 42-62 (2003); PDF
A polynomial-time algorithm for near-perfect phylogeny: D. Fernandez-Baca, J. Lagergren; SIAM Journal on Computing 32(5): 1115-1127 (2003); PDF
Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC: L. Arvestad, A.C. Berglund, J. Lagergren, and B. Sennblad; Bioinformatics (ISMB) 2003: 7-15; PDF
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm: Öjvind Johansson, W. Alkema, Wyeth W. Wasserman, and Jens Lagergren; Bioinformatics (ISMB) 2003: 169-176; PS PDF
Towards Identifying Lateral Gene Transfer Events: L. Addario-Berry, M. Hallett, J. Lagergren; Pacific Symposium on Biocomputing 2003: 279-290; PDF
Combining Polynomial Running Time and Fast Convergence for the Disk-Covering Method: J. Lagergren.; Journal of Computer and System Science, 65(3): 481-493 (2002)
Efficient Algorithms for Lateral Gene Transfer Problems.: M.T. Hallett and J. Lagergren.; In RECOMB´01, pages 149-156.
Hunting for Functionally Analogous Genes.: M.T. Hallett and J.Lagergren.; In FSTTCS´00.
New algorithms for the duplication-loss model.: M.T. Hallett and J.Lagergren.; In RECOMB´00, pages 138-146.; PDF
On the approximability of the Steiner tree problem in phylogeny: D. Fernandez-Baca, J. Lagergren; Discrete Applied Mathematics Special Issue on Computational Molecular Biology, 88 (1), pages 127-143, 1999
Upper bounds on the size of obstructions and intertwines.: Jens Lagergren.; Journal of Combinatorial Theory Series B, 73(1):7--40, May 1998.
Fitting Point on the Real Line and its Application to RH Mapping: J. Håstad, L. Ivansson, and J. Lagergren; ESA 98, pages 465-476, LNCS 1461, 1998. PostScript
Approximate Max k-Cut with subgraph guarantee.: Viggo Kann, Jens Lagergren, and Alessandro Panconesi.; Information Processing Letters, 65(3):145--150, 13 February 1998.
On the hardness of approximating max k-cut and its dual: Viggo Kann, Sanjeev Khanna, Jens Lagergren, and Alessandro Panconesi.; CJTCS-1997-2, June 3, 1997.
A polynomial time algorithm for near-perfect phylogeny.: D. Fernandez-Baca and J. Lagergren.; 23rd ICALP, pages 670-680, LNCS 1099, 1996.
Hypothesis testing in perfect phylogeny for a bounded number of characters.: J. Lagergren.; 13th STACS, pages 605--616, LNCS 1046, 1996.
Efficient parallel algorithms for graphs of bounded tree-width.: J. Lagergren.; Journal of Algorithms, 20:20--44, 1996.
Approximability of maximum splitting of k-sets and some other APX-complete problems.: Viggo Kann, Jens Lagergren, and Alessandro Panconesi.; Information Processing Letters, 58(3):105--110, 13 May 1996.
Equivalent definitions of recognizability for sets of graphs of bounded tree-width.: B. Courcelle and J. Lagergren.; Mathematical Structures in Computer Science, 2:141--165,1996.
On the approximability of the Steiner tree problem in phylogeny: D. Fernandez-Baca and J. Lagergren.; In 7th ISAAC,pages 65--74, 1996.
On the hardness of MAX k-CUT and its dual.: V. Kann, S. Kanna, J. Lagergren, and A. Panconesi.; In 4th ISTCS, pages 61--67, 1996.

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Latest change December 28, 2004
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