🧬Unlocking Long-Read Transcriptomics: A Deep Dive into SQANTI3 to master Isoform Quality Control
A Deep Dive Into SQANTI3 to Master Isoform Quality Control Tianyuan Liu, Doctoral Candidate at the Genomics of Gene Expression Lab (I2SysBio-CSIC), explains how to work with long-read transcriptomics data and have created a video-tutorial of the tool SQANTI3. Whether you are using PacBio or Oxford Nanopore technologies, accurate transcriptome characterization is the cornerstone of […]
👩🔬🌍 Research Mobility Experience – Carmen at CRG
Exploring the U12 introns biological role and conservation From November 1, 2024, to January 5, 2025, Carmen Lafuente Sanz, , LongTREC Doctoral Candidate at Genoscope, had the opportunity to carry out a research secondment at the Centre for Genomic Regulation (CRG), supervised by Prof. Roderic Guigó. This period was an enriching experience, both scientifically and […]
LongTREC presents: Profiling the epigenome using long-read sequencing
LongTREC presents: Profiling the epigenome using long-read sequencing Tianyuan Liu, Ana Conesa Every cell in our body carries the same DNA, yet a liver cell and a neuron behave very differently. Part of the explanation lies in the epigenome: chemical marks and packaging that act like switches and bookmarks, controlling which genes are turned on […]
👩🔬🌍 Research Mobility Experience – Yalan at BioBam
Long-Read Transcriptome Analysis at BioBam Bioinformatics From November 3, 2024 to January 3, 2025, Yalan Bi, LongTREC Doctoral Candidate at the Max Planck Institute for Molecular Genetics, had the opportunity to carry out a research secondment at BioBam Bioinformatics, supervised by Stefan Götz. This secondment offered valuable growth, both in scientific expertise and personal development. […]
👨🔬🌍 Research Mobility Experience – Fabian at SU
Improving Reference-Free Isoform Reconstruction at Stockholm University From August 19 to October 18, 2024, Fabian Jetzinger, LongTREC Doctoral Candidate at BioBam Bioinformatics, had the opportunity to carry out a research secondment at Stockholm University, supervised by Kristoffer Sahlin. This secondment offered valuable growth, both in scientific expertise and personal development. My goal? Contributing to the […]
👨🔬🌍 Research Mobility Experience – Fabio at Wobble Genomics
Transcript Normalisation for Genome Annotation at Wobble Genomics From September 2 to October 18, 2024, Fabio Zanarello, LongTREC Doctoral Candidate at the Centre for Genomic Regulation (CRG), had the opportunity to carry out a research secondment at Wobble Genomics, supervised by Björn Geigle. This secondment offered valuable growth, both in scientific expertise and personal development. […]
👩🔬📢 LongTREC in action: Carmen Lafuente Sanz Opens the Doors to DNA at the Fête de la Science
On 6 October 2024, Carmen Lafuente Sanz, Doctoral Candidate at CEA – Genoscope, took part in the Fête de la Science, when Genoscope, the French national sequencing centre, opened its doors free of charge to everyone who wanted to visit or join its science workshops and activities. Together with her colleagues, Carmen created two workshops […]
👨🔬🌍 Research Mobility Experience – Pablo at Oxford Nanopore
🧩 Exploring Haplotype Assembly and Methylation Pablo Angulo Lara enjoyed a fantastic opportunity to undertake a research secondment at Oxford Nanopore Technologies (ONT) from July to September 2024, under the guidance of Aino Järvelin. My main objective? To design a pipeline for performing haplotype assembly at the full-chromosome level in samples affected by aneuploidy and […]
👨🔬🌍 Research Mobility Experience – Eamon at Oxford Nanopore
Raw Signal and Modification Detection at Oxford Nanopore Technologies From June 24 to September 20, 2024, Eamon McAndrew, LongTREC Doctoral Candidate at IPMC (CNRS, Université Côte d’Azur), had the opportunity to carry out a research secondment at Oxford Nanopore Technologies, supervised by Aino Järvelin with scientific supervision support from Marcus Stoiber. This secondment offered valuable […]
LongTREC presents: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
LongTREC presents: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations Alicja Pacholewska, Matthias Lienhard, Mirko Brüggemann, Heike Hänel, Lorina Bilalli, Anja Königs, Felix Heß, Kerstin Becker, Karl Köhrer, Jesko Kaiser, Holger Gohlke, Norbert Gattermann, Michael Hallek, Carmen D. Herling, Julian König, Christina Grimm, Ralf Herwig, Kathi Zarnack, Michal R. […]
🧬 Unlocking Long-Read Transcriptomics: Combining Transcriptomes with TAMA Merge
Unlocking Long-Read Transcriptomics: Combining Transcriptomes with TAMA Merge Combining Transcriptomes with TAMA Merge In a recent BioBam article, Fabian Jetzinger, Doctoral Candidate, explains how to overcome the complexities of defining custom transcriptomes using TAMA Merge. While long-read sequencing reveals vast isoform diversity, researchers often struggle to identify rare or sample-specific isoforms that are missing from […]
👩🔬🌍 Research Mobility Experience – Nadja at UF
Learning, collaborating and growing From April to July 2024, Nadja Nolte, LongTREC Doctoral Candidate at the National Institute of Biology in Slovenia, had the incredible opportunity to undertake a research secondment at the University of Florida (UF) under the supervision of Lauren McIntyre. The goal? To deepen Nadja’s expertise in statistical methods for allele-specific expression (ASE) analysis—a […]