Fan Li

Fan Li
University of Pennsylvania | UP · Department of Biology

PhD

About

46
Publications
3,809
Reads
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980
Citations
Citations since 2016
0 Research Items
692 Citations
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
Additional affiliations
January 2014 - present
University of Pennsylvania
Position
  • PostDoc Position
Description
  • Bringing awk to the Gregory Lab bench.
August 2009 - December 2013
University of Pennsylvania
Position
  • PhD Student
Description
  • Genome-wide analysis of RNA secondary structure in eukaryotes. PIs: Brian D. Gregory and Li-San Wang
October 2007 - May 2008
University of California, Berkeley
Position
  • Undergraduate Reseacher
Description
  • Detection of conserved segments via hierarchical clustering.
Education
August 2009 - December 2013
University of Pennsylvania
Field of study
  • Genomics and Computational Biology
September 2004 - May 2008
University of California, Berkeley
Field of study
  • Electrical Engineering and Computer Sciences

Publications

Publications (46)
Article
Full-text available
Members of the Msi family of RNA-binding proteins have recently emerged as potent oncoproteins in a range of malignancies. MSI2 is highly expressed in hematopoietic cancers, where it is required for disease maintenance. In contrast to the hematopoietic system, colorectal cancers can express both Msi family members, MSI1 and MSI2. Here, we demonstra...
Article
Full-text available
The MSI2 RNA-binding protein is a potent oncogene playing key roles in haematopoietic stem cell homeostasis and malignant haematopoiesis. Here we demonstrate that MSI2 is expressed in the intestinal stem cell compartment, that its expression is elevated in colorectal adenocarcinomas, and that MSI2 loss-of-function abrogates colorectal cancer cell g...
Article
Full-text available
Empirical measurement of RNA secondary structure is an invaluable tool that has provided a more complete understanding of the RNA life cycle and functionality of this extremely important molecule. In general, methods for probing structural information involve treating RNA with either a chemical or an enzyme that preferentially targets regions of th...
Article
Full-text available
The RNase III enzyme DICER generates both microRNAs (miRNAs) and endogenous short interfering RNAs (endo-siRNAs). Both small RNA species silence gene expression post-transcriptionally in association with the ARGONAUTE (AGO) family of proteins. In mammals, there are four AGO proteins (AGO1-4), of which only AGO2 possesses endonucleolytic activity. s...
Article
Full-text available
To achieve the extreme nuclear condensation necessary for sperm function, most histones are replaced with protamines during spermiogenesis in mammals. Mature sperm retain only a small fraction of nucleosomes, which are, in part, enriched on gene regulatory sequences, and recent findings suggest that these retained histones provide epigenetic inform...
Article
Full-text available
Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP-RNA interactions. Here, we describe PIP-seq, a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites t...
Article
Full-text available
Persistent infection of the mouse central nervous system (CNS) with mouse hepatitis virus (MHV) induces a demyelinating disease pathologically similar to multiple sclerosis and is therefore used as a model system. There is little information regarding the host factors that correlate with and contribute to MHV-induced demyelination. Here, we detail...
Article
The eukaryotic transcriptome is regulated both transcriptionally and post-transcriptionally. Transcriptional control was the major focus of early research efforts, while more recently post-transcriptional mechanisms have gained recognition for their significant regulatory importance. At the heart of post-transcriptional regulatory pathways are cis-...
Article
Full-text available
RNAs fold into intricate structures that are determined by specific base pairing interactions encoded within their primary sequences. Recently, a number of transcriptome-wide studies have suggested that RNA secondary structure is a potent cis-acting regulator of numerous post-transcriptional processes in viruses and eukaryotes. However, the need fo...
Article
Full-text available
The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-deplete...
Article
Full-text available
RNA secondary structure is required for the proper regulation of the cellular transcriptome. This is because the functionality, processing, localization and stability of RNAs are all dependent on the folding of these molecules into intricate structures through specific base pairing interactions encoded in their primary nucleotide sequences. Thus, a...
Article
Full-text available
The secondary structure of RNA is necessary for its maturation, regulation, processing, and function. However, the global influence of RNA folding in eukaryotes is still unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach to identify the paired (double-stranded RNA [dsRNA]) and unpaired (single-stranded RNA [ssRNA]...
Data
Related to Figure 1. (A) Schematic of dsRNA-seq, a novel high-throughput sequencing methodology for identifying and characterizing the dsRNA component of the eukaryotic transcriptome genome-wide. See Text S1 (Supplemental Materials and Methods) for details on the methodology. (B) The relative dsRNA sequence coverage overall (black line) and for 10...
Data
Related to Figure 2 and Figure 3. (A) The distribution of wild-type Col-0 compared to rdr6 mutant 1 kb dsRNA-seq differentially expressed (DE) bins along the length of all Arabidopsis chromosomes. Each red dot denotes a specific 1 kb dsRNA-seq DE bin (fold change ≥2 and p<.001). Red dots with positive Lods-ratio values are dsRNA-seq DE bins where C...
Data
Related to Figure 5 and Figure 7. (A, B) Identification of widespread conserved functionality within non-coding portions (introns) of mRNA. (A) The top figure is a model demonstrating the position of the dsRNA ‘hotspot’ within the 3rd intron (from the 5′ end) of At1g67430. The black lines delineate the positions within the intron that are demonstra...
Data
Related to Figure 4, Figure 5, and Figure 7. (A) The distribution of dsRNA ‘hotspots’ identified using the normal (1X Ribominus) dsRNA-seq dataset along the length of all (as specified) Arabidopsis chromosomes. Red dots denote specific ‘hotspots’. (B) The distribution of dsRNA ‘hotspots’ identified using the 2X Ribominus dsRNA-seq dataset along the...
Data
Related to Figure 2 and Figure 3. (A) The size distribution of dsRNA-seq reads obtained from unopened flower buds of wild-type Col-0 plants using normal and 2X Ribominus dsRNA-seq approaches. The left graph shows the size distribution of all raw dsRNA-seq reads for wild-type Col-0 plants using the normal (yellow bars) and 2X (green bars) Ribominus...
Data
Supplemental text. (1.03 MB DOC)
Data
Related to Figure 6. Identification of novel, highly structured RNAs using dsRNA-seq. (A–D) Four examples of intergenic, highly base-paired transcripts (screenshots from http://tesla.pcbi.upenn.edu/annoj_at9). W (red bars) and C (green bars) indicate signal from Watson and Crick strands, respectively. (A) Two intergenic dsRNA ‘hotspots’ (h348 and h...
Data
Related to Figure 7. Highly base-paired segments of the Arabidopsis genome (dsRNA ‘hotspots’). (A) Approximate genomic distribution (∼100 kb resolution) and length of dsRNA ‘hotspots’ along Arabidopsis Chr. 1 identified using the 2X Ribominus dataset (B) Classification of dsRNA ‘hotspots’ identified using the 2X Ribominus dataset. TE, transposable...
Data
Related to Figure 2, Figure 3, Figure 4, and Figure 6. The smRNA component of the Arabidopsis unopened flower bud transcriptome. (A) The pie chart demonstrates the classification of smRNA sequencing data from Arabidopsis unopened flower buds. (B) Distribution of smRNA ‘hotspots’ along the length of Chromosome 1. Red dots denote specific smRNA ‘hots...
Data
RDR6 substrates that produce phased siRNAs. (0.03 MB XLS)
Data
Normal (1X Ribominus) dsRNA-seq novel RNAs. (0.30 MB XLS)
Data
2X Ribominus dsRNA-seq novel RNAs. (0.16 MB XLS)
Data
Primers used. (0.03 MB XLS)
Data
Related to Figure 4 and Figure S7. (A) The relative highly base-paired RNA (dsRNA ‘hotspot’) coverage overall (black line) and for 10 classes of RNA molecules (colored lines as specified in legend) as the library subset size changes for the 1X Ribominus dsRNA-seq methodology. (B) The relative highly base-paired RNA (dsRNA ‘hotspot’) coverage overal...
Data
2X Ribominus dsRNA-seq dsRNA ‘hotspots’. (2.24 MB XLS)
Data
Arabidopsis RDR6 substrates determined using the combination of dsRNA- and smRNA-seq. (0.06 MB XLS)
Data
Normal (1X Ribominus) dsRNA-seq dsRNA ‘hotspots’. (2.82 MB XLS)
Article
Full-text available
The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base...
Article
Full-text available
Recent advances in reconstruction and analytical methods for signaling networks have spurred the development of large-scale models that incorporate fully functional and biologically relevant features. An extended reconstruction of the human Toll-like receptor signaling network is presented herein. This reconstruction contains an extensive complemen...
Data
Full-text available
Intermediate reactions (0.01 MB PDF)
Data
TLR_model in Matlab format (zip file) (0.05 MB ZIP)
Data
Full-text available
Map of the reconstructed TLR signaling network (3.29 MB PDF)
Data
Full-text available
TLR network species (0.39 MB PDF)
Data
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TLR network outputs (0.01 MB PDF)
Data
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Critical network reactions (0.01 MB PDF)
Data
Full-text available
Reaction references (0.36 MB PDF)
Data
Full-text available
TLR network reactions (0.30 MB PDF)
Data
Full-text available
TLR network inputs (0.02 MB PDF)
Conference Paper
Have genomes; need help with downstream analyses? This workshop provides an overview and in-depth examples of the comparative genomics platform CoGe (http://genomevolution.org) focusing on: * Managing your genome: How to add your own genome to CoGe, add structural and functional annotations, keep it private, share it with collaborators, and make...
Conference Paper
Inexpensive sequencing technology permits the characterization of genome-wide epigenetic modifications. Some challenges facing epigenentic researchers are integrating their data so it may be dynamically viewed on genomic information, shared with collaborators, merged with publicly available datasets, and overlayed on comparative genomic analyses. T...
Conference Paper
Inexpensive sequencing technology permits the characterization of genome-wide epigenetic modifications. Some challenges facing epigenentic researchers are integrating their data so it may be dynamically viewed on genomic information, shared with collaborators, merged with publicly available datasets, and overlayed on comparative genomic analyses. T...

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