Publications by authors named "Andre Sim"

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A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.
Ying Chen, Nadia M Davidson, Yuk Kei Wan, Fei Yao, Yan Su, Andre Sim

Nat Methods· April 2025

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Andre D Sim

Nat Methods· July 2024

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Context-aware transcript quantification from long-read RNA-seq data with Bambu.
Ying Chen, Andre Sim, Yuk Kei Wan, Keith Yeo, Joseph Jing Xian Lee

Nat Methods· August 2023

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Andre D Sim

bioRxiv· July 2023

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Antisense RNAs Influence Promoter Usage of Their Counterpart Sense Genes in Cancer.
Fernando Bellido Molias, Andre Sim, Ka Wai Leong, Omer An, Yangyang Song

Cancer Res· December 2021

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BceAB-Type Antibiotic Resistance Transporters Appear To Act by Target Protection of Cell Wall Synthesis.
Carolin M Kobras, Hannah Piepenbreier, Jennifer Emenegger, Andre Sim, Georg Fritz

Antimicrob Agents Chemother· February 2020

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From Modules to Networks: a Systems-Level Analysis of the Bacitracin Stress Response in Bacillus subtilis.
Hannah Piepenbreier, Andre Sim, Carolin M Kobras, Jara Radeck, Thorsten Mascher

mSystems· February 2020

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Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains.
Rosie E Bradshaw, Andre D Sim, Pranav Chettri, Pierre-Yves Dupont, Yanan Guo

Mol Plant Pathol· June 2019

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Evolution of polyketide synthesis in a Dothideomycete forest pathogen.
I Kutay Ozturk, Pranav Chettri, Pierre-Yves Dupont, Irene Barnes, Rebecca L McDougal, Andre Sim

Fungal Genet Biol· September 2017

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Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation.
Murray P Cox, Georgi Hudjashov, Andre Sim, Olga Savina, Tatiana M Karafet

Mol Biol Evol· September 2016

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The venom gland transcriptome of the parasitoid wasp Nasonia vitripennis highlights the importance of novel genes in venom function.
Andre D Sim, David Wheeler

BMC Genomics· August 2016

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Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata.
Rosie E Bradshaw, Yanan Guo, Andre D Sim, M Shahjahan Kabir, Pranav Chettri

Mol Plant Pathol· February 2016

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