Search Results - "Bi, Chengpeng"

A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences by Bi, Chengpeng

“…Motif discovery methods play pivotal roles in deciphering the genetic regulatory codes (i.e., motifs) in genomes as well as in locating conserved domains in…”
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Proteomics of human liver membrane transporters: a focus on fetuses and newborn infants by van Groen, Bianca D., van de Steeg, Evita, Mooij, Miriam G., van Lipzig, Marola M.H., de Koning, Barbara A.E., Verdijk, Robert M., Wortelboer, Heleen M., Gaedigk, Roger, Bi, Chengpeng, Leeder, J. Steven, van Schaik, Ron H.N., van Rosmalen, Joost, Tibboel, Dick, Vaes, Wouter H., de Wildt, Saskia N.

“…Hepatic membrane transporters are involved in the transport of many endogenous and exogenous compounds, including drugs. We aimed to study the relation of age…”
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Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort by Cheung, Warren A., Johnson, Adam F., Rowell, William J., Farrow, Emily, Hall, Richard, Cohen, Ana S. A., Means, John C., Zion, Tricia N., Portik, Daniel M., Saunders, Christopher T., Koseva, Boryana, Bi, Chengpeng, Truong, Tina K., Schwendinger-Schreck, Carl, Yoo, Byunggil, Johnston, Jeffrey J., Gibson, Margaret, Evrony, Gilad, Rizzo, William B., Thiffault, Isabelle, Younger, Scott T., Curran, Tom, Wenger, Aaron M., Grundberg, Elin, Pastinen, Tomi

“…Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, and structural variants. Recent…”
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Pediatric growth patterns in youth‐onset type 2 diabetes mellitus: Implications for physiologically‐based pharmacokinetic models by Hosey, Chelsea M., Halpin, Kelsee, Shakhnovich, Valentina, Bi, Chengpeng, Sweeney, Brooke, Yan, Yun, Leeder, J. Steven

“…An accurate understanding of the changes in height and weight of children with age is critical to the development of models predicting drug concentrations in…”
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P458: Evaluating the impact of long read genomes in rare disease: A systematic analysis of 1000 HiFi genomes by Farrow, Emily, Thiffault, Isabelle, Cohen, Ana, Zion, Tricia, Walter, Adam, Gibson, Margaret, Bi, Chengpeng, Cheung, Warren, Johnston, Jeffrey, Pastinen, Tomi

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Alternative Splicing of the SLCO1B1 Gene: An Exploratory Analysis of Isoform Diversity in Pediatric Liver by Groen, Bianca D., Bi, Chengpeng, Gaedigk, Roger, Staggs, Vincent S., Tibboel, Dick, Wildt, Saskia N., Leeder, J. Steven

“…The hepatic influx transporter OATP1B1 (SLCO1B1) plays an important role in the disposition of endogenous substrates and drugs prescribed to children…”
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WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA by Bi, Chengpeng, Benham, Craig J.

“…WebSIDD is a Web-based service designed to predict locations and extents of stress-induced duplex destabilization (SIDD) that occur in a double-stranded DNA…”
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Evolutionary Metropolis Sampling in Sequence Alignment Space by Chengpeng Bi

“…Metropolis sampling is the earliest Markov chain Monte Carlo (MCMC) method and MCMC has been widely used in motif-finding via sequence local alignment. A key…”
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BIPAD: a web server for modeling bipartite sequence elements by Bi, Chengpeng, Rogan, Peter K

“…Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site…”
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A Comparative Study on Computational Two-Block Motif Detection: Algorithms and Applications by Bi, Chengpeng, Leeder, J. Steven, Vyhlidal, Carrie A

“…Since the completion of human genome sequencing, cataloging of all genomic functional elements has been one of the challenging problems in bioinformatics…”
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Deterministic local alignment methods improved by a simple genetic algorithm by Bi, Chengpeng

“…Multiple sequence local alignment, often deployed for de novo discovery of biological motifs hidden in a set of DNA or protein sequences, remains a challenge…”
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Memetic algorithms for de novo motif-finding in biomedical sequences by Bi, Chengpeng

“…Abstract Objectives The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to…”
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Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood by Bi, Chengpeng

“…Among a set of observed relevant DNA sequences coming from a set of co-regulated genes, there exist some short, functional yet hidden sub-sequence patterns…”
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Tackling the challenging motif problem through hybrid particle swarm optimized alignment clustering by Chengpeng Bi

“…Previous studies show that Gibbs sampling methods and the like desperately failed to solve the challenging motif problem. This paper proposes a new hybrid…”
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DNA motif alignment by evolving a population of Markov chains by Bi, Chengpeng

“…Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov…”
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Data Augmentation Algorithms for Detecting Conserved Domains in Protein Sequences: A Comparative Study by Bi, Chengpeng

“…Protein conserved domains are distinct units of molecular structure, usually associated with particular aspects of molecular function such as catalysis or…”
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A Genetic-Based EM Motif-Finding Algorithm for Biological Sequence Analysis by Chengpeng Bi

“…Motif-finding in biological sequence analysis remains a challenge in computational biology. Many algorithms and software packages have been developed to…”
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Characterization and visualization of tandem repeats at genome scale by Dolzhenko, Egor, English, Adam, Dashnow, Harriet, De Sena Brandine, Guilherme, Mokveld, Tom, Rowell, William J., Karniski, Caitlin, Kronenberg, Zev, Danzi, Matt C., Cheung, Warren A., Bi, Chengpeng, Farrow, Emily, Wenger, Aaron, Chua, Khi Pin, Martínez-Cerdeño, Verónica, Bartley, Trevor D., Jin, Peng, Nelson, David L., Zuchner, Stephan, Pastinen, Tomi, Quinlan, Aaron R., Sedlazeck, Fritz J., Eberle, Michael A.

“…Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate…”
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Abstract 243: Long-read sequencing of pediatric cancer genomes identifies multiple clinically relevant variants by Yoo, Byunggil, Cheung, Warren, Pushel, Irina, Lansdon, Lisa, Bi, Chengpeng, Guest, Erin, Pastinen, Tomi, Farooqi, Midhat

“…Abstract Genetic characterization of pediatric cancer samples clinically for diagnostic, prognostic, or therapeutic information currently relies on an…”
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Large-scale computation of pediatric growth percentiles with fuzzy logic justification of parameter selection by Chengpeng Bi, Leeder, J. S.

“…The electronic health record is now becoming a hot topic in the medical community largely owing to the rapid advances in both information technology and…”
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