20 papers · ranked by Valyu relevance
Th.I. Götz, X. Cong, S. Rauber, M. Angeli + 3 more
'C. Schmidkonz'] Analysis of gene expression at the single-cell level could help predict the effectiveness of therapies in the field of chronic inflammatory diseases such as arthritis. Here, we demonstrate an adopted approach for processing images from the Slide-seq method. Using a puck, which consists of about 50,000…
Samuel G. Rodriques, Robert R. Stickels, Aleksandrina Goeva, Carly A. Martin + 6 more
The spatial organization of cells in tissue has a profound influence on their function, yet a high-throughput, genome-wide readout of gene expression with cellular resolution is lacking. Here, we introduce Slide-seq, a highly scalable method that enables facile generation of large volumes of unbiased spatial…
Carolyn Brewster, Frederick G Mann Jr., Blair Benham-Pyle, Alejandro Sánchez Alvarado + 1 more
Spatial analysis of gene expression patterns has been a key technique for revealing the potential functions of genes. Traditionally, these analyses, conducted using in situ hybridizations and other labor-intensive protocols, were constrained to examining only a few candidate genes per sample. However, the advent of…
Diane Zhang, Asa Segerstolpe, Michal Slyper, Julia Waldman + 14 more
Solid tumors are spatially heterogeneous in their genetic, molecular and cellular composition, and this variation can be meaningful for diagnosis, prognosis and therapy. Recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to identify copy…
Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman + 16 more
'Evan Murray' 'Robert Strasser' 'Jan Watter' 'Ofir Cohen' 'Orr Ashenberg' 'Daniel Abravanel' 'Judit Jané-Valbuena' 'Simon Mages' 'Ana Lako' 'Karla Helvie' 'Orit Rozenblatt-Rosen' 'Scott Rodig' 'Fei Chen' 'Nikhil Wagle' 'Aviv Regev' 'Johanna Klughammer'] Solid tumors are spatially heterogeneous in their genetic…
Inbal Avraham-Davidi, Simon Mages, Johanna Klughammer, Noa Moriel + 25 more
While advances in single-cell genomics have helped to chart the cellular components of tumor ecosystems, it has been more challenging to characterize their specific spatial organization and functional interactions. Here, we combine single-cell RNA-seq, spatial transcriptomics by Slide-seq, and in situ multiplex RNA…
Javad Rahimikollu, Hanxi Xiao, Anna E. Rosengart, Tracy Tabib + 9 more
Modern multi-omic technologies can generate deep multi-scale profiles. However, differences in data modalities, multicollinearity of the data, and large numbers of irrelevant features make the analyses and integration of high-dimensional omic datasets challenging. Here, we present Significant Latent factor Interaction…
Liang, Xin, Zhang, Xiang + 6 more
Generating academic slides from scientific papers is a challenging multimodal reasoning task that requires both longcontext understanding and deliberate visual planning. Existing approaches largely reduce it to text-only summarization, overlooking the visual component and design-intensive nature of slide creation. In…
Yuting Ye, Jingyi Jessica Li
Background The advent of next-generation RNA sequencing (RNA-seq) has greatly advanced transcriptomic studies, including system-wide identification and quantification of mRNA isoforms under various biological conditions. A number of computational methods have been developed to systematically identify mRNA isoforms in a…
Jiaxin Ge, Zora Zhiruo Wang, Xuhui Zhou, Yi-Hao Peng + 7 more
'Sanjay Subramanian' 'Qinyue Tan' 'Maarten Sap' 'Alane Suhr' 'Daniel Fried' 'Graham Neubig' 'Trevor Darrell'] Designing structured visuals such as presentation slides is essential for communicative needs, necessitating both content creation and visual planning skills. In this work, we tackle the challenge of automated…
Suyash Maniyar, Vishvesh Trivedi, Ajoy Mondal, Anand Mishra + 1 more
Lecture slide element detection and retrieval are key problems in slide understanding. Training effective models for these tasks often depends on extensive manual annotation. However, annotating large volumes of lecture slides for supervised training is labor intensive and requires domain expertise. To address this, we…
Authors not listed
A thorough understanding of drug pharmacokinetics and target interaction within complex biological environments is critical for successful drug discovery. Quantitative matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI; qMSI) presents a promising avenue for such investigations. While…
Changqing Wang, Matthew E. Ritchie, Nadia M. Davidson
Visualizing and troubleshooting long-read sequencing data is a common task when analyzing novel protocols, but identifying several primer sequences from reads exceeding 2 kb with fuzzy matching is challenging for the human eye. Here, we present seqsizzle, a cross-platform terminal user interface (TUI) based tool for…
Kun Zhou, Jiakai He, Wenmian Yang, Zhensheng Wang + 2 more
Presentation slides are a primary medium for data-driven reporting, yet keeping complex, analytics-style decks up to date remains labor-intensive. Existing automation methods mostly follow fixed template filling and cannot support dynamic updates for diverse, user-authored slide decks. We therefore define "Dynamic…
Harold Pimentel, Pascal Sturmfels, Nicolas Bray, Páll Melsted + 1 more
Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is typically not easily usable in practice. We introduce a series of tools for processing and analyzing…
Ryota Tanaka, Kyosuke Nishida, Kosuke Nishida, Taku Hasegawa + 2 more
'Itsumi Saito' 'Kuniko Saito'] Visual question answering on document images that contain textual, visual, and layout information, called document VQA, has received much attention recently. Although many datasets have been proposed for developing document VQA systems, most of the existing datasets focus on understanding…
Jürgen Behr, Timm Michel, Maya Giridhar, Santra Santhosh + 11 more
Large- to ultra-large-scale synthesis of nucleic acids is becoming an increasingly important tool for understanding and manipulating biological systems, as well as for developing new technologies based on engineered biological materials, including DNA-based nanofabrication, aptamers and writing digital data at the…
David E. Hufnagel, Matthew B. Hufford, Arun S. Seetharam
PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its real-time sequencing methodology. Yet, hitherto no tool was available for analyzing the quality of, subsampling, and filtering PacBio data. Here we present…
Shannon Zhang, Yaping Zong
In the article, Scanner calibration revisited, BMC Bioinformatics 2010, 11:361, Dr. Pozhitkov used the Scanner Calibration Slide, a key product of Full Moon BioSystems to generate data in his study of microarray scanner PMT response and proposed a mathematic model for PMT response [1]. In the end, the author concluded…
Authors not listed
The analysis of macromolecules - such as proteins - pose a significant bottleneck in analytical science. We have developed surface treatment techniques utilising direct and radiofrequency current argon plasmas, able to quickly digest condensed-phase macromolecules while maintaining spatial resolution of analytes. We…