1. Designing effective image-based surveys for urban visual perception 

   Gu, Youlong; Quintana Rosales, Matias Alberto; Liang, Xiucheng; et al. (2025)

   Landscape and Urban Planning

   Urban visual perception is important for the human experience in cities, shaped by intertwined characteristics of urban landscapes. By quantifying and explaining these perceptual experiences, researchers can gain insights into human preferences and support decision-making in planning and design. However, past studies have shown inconsistencies in survey design and ambiguities in reporting, leading to concerns about the reliability and ...

   Journal Article

2. Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution 

   Qin Q.; Popic V.; Wienand K.; et al. (2025)

   Genome Research

   Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate short-read sequences. Recent advances in long-read isoform sequencing enable the detection ...

   Journal Article

3. Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids 

   Karakulak T.; Zajac N.; Bolck H.A.; et al. (2025)

   Genome Research

   Splicing is often dysregulated in cancer, leading to alterations in the expression of canonical and alternatively spliced isoforms. We used the multiplexed arrays sequencing (MAS-seq) protocol of PacBio to sequence full-length transcripts in patient-derived organoid (PDO) cells of clear cell renal cell carcinoma (ccRCC). The sequencing revealed a heterogeneous dysregulation of splicing across 2599 single ccRCC cells. The majority of novel ...

   Journal Article

4. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data 

   Dondi A.; Borgsmüller N.; Ferreira P.F.; et al. (2025)

   Genome Research

   In cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging high-quality LR scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy ...

   Journal Article

5. Repurposing shared bike frames into rural infrastructure 

   Qian C.; Ma Z. (2025)

   Journal of Environmental Management

   While bike-sharing systems have generated significant economic benefits, they have also faced challenges regarding the disposal and recycling of discarded bicycle frames. A potential solution to reuse these difficult-to-recycle frames for essential public service facilities in rural areas has not yet been thoroughly explored. Using shape grammar as a design method, this study examines two typical bicycle frame designs with different ...

   Journal Article

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