A5077269033- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Developmental Biology and Gene Regulation
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Pluripotent Stem Cells Research
- Chromosomal and Genetic Variations
- Machine Learning in Bioinformatics
- Invertebrate Immune Response Mechanisms
- Malaria Research and Control
- Advanced biosensing and bioanalysis techniques
- Plant Molecular Biology Research
- Insect Resistance and Genetics
- Fungal and yeast genetics research
- Scientific Computing and Data Management
- Congenital heart defects research
- Genetic Mapping and Diversity in Plants and Animals
- Cancer Genomics and Diagnostics
- Adipose Tissue and Metabolism
- Genomic variations and chromosomal abnormalities
Pennsylvania State University
2016-2025
Stanford University
2023
Cornell University
2021
Cancer Institute (WIA)
2005-2018
University of Limerick
2016
Massachusetts Institute of Technology
2010-2014
Brigham and Women's Hospital
2010-2012
Harvard University
2010-2012
Vassar College
2012
University of Pittsburgh
2005-2011
STAMP is a newly developed web server that designed to support the study of DNA-binding motifs. may be used query motifs against databases known motifs; software aligns input chosen database (or alternatively user-provided dataset), and lists highest-scoring matches are returned. Such similarity-search functionality expected facilitate identification transcription factors potentially interact with discovered also automatically builds multiple alignments, familial binding profiles similarity...
An essential component of genome function is the syntax genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program control. A precise characterization in vivo spacing constraints between key would reveal aspects this language. To discover novel factor spatial binding vivo, we developed new integrative computational method, wide event finding and motif discovery (GEM). GEM resolves ChIP data into explanatory motifs events at high resolution...
ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites variants. The current release comprises 30 145 records curated from 922 publications describing sequences over 3853 genes 465 factors 19 species. A new feature called the 'publication queue' allows users to input relevant papers scientific as targets annotation. queue contains 4438 gene...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence construct map of a major histocompatibility complex (MHC). MHC is most gene-dense region and critical immunity reproductive success. bridges phylogenetic gap between eutherian mammals minimal essential birds. Here we show that opossum gene dense complex, as in humans, but shares more organizational features with...
Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating receptor (RAR)-mediated transcription. RAR is thought to bind genome constitutively, and only induce transcription presence retinoid ligand. However, little known about where binds or how it selects target sites.We tested constitutive binding model using acid-driven differentiation mouse embryonic stem cells into differentiated neurons. We find that...
Recent experiments have provided Hi-C data at resolution as high 1 kbp. However, 3D structural inference from high-resolution datasets is often computationally unfeasible using existing methods.We developed miniMDS, an approximation of multidimensional scaling (MDS) that partitions a dataset, performs MDS separately on each partition, and then reassembles the low-resolution MDS. miniMDS faster, more accurate, uses less memory than methods for inferring human genome (10 kbp).A Python...
Transcription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression neighbouring genes. The evolution TF binding preference has been subject recent studies, in which generalized profiles have introduced used to improve prediction new target sites. Generalized are generated by aligning merging individual related TFs. However, distance metrics alignment algorithms compare not yet fully explored or optimized. As result, depend on...
Regulatory proteins can bind to different sets of genomic targets in various cell types or conditions. To reliably characterize such condition-specific regulatory binding we introduce MultiGPS, an integrated machine learning approach for the analysis multiple related ChIP-seq experiments. MultiGPS is based on a generalized Expectation Maximization framework that shares information across experiments event discovery. We demonstrate our enables simultaneous modeling sparse changes, sequence...
Gene expression is controlled by a variety of proteins that interact with the genome. Their precise organization and mechanism action at every promoter remains to be worked out. To better understand physical interplay among genome-interacting proteins, we examined temporal binding functionally diverse subset these proteins: nucleosomes (H3), H2AZ (Htz1), SWR (Swr1), RSC (Rsc1, Rsc3, Rsc58, Rsc6, Rsc9, Sth1), SAGA (Spt3, Spt7, Ubp8, Sgf11), Hsf1, TFIID (Spt15/TBP Taf1), TFIIB (Sua7), TFIIH...
Abstract Differentiation from asexual blood stages to mature sexual gametocytes is required for the transmission of malaria parasites. Here, we report that ApiAP2 transcription factor, PfAP2‐G2 (PF3D7_1408200) plays a critical role in maturation Plasmodium falciparum gametocytes. binds promoters wide array genes are expressed at many parasite life cycle. Interestingly, also find binding within gene body almost 3,000 genes, which strongly correlates with location H3K36me3 and several other...
Thousands of epigenomic data sets have been generated in the past decade, but it is difficult for researchers to effectively use all relevant their projects. Systematic integrative analysis can help meet this need, and VISION project was established
Precise Hox gene expression is crucial for embryonic patterning. Intra- transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling expression. However, quantifying their relative contributions has remained elusive. Here, we introduce “synthetic reconstitution,” a conceptual framework studying regulation, apply it to HoxA cluster. We synthesized delivered variant rat clusters (130 170 kilobases) an ectopic location in mouse genome. found...
Abstract Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number sequence-specific transcription factors (TFs). However, mechanisms which these TFs recognize genome-wide binding sites largely unknown. To address TF specificity, we investigated two subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized additional ApiAP2 TFs, PfAP2-G PfAP2-EXP, unique (GTAC TGCATGCA). We also interrogated impact chromatin context on P....