Gill Bejerano
Publications
- Enhancers: five essential questions. Nat Rev Genet. 2013; (4): 288-95
- Evolutionary biology for the 21st century. PLoS Biol. 2013; (1): e1001466
- PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res. 2013; (5): 889-904
- A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep. 2012; (4): 817-23
- A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Hum Mutat. 2012; (7): 1063-6
- Coding exons function as tissue-specific enhancers of nearby genes. Genome Res. 2012; (6): 1059-68
- Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet. 2012; (8): e1002852
- Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res. 2012; (22): 11463-76
- PESNPdb: a comprehensive database of SNPs studied in association with pre-eclampsia. Placenta. 2012; (12): 1055-7
- Control of pelvic girdle development by genes of the Pbx family and Emx2. Dev Dyn. 2011; (5): 1173-89
- Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 2011; (7337): 216-9
- Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging. PLoS One. 2011; (1): e16348
- Endangered species hold clues to human evolution. J Hered. 2010 Jul-Aug; (4): 437-47
- GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010; (5): 495-501
- Dispensability of mammalian DNA. Genome Res. 2008; (11): 1743-51
- Comparative genomic analysis using the UCSC genome browser. Methods Mol Biol. 2007: 17-34
- Human genome ultraconserved elements are ultraselected. Science. 2007; (5840): 915
- Thousands of human mobile element fragments undergo strong purifying selection near developmental genes Proc. Natl Acad. Sci. USA. 2007; (19): 8005-8010
- A Distal Enhancer and an Ultraconserved Exon are Derived From a Novel Retroposon Nature. 2006; (7089): 87-90
- Branch and bound computation of exact p-values. Bioinformatics. 2006; (17): 2158-9
- Forces Shaping the Fastest Evolving Regions in the Human Genome PLoS Genetics. 2006; (10): e168
- Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006; (4): e33
- The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006; (Database issue): D590-8
- Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods. 2005; (7): 535-45
- Evolutionarily Conserved Elements in Vertebrate, Fly, Worm, and Yeast Genomes Genome Research. 2005; (8): 1034-1050
- Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 2005; (6): 800-8
- Algorithms for variable length Markov chain modeling. Bioinformatics. 2004; (5): 788-9
- Efficient exact p-value computation for small sample, sparse and surprising categorical data J. Computational Biology. 2004; (5675): 867-886
- Extremely conserved non-coding sequences in the vertebrate genomes Proceedings of 4th International Conference on Bioinformatics of Genome Regulation and Structure. 2004
- Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics. 2004: i40-8
- Sequencing and comparative analysis of the chicken genome Nature. 2004; (7018): 695-716
- Ultraconserved elements in the human genome. Science. 2004; (5675): 1321-5
- A system for computer music generation by learning and improvisation in a particular style IEEE Computer J.. 2003; (10): 73-80
- Discriminative feature selection via multiclass variable memory Markov models EURASIP J. Applied Signal Processing. 2003: 93-102
- Efficient exact p-value computation and applications to biosequence analysis Proceedings of the 7th annual international conference on research in computational molecular biology. 2003
- Discriminative feature selection via multiclass variable memory Markov models Proceedings of 19th International Conference on Machine Learning. 2002
- A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites, 1st Workshop on Algorithms in Bioinformatics Lecture Notes in Computer Science. 2001; (2149): 278-293
- A variable memory Markovian modeling approach to unsupervised sequence segmentation Proceedings of 33rd Symposium on the Interface of Computing Science and Statistics. 2001
- Automated modeling of musical style Proceedings of the International Computer Music Conference. 2001
- Markovian domain fingerprinting: statistical segmentation of protein sequences. Bioinformatics. 2001; (10): 927-34
- Novel small RNA-encoding genes in Escherichia coli Current Biology. 2001; (12): 941-950
- Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol. 2001; (12): 941-50
- PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res. 2001; (1): 277
- Unsupervised sequence segmentation by a mixture of switching variable memory Markov sources Proceedings of 18th International Conference on Machine Learning. 2001
- Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bioinformatics. 2001; (1): 23-43
- Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space J. Computational Biology. 2000; (3-4): 381-393
- Optimal amnesic probabilistic automata, or, how to learn and classify proteins in linear time and space Proceedings of the 4th annual international conference on research in computational molecular biology. 2000
- Modeling protein families using probabilistic suffix trees, Proceedings of the 3rd annual international conference on research in computational molecular biology RECOMB. 1999
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