|
| 36692138 | NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration. | | 2023 |
| 37755132 | Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues. | | 2023 |
| 37333130 | Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues. | | 2023 |
| 37131703 | How host-like signals drive gene expression and gene expression drives capsule expansion in . | | 2023 |
| 35666184 | Predicting which genes will respond to transcription factor perturbations. | G3: Genes, Genomes, Genetics | 2022 |
| 33135076 | Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. | | 2021 |
| 33688010 | The Transcription Factor Pdr802 Regulates Titan Cell Formation and Pathogenicity of Cryptococcus neoformans. | mBio | 2021 |
| 32060051 | Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses. | Genome Research | 2020 |
| 29305388 | Unintended Side Effects of Transformation Are Very Rare in . | G3: Genes, Genomes, Genetics | 2018 |
| 28968736 | NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources. | Bioinformatics | 2018 |
| 29487137 | Seven-Up Is a Novel Regulator of Insulin Signaling. | Genetics | 2018 |
| 27716485 | SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. | Mol Cell | 2016 |
| 27094327 | Computational Analysis Reveals a Key Regulator of Cryptococcal Virulence and Determinant of Host Response. | mBio | 2016 |
| 27810962 | Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast. | Proc Natl Acad Sci U S A | 2016 |
| 27720190 | Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. | Trends in Genetics | 2016 |
| 26257285 | SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers. | Mol Cell | 2015 |
| 25644834 | Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation. | Genome Res | 2015 |
| 24747214 | Cryptococcus neoformans dual GDP-mannose transporters and their role in biology and virulence. | Eukaryot Cell | 2014 |
| 23355467 | Role of fat body lipogenesis in protection against the effects of caloric overload in Drosophila. | J Biol Chem | 2013 |
| 23636944 | Mapping functional transcription factor networks from gene expression data. | Genome Res | 2013 |
| 22252463 | Reduced DICER1 elicits an interferon response in endometrial cancer cells. | Molecular Cancer Research | 2012 |
| 22955987 | GENCODE: the reference human genome annotation for The ENCODE Project. | Genome Res | 2012 |
| 22174677 | Toward an integrated model of capsule regulation in Cryptococcus neoformans. | PLoS Pathogens | 2011 |
| 21179090 | The developmental transcriptome of Drosophila melanogaster. | Nature | 2011 |
| 21177962 | The transcriptional diversity of 25 Drosophila cell lines. | Genome Res | 2011 |
| 20810924 | A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription. | Proc Natl Acad Sci U S A | 2010 |
| 21177974 | Identification of functional elements and regulatory circuits by Drosophila modENCODE. | Science | 2010 |
| 19188190 | Benchmarking regulatory network reconstruction with GRENDEL. | | 2009 |
| 19767417 | The completion of the Mammalian Gene Collection (MGC). | Genome Res | 2009 |
| 19414532 | Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. | Bioinformatics | 2009 |
| 18087260 | Steady progress and recent breakthroughs in the accuracy of automated genome annotation. | Nature Reviews Genetics | 2008 |
| 18334530 | wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data. | Nucleic Acids Res | 2008 |
| 18428682 | Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences. | Current Protocols in Bioinformatics | 2007 |
| 17994087 | Evolution of genes and genomes on the Drosophila phylogeny. | Nature | 2007 |
| 17989246 | Targeted discovery of novel human exons by comparative genomics. | Genome Res | 2007 |
| 17210930 | A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. | Genome Research | 2007 |
| 17589517 | Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. | Nat Methods | 2007 |
| 17687368 | How does eukaryotic gene prediction work? | Nature Biotechnology | 2007 |
| 17571346 | Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. | Nature | 2007 |
| 17237054 | The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs. | Bioinformatics | 2007 |
| 16925837 | Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. | Genome Biol | 2006 |
| 16817966 | Using ESTs to improve the accuracy of de novo gene prediction. | BMC Bioinformatics | 2006 |
| 16464855 | Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches. | J Biol Chem | 2006 |
| 16651666 | Iterative gene prediction and pseudogene removal improves genome annotation. | Genome Research | 2006 |
| 16597247 | Using multiple alignments to improve gene prediction. | Journal of Computational Biology | 2006 |
| 16925842 | Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts. | Genome Biol | 2006 |
| 16925839 | Pairagon+N-SCAN_EST: a model-based gene annotation pipeline. | Genome Biol | 2006 |
| 16339376 | Genome annotation past, present, and future: how to define an ORF at each locus. | Genome Research | 2005 |
| 15924626 | Gene finding in the chicken genome. | BMC Bioinformatics | 2005 |
| 15867435 | Begin at the beginning: predicting genes with 5' UTRs. | Genome Research | 2005 |