-
In this study, we analyze discordance between the transcriptome and proteome using paired scRNA-Seq and multiplexed spatial proteomics data from HuBMAP. Our findings highlight persistent transcripts in key immune markers, including CD45-RO, Ki67, CD45, CD20, a…
arxiv
Jai Prakash Veerla, Jillur Rahman Saurav, Michael Robben, Jacob M Luber
2023-07-02T18:43:03Z
置信度 0.78
q-bio.TOq-bio.GN
-
Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum varies with differe…
arxiv
Thierry Rabilloud
2009-06-12T09:11:38Z
置信度 0.78
q-bio.GN
-
Cryo-electron tomography enables 3D visualization of cells in a near native state at molecular resolution. The produced cellular tomograms contain detailed information about all macromolecular complexes, their structures, their abundances and their specific sp…
arxiv
Min Xu, Elitza I Tocheva, Yi-Wei Chang, Grant J Jensen 等
2015-12-31T19:18:33Z
置信度 0.78
q-bio.QM
-
Mass spectrometry based proteomics enables large-scale identification, quantification, and characterization of proteins, post-translational modifications, and dynamic expression changes, providing critical insights into biological processes and disease mechani…
arxiv
Samuel de la Camara-Fuentes, Dolores Gutierrez-Blazquez, Maria Luisa Hernaez, Concha Gil
2024-12-20T11:27:16Z
置信度 0.78
stat.APq-bio.QM
-
There is the need to represent in a standard manner all the possible variations of a protein or peptide primary sequence, including both artefactual and post-translational modifications of peptides and proteins. With that overall aim, here, the Human Proteome …
arxiv
Richard D. LeDuc, Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers 等
2021-09-23T12:59:09Z
置信度 0.78
q-bio.BM
-
Spatial summary statistics based on point process theory are widely used to quantify the spatial organization of cell populations in single-cell spatial proteomics data. Among these, Ripley's K is a popular metric for assessing whether cells are spatially clus…
arxiv
Julia Wrobel, Hoseung Song
2024-12-11T16:01:09Z
置信度 0.78
stat.MEq-bio.GN
-
Database search and clustering are fundamental components of many data analytics problems, such as mass spectrometry-driven proteomics. Traditional full clustering and search algorithms suffer from high resource usage and long latencies. We introduce HERP, a l…
arxiv
Md Mizanur Rahaman Nayan, Zheyu Li, Flavio Ponzina, Sumukh Pinge 等
2025-11-05T12:55:35Z
置信度 0.78
cs.DBcs.ET
-
The ultimate target of proteomics identification is to identify and quantify the protein in the organism. Mass spectrometry (MS) based on label-free protein quantitation has mainly focused on analysis of peptide spectral counts and ion peak heights. Using seve…
arxiv
Biao He, Baochang Zhang, Yan Fu
2013-12-04T05:34:40Z
置信度 0.78
q-bio.QM
-
Here we present a structural similarity index measure (SSIM) guided conditional Generative Adversarial Network (cGAN) that generatively performs image-to-image (i2i) synthesis to generate photo-accurate protein channels in multiplexed spatial proteomics images…
arxiv
Jillur Rahman Saurav, Mohammad Sadegh Nasr, Paul Koomey, Michael Robben 等
2022-05-20T15:44:53Z
置信度 0.78
eess.IVcs.CVq-bio.QMq-bio.TO
-
Understanding the spatial architecture of the tumor microenvironment (TME) is critical to advance precision oncology. We present ProteinPNet, a novel framework based on prototypical part networks that discovers TME motifs from spatial proteomics data. Unlike t…
arxiv
Louis McConnell, Jieran Sun, Theo Maffei, Raphael Gottardo 等
2025-12-02T18:00:03Z
置信度 0.78
cs.LG
-
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate the…
arxiv
Bogdan Budnik, Ezra Levy, Guillaume Harmange, Nikolai Slavov
2018-08-01T23:50:47Z
置信度 0.78
q-bio.GNq-bio.QM
-
Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity modalities such as an…
arxiv
Alon Shtrikman, Nitzan Simchi, Michal Ran Shchory, Sagie Brodsky 等
2026-05-25T14:54:08Z
置信度 0.78
cs.LGcs.AIq-bio.BM
-
Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine. However, current analysis workflows remain fra…
arxiv
Yucheng Yuan, Yuanfeng Ji, Zhongxiao Li, Ruijiang Li
2026-06-23T07:24:23Z
置信度 0.78
cs.AI
-
Randomisation is used in experimental design to reduce the prevalence of unanticipated confounders. Complete randomisation can however create unbalanced designs, for example, grouping all samples of the same condition in the same batch. Block randomisation is …
arxiv
Bram Burger, Marc Vaudel, Harald Barsnes
2020-07-13T12:12:07Z
置信度 0.78
q-bio.QMstat.AP
-
In clinical proteomics, available input is often limited. In addition, phospho-proteomics is of particular interest since the dysregulation of these post-translational modifications (PTMs) has been implicated in various diseases such as cancer. We therefore as…
arxiv
Teresia Ndungu, Jana Zecha, Lisa Cazares, Sonja Hess
2025-11-04T19:31:10Z
置信度 0.78
q-bio.QMq-bio.GN
-
Quantitative measurements produced by mass spectrometry proteomics experiments offer a direct way to explore the role of proteins in molecular mechanisms. However, analysis of such data is challenging due to the large proportion of missing values. A common str…
arxiv
Haeun Moon, Jin-Hong Du, Jing Lei, Kathryn Roeder
2024-03-23T11:14:50Z
置信度 0.78
stat.MEstat.AP
-
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rel…
arxiv
Thierry Rabilloud, Ali R Vaezzadeh, Noelle Potier, Cécile Lelong 等
2009-09-23T09:29:36Z
置信度 0.78
q-bio.GN
-
Motivation: In transcriptomic and proteomics-based studies, the abundance of genes is often compared to functional pathways such as the Kyoto Encyclopaedia at Genes and Genomes (KEGG) to identify active metabolic processes. Even though a plethora of tools allo…
arxiv
Thomas Nussbaumer, Julia Polzin, Alexander Platzer
2017-08-24T16:47:20Z
置信度 0.78
stat.APq-bio.MN
-
In order to study unknown proteins on a large scale, a reference system has been set up for the three major eukaryotic lineages, built with 36 proteomes as taxonomically diverse as possible. Proteins from 362 eukaryotic proteomes with no known homologue in thi…
arxiv
Yves-Henri Sanejouand
2022-09-22T13:34:02Z
置信度 0.78
q-bio.GN
-
Redox proteomics generates bounded biochemical measurements that are categorically mismatched to conventional linear algebraic formalisms. This work introduces Oxi-Shapes, a tropical geometric framework for the measurement-native analysis of bounded redox prot…
arxiv
James N. Cobley
2026-02-09T16:01:49Z
置信度 0.78
q-bio.QM
-
Ripley's K-function is a widely used spatial summary statistic for assessing clustering in point patterns. However, existing K-based methods can be computationally prohibitive for large-scale data, particularly in high-throughput spatial proteomics, because th…
arxiv
Mingyu Go, Julia Wrobel, Hoseung Song
2026-06-10T12:45:50Z
置信度 0.78
stat.ME
-
Biomarker discovery for clinical purposes is one of the major areas in which proteomics is used. However, despite considerable effort, the successes have been relatively scarce. In this perspective paper, we try to highlight and analyze the main causes for thi…
arxiv
Pierre Lescuyer, Denis Hochstrasser, Thierry Rabilloud
2008-07-08T10:08:04Z
置信度 0.78
q-bio.GN
-
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific…
arxiv
Kasper P. Kepp
2020-03-03T15:53:13Z
置信度 0.78
q-bio.PEphysics.bio-ph
-
Deep Learning can significantly benefit cancer proteomics and genomics. In this study, we attempt to determine a set of critical proteins that are associated with the FLT3-ITD mutation in newly-diagnosed acute myeloid leukemia patients. A Deep Learning network…
arxiv
Christine A. Liang, Lei Chen, Amer Wahed, Andy N. D. Nguyen
2017-12-29T13:05:30Z
置信度 0.78
q-bio.QMcs.LGstat.ML
-
Network theory has proven invaluable in unraveling complex protein interactions. Previous studies have employed statistical methods rooted in network theory, including the Gaussian graphical model, to infer networks among proteins, identifying hub proteins bas…
arxiv
Seungjun Ahn, Eun Jeong Oh
2025-05-29T01:50:17Z
置信度 0.78
stat.MEq-bio.QMstat.AP
-
Objective: Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by unpredictable flares. This study aimed to develop a novel proteomics-based risk prediction model specifically for Asian SLE populations to enhance personalized disea…
arxiv
Liying Chen, Ou Deng, Ting Fang, Mei Chen 等
2024-11-18T01:50:36Z
置信度 0.78
q-bio.GNcs.LG
-
The integration of single-cell proteomic data is often hindered by the fragmented nature of targeted antibody panels. To address this limitation, we introduce scpFormer, a transformer-based foundation model designed for single-cell proteomics. Pre-trained on o…
arxiv
Qifeng Zhou, Lei Yu, Yuzhi Guo, Yuwei Miao 等
2026-04-21T21:27:04Z
置信度 0.78
q-bio.QMcs.AIcs.LG
-
Spatial proteomics technologies have transformed our understanding of complex tissue architecture in cancer but present unique challenges for computational analysis. Each study uses a different marker panel and protocol, and most methods are tailored to single…
arxiv
Johann Wenckstern, Eeshaan Jain, Yexiang Cheng, Benedikt von Querfurth 等
2025-01-10T15:17:27Z
置信度 0.78
q-bio.QMcs.AIcs.CVcs.LG
-
Regression analysis of correlated data, where multiple correlated responses are recorded on the same unit, is ubiquitous in many scientific areas. With the advent of new technologies, in particular high-throughput omics profiling assays, such correlated data i…
arxiv
Lu Xia, Ali Shojaie
2022-07-24T08:08:32Z
置信度 0.78
stat.ME
-
The ultimate goal of proteomic analysis of a cell compartment should be the exhaustive identification of resident proteins; excluding proteins from other cell compartments. Plant cell walls possess specific difficulties. Several reported procedures to isolate …
arxiv
Leila Feiz, Muhammad Irshad, Rafael F Pont-Lezica, Hervé Canut 等
2006-10-12T08:22:38Z
置信度 0.78
q-bio.GN
-
Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods require extensive e…
arxiv
Yuewen Zhang, Maya A. Wright, Pavan K. Challa, Kadi-Liis Saar 等
2019-10-25T17:40:39Z
置信度 0.78
physics.bio-phq-bio.BM
-
Mitochondria are complex organelles, and their proteomics analysis requires a combination of techniques. The emphasis in this chapter is made first on mitochondria preparation from cultured mammalian cells, then on the separation of the mitochondrial proteins …
arxiv
Thierry Rabilloud
2008-07-08T15:28:08Z
置信度 0.78
q-bio.GN
-
Negative control is a common technique in scientific investigations and broadly refers to the situation where a null effect (''negative result'') is expected. Motivated by a real proteomic dataset, we will present three promising and closely connected methods …
arxiv
Zijun Gao, Qingyuan Zhao
2023-03-02T19:53:20Z
置信度 0.78
stat.MEmath.STstat.AP
-
Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Herein, we present DeepRT, a deep learning based software for peptide retention time prediction. DeepRT automatically le…
arxiv
Chunwei Ma, Zhiyong Zhu, Jun Ye, Jiarui Yang 等
2017-05-15T10:13:36Z
置信度 0.78
q-bio.QM
-
Background In proteomics, the most probable localizations of post-translational modifications are assessed by localization scores evaluating the likelihood of a given modification to occupy a site on a peptide sequence. When identifying highly modified peptide…
arxiv
Dafni Skiadopoulou, Lukas Käll, Harald Barsnes, Veit Schwämmle 等
2025-05-23T11:24:41Z
置信度 0.78
q-bio.QM
-
Data-independent acquisition mass spectrometry (DIA-MS) has established itself as a cornerstone of proteomic profiling and large-scale systems biology, offering unparalleled depth and reproducibility. Current DIA analysis frameworks, however, require semi-supe…
arxiv
Yucheng Liao, Han Wen, Weinan E, Weijie Zhang
2026-02-02T07:55:24Z
置信度 0.78
cs.LGcs.AIq-bio.QM
-
Large language models (LLMs) have shown promise in various natural language processing tasks, including their application to proteomics data to classify protein fragments. In this study, we curated a limited mass spectrometry dataset with 1000s of protein frag…
arxiv
Taylor A Phillips, Alejandro W. Huskey, Patrick T. Huskey, Seth L. Robia 等
2025-02-26T21:33:26Z
置信度 0.78
q-bio.QM
-
Mass spectrometry proteomics, characterized by spiky, spatially heterogeneous functional data, can be used to identify potential cancer biomarkers. Existing mass spectrometry analyses utilize mean regression to detect spectral regions that are differentially e…
arxiv
Yusha Liu, Meng Li, Jeffrey S. Morris
2018-09-01T23:39:07Z
置信度 0.78
stat.ME
-
The term unfoldome has been recently used to indicate the universe of intrinsically disordered proteins. These proteins are characterized by an ensemble of high-flexible interchangeable conformations and therefore they can interact with many targets without re…
arxiv
Antonio Deiana, Andrea Giansanti
2010-12-29T11:15:53Z
置信度 0.78
q-bio.GN
-
Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable proteomes. Here, we analy…
arxiv
L. Felipe Benites, Louie Slocombe, Sara I. Walker
2026-05-19T04:14:11Z
置信度 0.78
q-bio.BMq-bio.PE
-
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the …
arxiv
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev 等
2022-07-19T12:19:10Z
置信度 0.78
q-bio.OT
-
Identification of nearly all proteins in a system using data-dependent acquisition (DDA) mass spectrometry has become routine for simple organisms, such as bacteria and yeast. Still, quantification of the identified proteins may be a complex process and requir…
arxiv
Jesse G. Meyer
2018-11-28T21:29:54Z
置信度 0.78
q-bio.QM
-
The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and prot…
arxiv
Tianyu Liu, Yijia Xiao, Xiao Luo, Hua Xu 等
2024-06-21T14:19:10Z
置信度 0.78
cs.LGcs.AIcs.CLq-bio.QM
-
It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a phylogenetic distan…
arxiv
Luca Ferraro, Andrea Giansanti, Giovanni Giuliano, Vittorio Rosato
2004-10-10T13:46:10Z
置信度 0.78
q-bio.MNq-bio.GNq-bio.PE
-
The TNF initiated processes are simulated using our integrative computational model with new quantitative proteomics data obtained on HeLa cell line. In spite of fact, that the model development is based on limited experimental information, with missing data e…
arxiv
Csilla Ulicna, Jozef Ulicny
2013-01-15T12:21:32Z
置信度 0.78
q-bio.MN
-
Two-dimensional mass spectrometry (2D MS) is a method for tandem mass spectrometry that enables the correlation between precursor and fragment ions without the need for ion isolation. On a Fourier transform ion cyclotron resonance mass spectrometer, the phase …
arxiv
Maria A van Agthoven, Marek Polák, Jan Fiala, Claude Nelcy Ounounou 等
2026-01-21T09:46:09Z
置信度 0.78
eess.SP
-
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in folded states of prot…
arxiv
Igor N. Berezovsky, William W. Chen, Paul J. Choi, Eugene I. Shakhnovich
2005-06-22T01:49:50Z
置信度 0.78
q-bio.BMcond-mat.softphysics.bio-phq-bio.GN
-
While prefractionation has previously been shown to improve results in MS analysis, a novel combination provides an additional dimension of separation: protein fractionation by SDS-PAGE followed by IEF of tryptic peptides before separation by RP-LC [Atanassov …
arxiv
Manuel Mayr, Thierry Rabilloud
2013-11-15T08:39:55Z
置信度 0.78
q-bio.GN
-
Protein length distributions across the tree of life carry a quantitative signature of organismal complexity. Nonextensive statistical mechanics, through the Tsallis generalized entropy formalism, provides a natural framework for describing complex systems cha…
arxiv
Sertac Eroglu
2026-06-26T11:32:33Z
置信度 0.78
cond-mat.stat-mechphysics.bio-ph
-
Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modified proteome. Standard database search algorithms suffer from a combinatorial exp…
arxiv
Yuhan Chen, Shang Qu, Zhiqiang Gao, Yuejin Yang 等
2025-12-13T10:27:14Z
置信度 0.78
q-bio.QMcs.AI
-
Motivation: Accurate estimation of false discovery rate (FDR) of spectral identification is a central problem in mass spectrometry-based proteomics. Over the past two decades, target decoy approaches (TDAs) and decoy-free approaches (DFAs), have been widely us…
arxiv
Yisu Peng, Shantanu Jain, Yong Fuga Li, Michal Gregus 等
2020-09-17T02:22:15Z
置信度 0.78
q-bio.QM
-
Motivation: Target-decoy search (TDS) is currently the most popular strategy for estimating and controlling the false discovery rate (FDR) of peptide identifications in mass spectrometry-based shotgun proteomics. While this strategy is very useful in practice …
arxiv
Kun He, Yan Fu, Wen-Feng Zeng, Lan Luo 等
2015-01-03T07:20:05Z
置信度 0.78
stat.APmath.ST
-
The use of an extra SDS separation in a different buffer system provide a technique for deconvoluting 2D gel spots made of several proteins (Colignon et al. Proteomics, 2013, 13, 2077-2082). This technique keeps the quantitative analysis of the protein amounts…
arxiv
Thierry Rabilloud
2013-11-15T08:39:25Z
置信度 0.78
q-bio.GN
-
Objectives This study aimed to elucidate the potential mechanisms of electroacupuncture (EA) in restoring detrusor-bladder neck dyssynergesia (DBND) following suprasacral spinal cord injury. Methods A total of 52 adult female Sprague-Dawley rats were randomly …
arxiv
Liya Tang, Qirui Qu, Yiying Long, Xia Wu 等
2025-03-08T08:35:24Z
置信度 0.78
q-bio.BM
-
Imaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of tens of thousands of …
arxiv
Lyron J. Winderbaum, Inge Koch, Ove J. R. Gustafsson, Stephan Meding 等
2014-10-07T07:24:24Z
置信度 0.78
stat.APq-bio.QM
-
Understanding sub-cellular protein localisation is an essential component to analyse context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to sub-cellular location…
arxiv
Oliver M. Crook, Kathryn S. Lilley, Laurent Gatto, Paul D. W. Kirk
2019-03-07T13:52:43Z
置信度 0.78
stat.AP
-
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