Deild:  


Bjarni Vilhjálmur Halldórsson, Associate Professor

School:School of Technology / Department of Engineering 
Location:Venus, 2.2.41b 
Office hours:By appointment 
Phone:5701808 
Email:bjarnivhru.is 
Website:https://www.ru.is/haskolinn/starfsfolk/bjarnivh
bioinformatics.ru.is/bjarni

Curriculum Vitae

www.math.ru.is/bjarni


Education

2001  Carnegie Mellon University, PhD Algorithms, Combinatorics and Optimization
1998  Carnegie Mellon University, MS Algorithms, Combinatorics and Optimization
1996  Unversity of Iceland, BSc Mathematics


Career

2001-4,  Celera Genomics/Applied Biosystems, Sr. Scientist
2004-10,  deCODE Genetics, statistician

RU teaching record

More...

Research

Algorithms in Bioinformatics. Algorithms; design, analysis, implementation and application. Computational Biology, Bioinformatics, Combinatorics, Optimization.

Honours and grants

Graduate Student Research Award, Dept. Math. Sciences, Carnegie Mellon University, 2001 Merck Computational Biology and Chemistry Program Graduate Fellowship 2000-2001. Helga Jonsdottir and Sigurlidi Kristjansson memorial fund fellowship 2000. Thor Thors memorial fund fellowship 2000. Fulbright Fellowship 1996. International Mathematical Olympiad, Sweden 1991, Moscow 1992 (Honorable Mention), Istanbul 1993. Baltic-Way, Vilnus 1992. Nordic Mathematical Contest, 1993. 1st place, out of 120 finalists. Icelandic Mathematical Contest, 1991 (1st place in younger division), 1992 (1st place, older division and finals), 1993 (1st place, older division and finals).

Subject field

Algorithms in Bioinformatics

Business relations

Statistics consultant, deCODE Genetics

Services

Reviewing

SIAM Journal of Computing Discrete Mathematics (2)

Discrete Applied Mathematics (2)

Journal of Computational Biology (12)

Bioinformatics (3)

BMC Bioinformatics (2)

Journal of Bioinformatics and Computational Biology (2)

IEEE/ACM Transaction on Compuational Biology and Bioinformatics (4)

American Journal of Human Genetics

Genome Research

Genomics

Conferences: FOCS 2000, ESA 2000, SWAT 2000, COCOON 2001, RECOMB 2003, FCT 2003, FST-TCS 2003, PSB 2004, RECOMB 2004, SWAT 2004, BIOCONCUR 2004, PSB 2005, RECOMB 2005, SWAT 2006, ESA 2006, SODA 2006.

Program Committee, Session Chair: Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, Pittsburgh, PA, 2004.

Iceland Center of Excellence for Theoretical Computer Science (ICE-TCS) member 2004-.

EURO working group on computational biology, events organizer, 2006-2007.

Organized the weekly seminar in Algorithms, Combinatorics and Optimization 1998-1999.

CMU Algorithms,Combinatorics and Optimization web-page maintenance, 1997-2001.

Student representative to University of Iceland, Faculty of Sciences Board of Directors meetings and Faculty meetings, 1995-1996.

Student representative to University of Iceland, Dept. of Mathematics Faculty meetings, 1994-1995.


Publications


Refereed Journals

 

.Avgustinovich, A. Glen, B. V. Halldorsson, S. Kitaev,
On shortest crucial words avoiding abelian powers Discrete Applied Mathematics 2010 March, 606-608.

H.J. Kerkhof et al. A genome-wide association study identifies
an osteoarthritis susceptibility locus on chromosome 7q22.} Arthritis Rheum. 2010 Feb;62(2):499-510.

A.M Kung Association of JAG1 with Bone Mineral Density
and Osteoporotic
Fractures: A Genome-wide Association Study and Follow-up Replication Studies Am J Hum Genet. 2010 Feb 12;86(2):229-239

J.B. Richards Collaborative meta-analysis: associations
of 150 candidate genes with osteoporosis and osteoporotic fracture Ann Intern Med. 2009 Oct 20;151(8):528-37.

Thorleifsson, G; Holm, H; Edvardsson, V; Walters, GB; Styrkarsdottir, U; Gudbjartsson, DF; Sulem, P; Halldorsson, BV; et al. Sequence variants in the CLDN14 gene associate with kidney stones and bone mineral density NATURE GENETICS       Volume: 41   Issue: 8   Pages: 926-U92

Evangelou, E; ... Halldorsson, BV; et al. Large-Scale Analysis of Association Between GDF5 and FRZB Variants and Osteoarthritis of the Hip, Knee, and Hand   ARTHRITIS AND RHEUMATISM, JUN, 2009, 60, 1710-1721

Styrkarsdottir, U; Halldorsson, BV;  et al. New sequence variants associated with bone mineral density NATURE GENETICS JAN     2009 15-17

Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies.
the Genetic Factors for Osteoporosis (GEFOS) Consortium, Rivadeneira F, Styrkársdottir U, Estrada K, Halldórsson BV et al.
Nat Genet. 2009 Oct 4. [Epub ahead of print]

Large recurrent microdeletions associated with schizophrenia. Stefansson H, Rujescu D, Cichon S, Pietiläinen OP, Ingason A, Steinberg S, Fossdal R, Sigurdsson E, Sigmundsson T, Buizer-Voskamp JE, Hansen T, Jakobsen KD, Muglia P, Francks C, Matthews PM, Gylfason A, Halldorsson BV, Gudbjartsson D, Thorgeirsson TE, Sigurdsson A, Jonasdottir A, Jonasdottir A, Bjornsson A, Mattiasdottir S, Blondal T, Haraldsson M, Magnusdottir BB, Giegling I, Möller HJ, Hartmann A, Shianna KV, Ge D, Need AC, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Paunio T, Toulopoulou T, Bramon E, Di Forti M, Murray R, Ruggeri M, Vassos E, Tosato S, Walshe M, Li T, Vasilescu C, Mühleisen TW, Wang AG, Ullum H, Djurovic S, Melle I, Olesen J, Kiemeney LA, Franke B, Sabatti C, Freimer NB, Gulcher JR, Thorsteinsdottir U, Kong A, Andreassen OA, Ophoff RA, Georgi A, Rietschel M, Werge T, Petursson H, Goldstein DB, Nöthen MM, Peltonen L, Collier DA, St Clair D, Stefansson K. Nature. 2008 Sep 11;455(7210):232-6.

Impact of genetics on low bone mass in adults. Sigurdsson G, Halldorsson BV, Styrkarsdottir U, Kristjansson K, Stefansson K. J Bone Miner Res. 2008 Oct;23(10):1584-90.

Multiple genetic loci for bone mineral density and fractures. Styrkarsdottir U, Halldorsson BV, Gretarsdottir S, Gudbjartsson DF, Walters GB, Ingvarsson T, Jonsdottir T, Saemundsdottir J, Center JR, Nguyen TV, Bagger Y, Gulcher JR, Eisman JA, Christiansen C, Sigurdsson G, Kong A, Thorsteinsdottir U, Stefansson K. N Engl J Med. 2008 May 29;358(22):2355-65. Epub 2008 Apr 29.

Many sequence variants affecting diversity of adult human height. Gudbjartsson DF, Walters GB, Thorleifsson G, Stefansson H, Halldorsson BV, Zusmanovich P, Sulem P, Thorlacius S, Gylfason A, Steinberg S, Helgadottir A, Ingason A, Steinthorsdottir V, Olafsdottir EJ, Olafsdottir GH, Jonsson T, Borch-Johnsen K, Hansen T, Andersen G, Jorgensen T, Pedersen O, Aben KK, Witjes JA, Swinkels DW, den Heijer M, Franke B, Verbeek AL, Becker DM, Yanek LR, Becker LC, Tryggvadottir L, Rafnar T, Gulcher J, Kiemeney LA, Kong A, Thorsteinsdottir U, Stefansson K. Nat Genet. 2008 May;40(5):609-15. Epub 2008 Apr 6.

Lessons from the past: familial aggregation analysis of fatal pandemic influenza (Spanish flu) in Iceland in 1918. Gottfredsson M, Halldórsson BV, Jónsson S, Kristjánsson M, Kristjánsson K, Kristinsson KG, Löve A, Blöndal T, Viboud C, Thorvaldsson S, Helgason A, Gulcher JR, Stefánsson K, Jónsdóttir I. Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1303-8. Epub 2008 Jan 23.

Roded Sharan, Bjarni V. Halldorsson, Sorin Istrail, Islands of tractability of parsimony haplotyping, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006, To Appear.

Dannie Durand, Bjarni V. Halldorsson, Benjamin Vernot, A hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction, Journal of Computational Biology, 2006, 13:320-335.

Bjarni V. Halldorsson, Sorin Istrail, Fransisco M. De La Vega, Optimal selection of SNP markers for disease association studies, Human Heredity, 2004;58(3-4):190-202.

F. M. De La Vega, H. Avi-Itzhak, A. Collins, C.R. Scafe, B. V. Halld\´orsson, X. Su, R. A. Lippert, Y. Wang, M. Laig-Webster, R. T. Koehler, J.S. Ziegle, L.T. Wogan, J.F. Stevens, K.M. Leinen, S.J. Olson, K.J. Guegler, X. You, L.H. Xu., H.G. Hemken, F. Kalush, A. G. Clark, S. Istrail, M. W. Hunkapiller, E. G. Spier, D. A. Gilbert, The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common recombination pattern, Genome Research,

Bert Gold, Francis Kalush, Julie Bergeron, Kevin Scott, Nandita Mitra, Kelly Wilson, Nathan Ellis, Helen Huang, Michael Chen, Ross Lippert, Bjarni V. Halld\´orson, Beth Woodworth, Thomas White, Andrew G. Clark, Fritz F. Parl, Samuel Broder, Michael Dean and Kenneth Offit Estrogen Receptor Genotypes and Haplotypes Associated with Breast Cancer Risk. Cancer Research.

Sorin Istrail, Liliana Florea, Bjarni V. Halldorsson, Oliver Kohlbacher, Russell S. Schwartz, Von Bing Yap, Jonathan Yewdell, Stephen Hoffman, Comparative Immuno-Peptidomics of Humans and their Pathogens Proceedings of the National Academy of Sciences, 2004, 101(36):13268-72

Bjarni V. Halldorsson, Vineet Bafna, Ross Lippert, Russell S. Schwartz, Francisco M. De La Vega, Andrew G. Clark, Sorin Istrail, Optimal haplotype block free selection of tagging SNPs for genome-wide association studies Genome Research, 2004, 14(8):1633-40.

Sorin Istrail, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, Brian Walenz, Hagit Shatkay, Ian Dew, Jason R. Miller, Michael J. Flanigan, Nathan J. Edwards, Randall Bolanos, Daniel Fasulo, Bjarni V. Halldorsson, Sridhar Hannenhalli, Russell Turner, Shibu Yooseph, Fu Lu, Deborah R. Nusskern, Bixiong Chris Shue, Xiangqun Holly Zheng, Fei Zhong, Arthur L. Delcher, Daniel H. Huson, Saul A. Kravitz, Laurent Mouchard, Knut Reinert, Karin A. Remington, Andrew G. Clark, Michael S. Waterman, Evan E. Eichler, Mark D. Adams, Michael W. Hunkapiller, Eugene W. Myers, J. Craig Venter Whole Genome Shotgun Assembly and Comparison of Human Genome Assemblies Proceedings of the National Academy of Sciences, 2004, 101:1916-21.

Russell S. Schwartz, Bjarni V. Halldorsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail Robustness of Inference of Haplotype Block Structure. Journal of Computational Biology, 2003, 10:13-19.

Koen M.J. De Bontridder, Bjarni V. Halld\´orsson, Magn\´us M. Halld\´orsson, Cor A.H. Hurkens, Jan K. Lenstra, R. Ravi, Leen Stougie, {\em Approximation algorithms for test cover problem.} Published as: Technical University Eindhoven SPOR-Report 2002-10. Mathematical Programming-B; (2003) 98(1-3):477 - 491.

Alan M. Frieze, Bjarni V. Halld\´orsson Optimal Sequencing by Hybridization in Rounds, Journal of Computational Biology, (2002), 9:355-369.

Bjarni V. Halldorsson, Reha Tutuncu, An Interior-Point Method for a Class of Saddle-Point Problems. Published as CMU Center for Nonlinear Analysis Research Report No. 00-CNA-006. Journal of Optimization Theory and Applications, (2003), 116(3):559-590.

Refereed Conference Proceedings

Bjarni V. Halldorsson,, Derek Aguiar, Ryan Tarpine, Sorin Istrail
 The Clark Phase-able Sample Size Problem:Long-range Phasing and Loss of Heterozygosity in GWAS RECOMB 2010

Amy Glen, Bjarni V. Halldorsson, Sergey Kitaev, Crucial Words for Abelian Powers, Developments in Language Theory, 2009, 264-275.


 

Roded Sharan, Bjarni V. Halldorsson, Sorin Istrail, Islands of tractability of parsimony haplotyping, IEEE Computational Systems Biology (CSB), 2005, 65-72.

Dannie Durand, Bjarni V. Halldorsson, Benjamin Vernot, A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction, RECOMB 2005, LNBI 3500, Springer Verlag, 250-264.

Bjarni V. Halldorsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail A survey of computational methods for determining haplotypes, In Computational Methods for SNPs and Haplotype Inference (LNCS 2983), pp. 26-47.

Bjarni V. Halldorsson, Vineet Bafna, Nathan Edwards, Ross Lippert, Shibu Yooseph, Sorin Istrail Combinatorial problems arising in SNP and haplotype analysis, In Proceedings of the Fourth International Conference on Discrete Mathematics and Theoretical Computer Science, CDMTCS 2003, pp. 26-47.

Liliana Florea, Bjarni V. Halldorsson, Oliver Kohlbacher, Russell S. Schwartz, Stephen Hoffman, Sorin Istrail, Epitope prediction algorithms for peptide-based vaccine design In Proceedings of the Second Annual IEEE Computer Society Bioinformatics Conference (CSB 2003), pp. 17-26.

Vineet Bafna, Bjarni V. Halld\´orsson, Russell S. Schwartz, Andrew G. Clark, Sorin Istrail, Haplotypes and Informative SNP Selection Algorithms: Don´t Block Out Information. Proceedings of the 7th Annual International Conference on Computational Molecular Biology ({RECOMB}-03), pp. 19-27.

Bjarni V. Hallld\´orsson, Magnus M. Halld\´orsson and R. Ravi, On the approximability of the minimum test collection problem.} Proceedings of the 9th Annual European Symposium on Algorithms (ESA-01), pp. 158-169.

Alan M. Frieze, Bjarni V. Halldorsson Optimal Sequencing by Hybridization in Rounds}, Proceedings of the 5th Annual International Conference on Computational Molecular Biology ({RECOMB}-01), pp. 144-151.

Technical Reports

Bjarni V. Halldorsson, Erlendur S. Thorsteinsson and Bjarni Kristjansson, Modeling Interface to Non-Linear Programming Solvers, An Instance: xMPS - the extended MPS format. Maximal Software white paper, 2000.

Bjarni V. Halldorsson, Jonathan S. Minden, R. Ravi Protein Identification by Epitope Recognition. Currents in computational molecular biology, 2001. pp. 109-110.

Bjarni V. Halldorsson, Magnus M. Halldorsson, Empirical Study of some Clique Heuristics Motivated by Worst-Case Results. University of Iceland Science Institute Technical Report RH-2000-21.

Bjarni V. Halldorsson, Component Software for Optimization:OOODL-Object Oriented Optimization Decomposition Library & LPSolver, Argonne National Laboratories summer report 1999.

Patents Pending

Jonathan S. Minden, R. Ravi, Alan Koretsky, Bjarni V. Halldorsson Methods and systems for identifying proteins, USPTO Appl. No. 20030054408.

Sorin Istrail, Liliana Florea, Bjarni V. Halldorsson, Russell S. Schwartz, Oliver Kohlbacher, Stephen Hoffman Methods for peptide protein binding prediction, USPTO Appl. No. 20040072249.

Bjarni V. Halldorsson, Vineet Bafna, Ross Lippert, Russell Schwartz, Andrew Clark, Sorin Istrail, Franscisco M. De La Vega,  Identification of informative genetic markers, USPTO Appl. No. 20060046256


Other websites

www.math.ru.is/bjarni