News
- 2023.11.07
- Manuscript submitted: "Detectability of Varied Hybridization Scenarios Using Genome-Scale Hybrid Detection Methods"
- 2023.07.14
- Manuscript submitted: "Infection induced inflammation impairs wound healing through IL-1β signaling"
- 2023.02.20
- Paper published in Blood Advances: "RNA-Regulatory Exosome Complex Suppresses an Apoptotic Program to Confer Erythroid Progenitor Cell Survival in Vivo"
- 2023.02.01
- Paper published in Computational Biology and Chemistry: "A Nile Rat Transcriptomic Landscape across 22 Organs by Ultra-Deep Sequencing and Comparative RNA-Seq Pipeline (CRSP)"
- 2022.09.16
- Paper published in iScience: "Distinctive Populations of CD4+T Cells Associated with Vaccine Efficacy"
- 2022.02.16
- Paper published in Front Immunol: "Cell Type-Specific Transcriptome Profiling Reveals a Role for Thioredoxin During Tumor Initiation"
- 2021.06.01
- Paper published in Nucleic Acids Research: "RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis"
- 2021.09.17
- Paper published in STAR Protocols: "Annotating cell types in human single-cell RNA-seq data with CellO"
- 2021.01.22
- Paper published in iScience: "CellO: Comprehensive and hierarchical cell type classification of human cells with the Cell Ontology"
- 2021.01.01
- Paper published in Molecular Cancer Therapeutics: "PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways"
- 2020.09.21
- Paper published in Genome Research: "PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments"
- 2020.07.10
- Manuscript submitted: "CellO: Comprehensive and hierarchical cell type classification of human cells with the Cell Ontology"
- 2020.06.12
- Paper published in Genome Biology and Evolution: "Giant Island Mice Exhibit Widespread Gene Expression Changes in Key Metabolic Organs"
- 2019.12.12
- Manuscript submitted: "Cell type specific gene expression profiling reveals a role for the complement component C3A in neutrophil migration to tissue damage"
- 2019.07.06
- Book chapter published in Evolutionary Genomics: "Whole-genome alignment"
- 2019.05.13
- Manuscript submitted: "PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments"
- 2019.04.23
- Paper published in PNAS: "Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase"
- 2018.07.01
- Promoted to Professor!
- 2017.08.07
- Paper published in Developmental Cell: "GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia"
- 2017.07.06
- Paper published in Developmental Biology: "Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis"
- 2017.05.23
- Paper published in Bioinformatics: "MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive"
- 2016.07.27
- Paper published in Developmental Biology: "Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability"
- 2016.07.12
- Paper published in Genome Research: "Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq"
- 2016.01.06
- Named a Vilas Associate
- 2015.12.16
- Group member Nathanael Fillmore successfully defends his PhD thesis: "Generative models for transcriptome assembly and analysis"
- 2015.12.23
- Paper published in EMBO Reports: "Mechanism Governing Heme Synthesis Reveals a GATA Factor-Heme Circuit that Controls Differentiation"
- 2015.10.20
- Paper published in PLoS Computational Biology: "Perm-seq: Mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping"
- 2015.09.04
- Paper published in Science Advances: "Cis-regulatory mechanisms governing stem and progenitor cell transitions"
- 2015.07.02
- Paper published in Molecular Cell: "Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome"
- 2015.04.20
- Grant awarded by NIH: "Integrated biochemical and bioinformatic technologies for accurate transcriptome-wide full-length RNA assembly." (Co-PI w/ M. Lodes, Lucigen)
- 2015.04.05
- Paper published in Bioinformatics: "EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments"
- 2014.12.21
- Paper published in Genome Biology: "Evaluation of de novo transcriptome assemblies from RNA-Seq data"
- 2014.09.29
- Grant awarded by NIH: "The Center for Predictive Computational Phenotyping." (Project lead w/ M. Craven, Director)
- 2013.12.02
- Paper published in Journal of Experimental Medicine: "Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo"
- 2013.09.23
- Paper published in RNA: "Bicaudal-C spatially controls translation of vertebrate maternal mRNAs"
- 2013.07.11
- Paper published in Bioinformatics: "Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs"
- 2013.07.11
- Paper published in Nature Protocols: "De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis"
- 2013.07.05
- Grant awarded by NIH: "Defining the Xenopus translatome." (Co-investigator w/ M. Sheets (PI))
- 2013.03.07
- Paper published in PLoS Computational Biology: "Comparative RNA-seq analysis in the unsequenced axolotl: The oncogene burst highlights early gene expression in the blastema"
- 2013.01.09
- Paper published in Nucleic Acids Research: "Rbm20 regulates titin alternative splicing as a splicing repressor"
- 2012.10.01
- Paper published in Genetics: "Genomic variation in natural populations of Drosophila melanogaster"
- 2012.09.17
- Grant awarded by NIH: "Statistical methods for annotating repetitive genomic regions through ENCODE-derived data." (Co-PI w/ S. Keles (PI) and E. Bresnick)
- 2012.09.10
- Grant awarded by NIH: "The genetics and evolution of extreme body size in mice from Gough Island." (Co-investigator w/ B. Payseur (PI) and K. Broman)
- 2012.07.01
- Promoted to Associate Professor with tenure!
- 2012.03.12
- Book chapter published in Evolutionary Genomics : "Whole-Genome Alignment"
- 2011.11.23
- Paper published in IEEE transactions on visualization and computer graphics : "Sequence Surveyor: leveraging overview for scalable genomic alignment visualization"
- 2011.09.23
- RSEM paper acquires designation of "Highly accessed"
- 2011.08.04
- Paper published in BMC Bioinformatics: "RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome"
- 2011.07.14
- Paper published in PLoS Computational Biology: "Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-seq data"
- 2011.06.24
- Paper published in Briefings in Bioinformatics: "Positional orthology: putting genomic evolutionary relationships into context".
- 2010.09.21
- Paper published in Bioinformatics: "BUCKy: Gene Tree / Species Tree Reconciliation with Bayesian Concordance Analysis".
- 2010.06.30
- Grant awarded by NIH: "Computational methods for the analysis of RNA-Seq data."
- 2010.04.27
- Grant awarded by WisCID: "Small RNAs of the human intestinal microbiome." (Co-PI w/ H. Goodrich-Blair, N. Safdar, and J. Sonnenburg)
- 2009.12.18
- Paper published in Bioinformatics: "RNA-Seq gene expression estimation with read mapping uncertainty".
- 2009.12.15
- Paper accepted in Bioinformatics: "RNA-Seq gene expression estimation with read mapping uncertainty".
- 2009.11.20
- Paper published in PLoS Genetics: "Fine scale phylogenetic discordance across the house mouse genome".
- 2009.05.29
- Paper published in PLoS Computational Biology: "Fast Statistical Alignment".
- 2009.03.28
- Paper accepted in PLoS Computational Biology: "Fast Statistical Alignment".
- 2008.12.03
- Teaching Science Masters Institute course on "Genetics, Natural Selection & Evolution" July 13-16, 2009.
- 2008.05.13
- Teaching BMI/CS 576 "Advanced Bioinformatics" during the Fall 2008 semester.
- 2008.05.13
- Teaching Science Masters Institute course on "Genetics, Natural Selection & Evolution" June 23-26, 2008.
- 2008.01.22
- Teaching BMI/CS 776 "Advanced Bioinformatics" during the Spring 2008 semester.
- 2007.11.12
- Teaching Science Masters Institute course on "Natural Selection & Evolution" Nov 12, 17, 26, & Dec 1
- 2007.11.08
- Paper published in Nature: "Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures"
- 2007.11.06
- Paper published in PLoS Biology: "Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans"
- 2007.06.14
- ENCODE pilot project results in the media: BBC, Boston Globe, Washington Post
- 2007.06.14
- Paper published in Genome Research: "Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome"
- 2007.06.14
- Paper published in Nature: "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project"
- 2007.06.07
- Joined UW Comprehensive Cancer Center as member.
- 2007.01.23
- Teaching BMI/CS 776 "Advanced Bioinformatics" during the Spring 2007 semester.
- 2006.12.08
- Paper published in BMC Genomics: "Compensatory relationships between splice sites and exonic splicing signals depending on the length of vertebrate introns"
- 2006.11.22
- Joined the Computation and Informatics in Biology and Medicine program as faculty trainer.
- 2006.09.22
- Joined the Genomic Sciences Training Program as faculty trainer.
- 2006.08.09
- Joined the Computer Sciences Department as affiliate faculty member.
- 2006.08.01
- Joined the Genome Center of Wisconsin as member.
- 2006.08.01
- Joined the Biostatistics and Medical Informatics Department as assistant professor.
