BeeSpace at UIUC logo

Quick links

 BeeSpace Navigator version 4 (Software)

 BeeSpace Software Training Workshop (April 2010)

 Arthropod Genomics Symposium (June 2009)

 Final BeeSpace Project Workshop (May 2009)

 Electronic BeeSpace (Education)

Papers

2011

S. Chandrasekaran, S. Ament, J. Eddy, S. Rodriguez-Zas, B. Schatz, N. Price, G. Robinson, 2011. Behavior-specific Changes in Transcriptional Modules lead to Distinct and Predictable Neurogenomic States. Proceedings National Academy Sciences PNAS, September 29, cite as doi:10.1073/pnas.1114093108, access at http://www.pnas.org/cgi/doi/10.1073/pnas.1114093108

M. Sen Sarma, D. Arcoleo, R. Khetani, B. Chee, X. Ling, X.He, J. Jiang, Q. Mei, C. Zhai, B. Schatz, 2011. BeeSpace Navigator: Exploratory Analysis of Gene Function using Semantic Indexing of Biological Literature, Nucleic Acids Research, Web Server Issue, vol 39, 9 May 2011. cite as doi: 10.1093/nar/gkr285. access at http://nar.oxfordjournals.org/cgi/reprint/gkr285?ijkey=jsrmZZPv8lqK7ZL&keytype=ref

D. Stone, J. Buell, N. Naeger, 2011. Electronic BeeSpace: A Video Curriculum for Behavioral Genomics, The Science Teacher, National Science Teachers of America journal, pp 58-60, February.

2010

X. He, Y. Li, R. Khetani, B. Sanders, Y. Lu, X. Ling, C. Zhai, B. Schatz, 2010. BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects, Nucleic Acids Research, Web Server Issue, p W175, vol 38.

X. He, M. Sen Sarma, X. Ling, B. Chee, C. Zhai, B. Schatz, 2010. Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model, BMC Bioinformatics, p. 272, vol. 11. doi 10.1186/1471-2105-11-272

M. Sen Sarma, S. Rodriguez-Zas, T. Gernat, T. Nguyen, T. Newman, G. Robinson, 2010. Distance responsive genes found in dancing bees, Genes, Brain and Behavior, p. 825, vol. 9. doi: 10.1111/j.1601-183X.2010.00622.

D. Stone, J. Buell, B. Schatz, 2010. Electronic BeeSpace: A Video Curriculum for Teaching Genomic Research about Arthropods to High School Students, Invertebrates in Education and Conservation Conference, Tucson Arizona, August.

N. Naeger, B. Nest, J. Johnson, S. Boyd, S. Rodriguez-Zas, D. Moore, G. Robinson, 2010. Neurogenomic signatures of spatiotemporal memories in time-trained forager honey bees, in preparation.

S. Ament, R. Velarde, M. Kolodkin, D. Moyse, G. Robinson, 2010. Neuropeptide Y-like signaling and nutritionally-mediated gene expression and behavior in the honey bee,in preparation.

S. Ament, Y. Wang, F. Hong, C. Chen, C. Mizzen, S. Sinha, S. Zhong, G. Robinson, 2010. A hormonally regulated transcriptional switch underlies phenotypic plasticity in the honey bee,in preparation.

S. Liang, H. Vu, S. Rodriguez-Zas, G. Robinson, 2010. Monoamine and glutamine systems influence scouting behavior in honey bees,in preparation.

2009

B. Chee, R. Berlin, B. Schatz, 2009. Measuring Population Health using Personal Health Messages, Annual Meeting of American Medical Informatics Association, San Francisco, November, full paper.

B. Chee, R. Berlin, B. Schatz, 2009. Information Visualization of Drug Regimens from Health Messages, Joint Conference on Biomedical Engineering, Porto Portugal, January, full paper.

J. Buell, D. Stone, N. Naeger, S. Fahrbach, C. Bruce, B. Schatz, 2009. Experiencing BeeSpace: Educational Explorations in Behavioral Genomics for High School and Beyond, Annual Meeting of American Association for Advancement of Science, Chicago, February, poster.

C. Alaux, S. Sinha, L. Hasadsri, G. Hunt, E. Guzman-Novoa, G. Degrandi-Hoffman, J. Uribe-Rubio, S. Rodriguez-Zas, G. Robinson, 2009. Honeybee Aggression Supports a Link Between Gene Regulation and Behavioral Evolution, Proceedings National Academy Sciences PNAS, August.

C. Alaux, Y. LeConte, H. Adams, S. Rodriguez-Zas, S. Sinha, G. Robinson, 2010. Regulation of brain gene expression in honey bees by brood pheromone, Gene, Brain, and Behavior, p. 309, vol. 8,

C. Alaux, N. Duong, S. Schneider, B. Southey, S. Rodriguez-Zas, G. Robinson. Modulatory communication signal performance is associated with a distinct neurogenomic state in honey bees, PLoS One, July.

M. Sen Sarma, S. Rodriguez-Zas, F. Hong, S. Zhong, G. Robinson, 2009. Transcriptomic Profiling of Central Nervous System Regions in Three Species of Honey Bee During Dance Communication Behavior, PLoS One, May.

R. Velarde and S. Fahrbach, 2009. Neuropeptide precursor genes in the honey bee: Expression profiles and mRNA localization in the adult worker honey bee, Annual Meeting of Society for Neuroscience, Chicago, October, full paper.

Y. Lv, C. Zhai, 2009. Adaptive Relevance Feedback in Information Retrieval, Proceedings 18th ACM International Conference on Information and Knowledge Management ( CIKM'09), full paper, Hong Kong, November.

Y. Ko, C. Zhai, S. Rodriguez-Zas, 2009. Inference of Gene Pathways using Mixture Bayesian Networks, BMC Systems Biology, 3:54, 2009, doi:10.1186/1752-0509-3-54.

Y. Lu, C. Zhai, N. Sundaresan, 2009. Rated Aspect Summarization of Short Comments, Proceedings of the World Wide Conference 2009 ( WWW'09), pages 131-140, Madrid, May.

Y. Lu, H. Fang, C. Zhai, 2009. An Empirical Study of Gene Synonym Query Expansion in Biomedical Information Retrieval, Journal of Information Retrieval, Volume 12, Number 1, Feb. 2009, Pages 51-68.

2008

X. Ling, Q. Mei, C. Zhai, B. Schatz, 2008. Mining multi-faceted overviews of arbitrary topics in a text collection, Proceedings of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'08), pages 497-505, 2008.

Q. Mei, D. Zhang, C. Zhai, 2008. Smoothing Language Models with Document and Word Graphs, Proceedings 31st Annual International ACM SIGIR Conference on Research and Development in Information Retrieval ( SIGIR'08 ), pages 611-618.

A. Shakery, C. Zhai, 2008. Smoothing Document Language Models with Probabilistic Term Count Propagation, Information Retrieval, 11(2), 2008, pages 139-164.

2007

B. Chee, B. Schatz. 2007. Document clustering using small world communities. In Proceedings of the 7th ACM/IEEE-CS Joint Conference on Digital Libraries JCDL '07. [Link] [slideset as PDF]

J. Jiang, C.X. Zhai. 2007. A two-stage approach to domain adaptation for statistical classifiers. In Proceedings of the ACM 16th Conference on Information and Knowledge Management (CIKM'07).

J. Jiang, C.X. Zhai. 2007. Instance weighting for domain adaptation in NLP. In Proceedings of the 45th Annual Meeting of the Association for Computational Linguistics (ACL'07), pages 264-271, 2007. [PDF] [BIB] [slides (PPT)] [slides (PDF)]

X. Ling, J. Jiang, X. He, Q. Mei, C.X. Zhai, B. Schatz. 2007. Generating gene summaries from biomedical literature: A study of semi-structured summarization. Information Processing and Management, 43: 1777-1791. Link

Y. Lu, J. Jiang, X. He, C.X. Zhai. 2007. Language models for Genomics Information Retrieval: UIUC at TREC 2007 Genomics Track. [PDF]

Q. Mei, X. Shen, C.X. Zhai. 2007. Automatic Labeling of Multinomial Topic Models, Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD' 07), pages 490-499. http://sifaka.cs.uiuc.edu/czhai/pub/kdd07-label.pdf . Runner-up Best Student Paper Award (link).

2006

The Honeybee Genome Sequencing Consortium. 2006. Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443, 931-949. Abstract | Full Text | PDF (4,656K)

A. B. Hummon, et al. 2006. From the genome to the proteome: Uncovering peptides in the Apis brain. Science 27 October 2006: Vol. 314. no. 5799, pp. 647 - 649. Link 

X. Ling, J. Jiang,  X. He, Q. Mei, C. X. Zhai, B. Schatz. 2006. Automatically generating gene summaries from biomedical literature. Proceedings of the Pacific Symposium on Biocomputing (PSB 2006), pages 40-51. [PDF]

J. Jiang, C.X. Zhai. 2006. Exploiting Domain Structure for Named Entity Recognition. 2006. Proceedings of HLT/NAACL 2006. [PDF] [PPT]

Q. Mei, C. Liu, H. Su, C.X. Zhai. 2006. A Probabilistic Approach to Spatiotemporal Theme Pattern Mining on Weblogs. Proceedings of the World Wide Web Conference 2006 ( WWW'06). [PDF]

Q. Mei, D. Xin, H. Cheng, J.W. Han, C.X. Zhai. 2006. Generating Semantic Annotations for Frequent Patterns with Context Analysis, Proceedings of the 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD' 06), pages 337-346. http://sifaka.cs.uiuc.edu/czhai/pub/kdd06-sem.pdf . Runner-up Best Student Paper Award (link).

G. E. Robinson, J. D. Evans, R. Maleszka, H. M. Robertson, D. B. Weaver, K. Worley, R. A. Gibbs, G. M. Weinstock. 2006. Sweetness and light: Illuminating the honey bee genome. Insect Molecular Biology 2006, 15:5, p. 535. Summary | Full Text | PDF 

S. Sinha, X. Ling, C. W. Whitfield, C. X. Zhai, G. E. Robinson. 2006. Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees. PNAS, 103(44): 16352 - 16357. Abstract | PDF

T. Tao, X. Wang, Q. Mei, C.X. Zhai. 2006. Language Model Information Retrieval with Document Expansion. Proceedings of HLT/NAACL 2006. [PDF]

R. Velarde, G. E. Robinson, S. E. Fahrbach. Nuclear receptors of the honey bee: annotation and expression in the adult brain. Insect Molecular Biology 2006, 15:5, p. 583. Summary | Full Text | PDF

C. W. Whitfield, Y. Ben-Shahar, C. Brillet, I. Leoncini, D. Crauser, Y. LeConte, S. Rodriguez-Zas, G. E. Robinson. 2006. Thrice out of Africa: ancient and recent expansions of the honey bee, Apis mellifera. Science 27 October 2006: Vol. 314. no. 5799, pp. 642 - 645. Link

C.X. Zhai and J. Lafferty. 2006. A risk minimization framework for information retrieval, Information Processing and Management ( IP &M ), 42(1), Jan. 2006. pages 31-55. [URL]

2005 

M. J. Fitzpatrick, Y. Ben-Shahar, H. M. Smid, L. E. M. Vet, G. E. Robinson, M. B. Sokolowski. 2005. Candidate genes for behavioural ecology. TRENDS in Ecology and Evolution, 20(2): 96-104. [PDF]

G. E. Robinson, C. M. Grozinger, C. W. Whitfield. 2005. Sociogenomics: social life in molecular terms. Nature Reviews: Genetics, 6(April): 257-271. [PDF]

C.X. Zhai, X. Lu, X. Ling, X. He, A. Velivelli, X. Wang, H. Fang, and A. Shakery. 2005. UIUC/MUSC at TREC 2005 Genomics Track. [PDF]


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