10 papers · ranked by Valyu relevance
Witold E. Wolski, Leonardo Schwarz, Christian Trachsel, Martina Zanella + 6 more
Mass spectrometry laboratories must turn lists of submitted samples into acquisition queues. The run order and the placement of quality-control (QC) injections determine whether a design controls batch effects and signal drift, and whether those effects stay correctable afterward. Yet operators usually set them by hand…
Muaaz Gul Awan, Fahad Saeed
Mass Spectrometry (MS) based proteomics has become an essential tool in the study of proteins. The big data from MS machines has led to the development of novel serial and parallel algorithmic tools. However, the absence of data benchmarks and ground truth makes the algorithmic integrity testing and reproducibility a…
Alexander R. Bricco, Iliya Miralavy, Shaowei Bo, Or Perlman + 4 more
Proteins are used by scientists to serve a variety of purposes in clinical practice and laboratory research. To optimize proteins for greater function, a variety of techniques have been developed. For the development of reporter genes used in Magnetic Resonance Imaging (MRI) based on Chemical Exchange Saturation…
Manuel Corpas
Large language model (LLM) agents are typically deployed as clones: identical copies of a single configuration with no mechanism for heritable variation or population-level dynamics. Here we introduce Genomebook, a designed evolutionary system that encodes 26 behavioural traits across 60 diploid loci using additive…
Jia Lu, Ryan Tsoi, Nan Luo, Yuanchi Ha + 8 more
Dynamical systems often generate distinct outputs according to different initial conditions, and one can infer the corresponding input configuration given an output. This property captures the essence of information encoding and decoding. Here, we demonstrate the use of self-organized patterns, combined with machine…
Elizabeth Tseng, Qiandong Zeng, Lax Iyer
We had developed VCFCons to address urgent need for a robust consensus sequence generator for SARS-CoV-2 viral surveillance, which presented several unique requirements, including: (a) low coverage areas should be noted with ‘N’s, (b) low frequency or suspicious variant calls need to be filtered. We have found that…
Lucien Piat, Sukanya Denni, Siegfried Dubois, Benjamin Linard + 1 more
Pangenome variation graphs (PVGs) are increasingly used to represent genomic diversity, yet there is currently no general framework for generating population pangenomes directly from explicit evolutionary histories. Existing simulators typically focus on individual classes of variation and do not integrate these…
F. Tessari, N. Hogan
Humans have a remarkable ability to manage physical interaction despite a tremendously complex musculoskeletal system, comparatively slow muscles and slow neural communication. Most physical interaction tasks require force generation, and that can compromise stability. To ensure stability, muscles are required to…
Yuxuan Zeng, Zitong Lu, Ren E Hentz, David E Osher
Holistic processing has traditionally been regarded as unique to faces, attributed to the spatial layout across facial features and their variability across individuals. However, whether such processing can occur in stimuli other than faces has remained an open and contentious question. Here, we show that novel…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…