Publications by authors named "Chengpeng Bi"

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Clinical Long-Read Sequencing Test for Genetic Disease Diagnosis.
Isabelle Thiffault, Emily Farrow, Cassandra Barrett, Meadow Scott, Amy Ross, Chengpeng Bi

JAMA Pediatr· December 2025

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Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.
Jimin Park, Daniel E Cook, Pi-Chuan Chang, Alexey Kolesnikov, Lucas Brambrink, Chengpeng Bi, Nicolas Robine

Nat Biotechnol· October 2025

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Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.
Ayse G Keskus, Asher Bryant, Tanveer Ahmad, Byunggil Yoo, Sergey Aganezov, Chengpeng Bi, Nicolas Robine

Nat Biotechnol· April 2025

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Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing.
Lisa A Lansdon, Byunggil Yoo, Ayse Keskus, Irina Pushel, Chengpeng Bi

medRxiv· November 2024

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Characterization and visualization of tandem repeats at genome scale.
Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, Chengpeng Bi

Nat Biotechnol· October 2024

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DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.
Jimin Park, Daniel E Cook, Pi-Chuan Chang, Alexey Kolesnikov, Lucas Brambrink, Chengpeng Bi, Nicolas Robine

bioRxiv· August 2024

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Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort.
Warren A Cheung, Adam F Johnson, William J Rowell, Emily Farrow, Richard Hall, Chengpeng Bi

Nat Commun· May 2023

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Pediatric growth patterns in youth-onset type 2 diabetes mellitus: Implications for physiologically-based pharmacokinetic models.
Chelsea M Hosey, Kelsee Halpin, Valentina Shakhnovich, Chengpeng Bi, Brooke Sweeney

Clin Transl Sci· April 2022

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Alternative Splicing of the SLCO1B1 Gene: An Exploratory Analysis of Isoform Diversity in Pediatric Liver.
Bianca D van Groen, Chengpeng Bi, Roger Gaedigk, Vincent S Staggs, Dick Tibboel

Clin Transl Sci· May 2020

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Proteomics of human liver membrane transporters: a focus on fetuses and newborn infants.
Bianca D van Groen, Evita van de Steeg, Miriam G Mooij, Marola M H van Lipzig, Barbara A E de Koning, Chengpeng Bi

Eur J Pharm Sci· November 2018

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Ontogeny-related pharmacogene changes in the pediatric liver transcriptome.
Richard Meier, Chengpeng Bi, Roger Gaedigk, Daniel P Heruth, Shui Qing Ye

Pharmacogenet Genomics· March 2018

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Dynamics of Cytosine Methylation in the Proximal Promoters of CYP3A4 and CYP3A7 in Pediatric and Prenatal Livers.
Carrie A Vyhlidal, Chengpeng Bi, Shui Qing Ye, J Steven Leeder

Drug Metab Dispos· July 2016

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Central nervous system lymphoma in immunocompetent patients: the North Shore-Long Island Jewish Health System experience.
Xinmin Zhang, Qiang Hua Chen, Peter Farmer, Mansoor Nasim, Alexis Demopoulos, Chengpeng Bi

J Clin Neurosci· January 2013

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Memetic algorithms for de novo motif-finding in biomedical sequences.
Chengpeng Bi

Artif Intell Med· September 2012

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Allele drop-out in the MECP2 gene due to G-quadruplex and i-motif sequences when using polymerase chain reaction-based diagnosis for Rett syndrome.
Carol J Saunders, Michael J Friez, Melanie Patterson, Masha Nzabi, Weiwei Zhao, Chengpeng Bi

Genet Test Mol Biomarkers· April 2010

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A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences.
Chengpeng Bi

IEEE/ACM Trans Comput Biol Bioinform· November 2009

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DNA motif alignment by evolving a population of Markov chains.
Chengpeng Bi

BMC Bioinformatics· January 2009

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A comparative study on computational two-block motif detection: algorithms and applications.
Chengpeng Bi, J Steven Leeder, Carrie A Vyhlidal

Mol Pharm· April 2008

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Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study.
Chengpeng Bi

J Proteome Res· January 2008

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SEAM: a Stochastic EM-type Algorithm for Motif-finding in biopolymer sequences.
Chengpeng Bi

J Bioinform Comput Biol· February 2007

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Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy.
Jürgen Bode, Silke Winkelmann, Sandra Götze, Steven Spiker, Ken Tsutsui, Chengpeng Bi

J Mol Biol· April 2006

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BIPAD: a web server for modeling bipartite sequence elements.
Chengpeng Bi, Peter K Rogan

BMC Bioinformatics· February 2006

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The analysis of stress-induced duplex destabilization in long genomic DNA sequences.
Craig J Benham, Chengpeng Bi

J Comput Biol· January 2005

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Bipartite pattern discovery by entropy minimization-based multiple local alignment.
Chengpeng Bi, Peter K Rogan

Nucleic Acids Res· September 2004

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WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA.
Chengpeng Bi, Craig J Benham

Bioinformatics· June 2004

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