Michael Lachmann
   
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Publications

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. (2014)
Khrameeva E.E., K Bozek, L He, Z Yan, X Jiang, Y Wei, K Tang, ...
Nature communications 5 [pdf] [journal]

The complete genome sequence of a Neanderthal from the Altai Mountains. (2014)
Prüfer K, F Racimo, N Patterson, F Jay, S Sankararaman, S Sawyer, ...
Nature 505 (7481), 43-49 [pdf] [journal]

When unreliable cues are good enough. (2013)
Donaldson-Matasci M.C., CT Bergstrom, M Lachmann
The American Naturalist 182 (3), 313-327. [pdf] [journal]

On the role of resonance in drug failure under HIV treatment interruption. (2013)
Oña L, RD Kouyos, M Lachmann, S Bonhoeffer
Theoretical Biology and Medical Modelling 10 (1), 44. [pdf] [journal]

Great ape genetic diversity and population history. (2013)
Prado-Martinez J, PH Sudmant, JM Kidd, H Li, JL Kelley, ...
Nature 499 (7459), 471-475. [pdf] [journal]

The value of information in signals and cues. (2013)
Lachmann M
Animal Communication Theory: Information and Influence, 357. [pdf] [book]

Inferring the history of population size change from genome-wide SNP data. (2012)
Theunert C, K Tang, M Lachmann, S Hu, M Stoneking
Molecular biology and evolution 29 (12), 3653-3667. [pdf] [journal]

The bonobo genome compared with the chimpanzee and human genomes. (2012)
Prüfer K, K Munch, I Hellmann, K Akagi, JR Miller, B Walenz, S Koren, ...
Nature. [pdf] [journal]

'maskBAD'-a package to detect and remove Affymetrix probes with binding affinity differences. (2012)
Dannemann M, M Lachmann, A Lorenc
BMC bioinformatics 13 (1), 56. [pdf] [journal]

Analysis of human accelerated DNA regions using archaic hominin genomes. (2012)
Burbano H.A., RE Green, T Maricic, C Lalueza-Fox, M de La Rasilla, ...
PloS one 7 (3), e32877. [pdf] [journal]

Ant aggression and evolutionary stability in plant–ant and plant–pollinator mutualistic interactions. (2011)
Oña L, M Lachmann
Journal of evolutionary biology 24 (3), 617-629. [pdf] [journal]

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain. (2010)
Somel M., S Guo, N Fu, Z Yan, HY Hu, Y Xu, Y Yuan, Z Ning, Y Hu, ...
Genome research 20 (9), 1207-1218. [pdf] [journal]

Targeted investigation of the Neandertal genome by array-based sequence capture. (2010)
Burbano H.A., E Hodges, RE Green, AW Briggs, J Krause, M Meyer, ...
science 328 (5979), 723-725. [pdf] [journal] [sup]

A draft sequence of the Neandertal genome. (2010)
Green R.E., J Krause, AW Briggs, T Maricic, U Stenzel, M Kircher, et. al.
science 328 (5979), 710-722. [pdf] [journal] [sup]

The fitness value of information. (2010)
Donaldson‐Matasci M.C., CT Bergstrom, M Lachmann
Oikos 119 (2), 219-230. [pdf] [journal]

The effects of probe binding affinity differences on gene expression measurements and how to deal with them. (2009)
Dannemann M, A Lorenc, I Hellmann, P Khaitovich, M Lachmann
Bioinformatics 25 (21), 2772-2779. [pdf] [journal] [sup]

Linkage disequilibrium extends across putative selected sites in FOXP2. (2009)
Ptak S.E., W Enard, V Wiebe, I Hellmann, J Krause, M Lachmann, S Pääbo
Molecular biology and evolution 26 (10), 2181-2184. [pdf] [journal] [sup]

The Neandertal genome and ancient DNA authenticity. (2009)
Green R. E., AW Briggs, J Krause, K Prüfer, HA Burbano, M Siebauer, M Lachmann, S Pääbo.
The EMBO journal 28 (17), 2494-2502. [pdf] [journal]

Transcriptional neoteny in the human brain. (2009)
Somel M, H Franz, Z Yan, A Lorenc, S Guo, T Giger, J Kelso, B Nickel, M Dannemann, S Bahn, M J Webster, C S Weickert, M Lachmann, S Pääbo, P Khaitovich
Proceedings of the National Academy of Sciences 106 (14), 5743-5748. [pdf] [journal]

PatMaN: rapid alignment of short sequences to large databases. (2008)
Prüfer K, U Stenzel, M Dannemann, RE Green, M Lachmann, J Kelso
Bioinformatics 24 (13), 1530-1531. [pdf] [journal]

Phenotypic diversity as an adaptation to environmental uncertainty. (2008)
Donaldson-Matasci M.C., M Lachmann, CT Bergstrom
Evolutionary Ecology Research 10 (4), 493-515. [pdf]

Human and chimpanzee gene expression differences replicated in mice fed different diets. (2008)
Somel M, H Creely, H Franz, U Mueller, M Lachmann, P Khaitovich, S Pääbo.
PLoS One 3 (1), e1504. [pdf] [journal]

Building trust by wasting time. (2008)
Bergstrom C.T., B Kerr, M Lachmann
Moral markets: The critical role of values in the economy, 142-156. [pdf]

Patterns of damage in genomic DNA sequences from a Neandertal. (2007)
Briggs A.W., U Stenzel, PLF Johnson, RE Green, J Kelso, K Prüfer, Matthias Meyer, J Krause, M T Ronan, M Lachmann, S Pääbo
Proceedings of the National Academy of Sciences 104 (37), 14616-14621. [pdf] [journal]

The evolution of functionally referential meaning in a structured world. (2007)
Donaldson M.C., M Lachmann, CT Bergstrom
Journal of theoretical biology 246 (2), 225-233. [pdf] [journal]

FUNC: a package for detecting significant associations between gene sets and ontological annotations. (2007)
Prüfer K, B Muetzel, HH Do, G Weiss, P Khaitovich, E Rahm, S Pääbo, M Lachmann, W Enard
BMC bioinformatics 8 (1), 41. [pdf] [journal]

Functionality of intergenic transcription: an evolutionary comparison. (2006)
Khaitovich P, J Kelso, H Franz, J Visagie, T Giger, S Joerchel, E Petzold, R.E. Green, M. Lachmann, S. Pääbo.
PLoS genetics 2 (10), e171. [pdf] [journal]

Evolution of primate gene expression. (2006)
Khaitovich. P., W Enard, M Lachmann, S Pääbo
Nature Reviews Genetics 7 (9), 693-702. [pdf] [journal]

Positive selection on gene expression in the human brain. (2006)
Khaitovich P., K Tang, H Franz, J Kelso, I Hellmann, W Enard, M. Lachmann, S. Pääbo
Current Biology 16 (10), R356-R358. [pdf] [journal]

Gene expression becomes heterogeneous with age. (2005)
Somel M., P. Khaitovich, S. Bahn, S. Pääbo, M. Lachmann
Current Biology 16 (10), R359-R360. [pdf] [journal]

Quasispecies made simple. (2005)
Bull J.J.L.A. Meyers, M. Lachmann
PLoS computational biology 1 (6), e61. [pdf] [journal]

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. (2005) Khaitovich, P., I. Hellmann, W. Enard, K. Nowick, M. LeinweberH. FranzG. Weiss, M. Lachmann, S. Pääbo. Science 309 (5742), 1850-1854. [pdf] [journal]

Evolution of genetic potential
Meyers, L.A., F.D. Ancel, M. Lachmann. (2005)
PLoS computational biology 1 (3), e32 [pdf][journal]

Shannon information and biological fitness
Bergstrom, C.T. , M. Lachmann (2004)
Information Theory Workshop, IEEE, 50-54. [pdf]

Regional patterns of gene expression in human and chimpanzee brains.
Khaitovich P, B. Muetzel, X. W. She, M. Lachmann, I. Hellmann, J. Dietzsch, S. Steigele, H. H. Do, G. Weiss W. Enard, F. Heissig, T. Arendt, K. Nieselt-Struwe, E. E. Eichler, and S. Pääbo S (2004) . Genome Res. 14(8):1462-1473. [pdf] [journal]

A neutral model of transcriptome evolution.
Khaitovich, P., G. Weiss, M. Lachmann, I. Hellmann, W. Enard, B. Muetzel, U. Wirkner, W. Ansorge, and S. Pääbo (2004) PLoS Biology 2:682-689. [pdf] [journal]

The disadvantage of combinatorial communication.
Lachmann M. and C. T. Bergstrom (2004). Proceedings of the Royal Society: Biological Sciences 271:2337-2343. [pdf][journal]

The Physical Limits of Communication or Why any sufficiently advanced technology is indistinguishable from noise
Lachmann M., M. E. J. Newman, and C. Moore (2004). Am. J. Phys. 72(10):1290-1293. SFI working paper 99-07-054. [pdf]

Cooperation and conflict in the evolution of genomes, cells and multicellular organisms.
Lachmann, M., N. W. Blackstone, D. Haig, A. Kowald, R. E. Michod, E. Szathmáry, J. H. Werren, and L. Wolpert (2003). Chapter 18 in P. Hammerstein, ed., Genetic and Cultural Evolution of Cooperation.Cambridge: MIT Press. [pdf]

The Red King Effect: When the slowest runner wins the coevolutionary race.
Bergstrom, C. T. and M. Lachmann (2003). Proceedings of the National Academy of Sciences, USA 100(2): 593-598. SFI working paper 02-09-048. [pdf] [ps]

Separating equilibria in continuous signalling games.
Bergstrom C. T., S. Számadó, and M. Lachmann (2002). Philosophical Transactions: Biological Sciences 357(1427):1595-1606. [pdf] SFI working paper 02-09-044 [pdf] [ps]

On the evolution of polygamy: a theoretical examination of the polygamy threshold model.
Ptak S. and M. Lachmann (2001). SFI working paper 01-01-001. [pdf] [ps] Behavioral Ecology, in press.

Cost and conflict in animal signals and human language
Lachmann M., C. T. Bergstrom, and S. Számadó (2001). Proceedings of the National Academy of Sciences USA. 98:13189-13194. [pdf] (other versions of this material appeared as Santa Fe Institute Working Papers, 01-05-27, "The peacock, the sparrow, and the evolution of human language," and 00-12-74, "The death of costly signalling?".)

Alarm Calls as Costly Signals of Anti-Predator Vigilance: The Watchful Babbler Game.
Bergstrom, C. T. and M. Lachmann (2001). SFI working paper 00-02-009. Animal Behavior 61(3):535-543. [pdf]

The Role of signalling and sibling competition in begging strategies.
Rodriguez-Girones, M. A., M. Enquist and M. Lachmann (2001). SFI working paper 01-01-002. Animal Behaviour 61(4):733-745. [pdf]

On the Dynamic Persistence of Cooperation: How Lower Fitness Induces Higher Survivability.
Sella, G. and M. Lachmann (2000). SFI working paper 99-03-017. Journal of Theoretical Biology 206:465-485. Also appeared in Evolutionary Dynamics: Exploring the Interplay of Selection, Accident, Neutrality, and Function. James P. Crutchfield and Peter Schuster (eds.) Oxford U. Press, 2002. [pdf]

On Information Sharing and the Evolution of Collectives.
Lachmann, M., G. Sella, and E. Jablonka (2000). SFI working paper 99-03-018. Proc. of the Royal Society: Biological Sciences, 267:1265-1374. [pdf]

Who wins Domineering on Rectangular Boards?
Lachmann M. and C. Moore (2000). presented by C. Moore in Combinatorial Game Theory, July 2000, MSRI Berkeley. SFI working paper 00-04-026. [pdf] [ps] (not peer reviewed)

Adopting adoption.
Avital, E., E. Jablonka and M. Lachmann (1998). Animal Behaviour 55(6):1451-1459. [pdf]

Signalling among relatives. III. Talk is cheap among relatives.
Bergstrom, C. T. and M. Lachmann (1998). Proceedings of the National Academy of Sciences, USA 95:5100-5105. [pdf]

Signalling among relatives. II. Beyond the Tower of Babel.
Lachmann, M. and C. T. Bergstrom (1998). Theoretial Population Biology, 54:146-160. [pdf]

Signalling among relatives. I. When is signalling too costly?
Bergstrom, C. T. and M. Lachmann (1997). Philosophical Transactions of the Royal Society Series B 352(1353):609-617. [pdf]

Heredity systems in a periodically fluctuating environment
Lachmann-Tarkhanov, M. and E. Jablonka (1996). Journal of Theoretical Biology. 181:1-9. [ps] [pdf] [html]

The computationally complete Ant Colony: Global Coordination in a System with no Hierarchy.
Lachmann, M. and G. Sella (1995). Presented in ECAL95. Published in F. Moran, A. Moreno, J.J. Merelo, and P Chacon (Ed.) Advances in Artificial Life, proceedings of the third European Conference on Artificial Life, Granada, Spain. Springer-Verlag 1995. [ps]

The Alternative Fitness Sets Which Preserve Allele Trajectories: A General Treatment
Lachmann-Tarkhanov, M. and S. Sarkar (1994). Genetics 138(4):1323-1330. [ps]

Evidence, mechanisms and models for the inheritance of acquired characters.
Jablonka, E., M. Lachmann, and M. J. Lamb (1992). Journal of Theoretical Biology. 158: 245-268. [pdf]

Origins of Evolution
Lachmann, M (1991). IJCAI-91 workshop on evolution and chaos in cognitive processing. [html] [pdf]