On the public citation graph

xiView: A common platform for the downstream analysis of Crosslinking Mass Spectrometry data

https://doi.org/10.1101/561829
0 signed · 121 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.jprot.2015.01.013openalex-snapshot
SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis
inferredcites →https://doi.org/10.1016/j.jsb.2010.10.014openalex-snapshot
The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes
inferredcites →https://doi.org/10.1021/acs.jproteome.6b00274openalex-snapshot
ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data
inferredcites →https://doi.org/10.1021/acs.jproteome.7b00205openalex-snapshot
CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization
inferredcites →https://doi.org/10.1021/pr301162jopenalex-snapshot
XLink-DB: Database and Software Tools for Storing and Visualizing Protein Interaction Topology Data
inferredcites →https://doi.org/10.1038/nsb1203-980openalex-snapshot
Announcing the worldwide Protein Data Bank
inferredcites →https://doi.org/10.1074/mcp.m117.068429openalex-snapshot
The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics
inferredcites →https://doi.org/10.1074/mcp.o114.042259openalex-snapshot
xiNET: Cross-link Network Maps With Residue Resolution
inferredcites →https://doi.org/10.1074/mcp.r110.000133openalex-snapshot
mzML—a Community Standard for Mass Spectrometry Data
inferredcites →https://doi.org/10.1074/mcp.r112.019695openalex-snapshot
File Formats Commonly Used in Mass Spectrometry Proteomics
inferredcites →https://doi.org/10.1093/nar/gku989openalex-snapshot
UniProt: a hub for protein information
inferredcites →https://doi.org/10.1093/nar/gkv402openalex-snapshot
NGL Viewer: a web application for molecular visualization
inferredcites →https://doi.org/10.1093/nar/gkv463openalex-snapshot
xVis: a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints
inferredcites →https://doi.org/10.1093/nar/gky353openalex-snapshot
xiSPEC: web-based visualization, analysis and sharing of proteomics data
inferredcites →https://doi.org/10.1101/424697openalex-snapshot
Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1109/cmv.2007.20openalex-snapshot
State of the Art: Coordinated & Multiple Views in Exploratory Visualization

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/prot.26807openalex-snapshot
The Actin‐Binding Prolyl‐Isomerase Par17 Sustains Its Substrate Selectivity by Interdomain Allostery
inferred← citeshttps://doi.org/10.1007/978-1-0716-1024-4_26openalex-snapshot
Quantitative Cross-Linking of Proteins and Protein Complexes
inferred← citeshttps://doi.org/10.1007/978-1-0716-3734-0_16openalex-snapshot
Characterization of β-Barrel Outer Membrane Proteins and Their Interactions with Chaperones by Chemical-Crosslinking Mass Spectrometry
inferred← citeshttps://doi.org/10.1007/s00018-025-05614-yopenalex-snapshot
Occlusion of TCR binding to HLA-A*11:01 by a non-pathogenic human alloantibody
inferred← citeshttps://doi.org/10.1016/j.cell.2022.11.014openalex-snapshot
Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT
inferred← citeshttps://doi.org/10.1016/j.cell.2024.03.002openalex-snapshot
The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity
inferred← citeshttps://doi.org/10.1016/j.cell.2024.06.041openalex-snapshot
Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport
inferred← citeshttps://doi.org/10.1016/j.celrep.2020.03.080openalex-snapshot
Integrative Modeling of a Sin3/HDAC Complex Sub-structure
inferred← citeshttps://doi.org/10.1016/j.devcel.2024.11.019openalex-snapshot
An amino acid-resolution interactome for motile cilia identifies the structure and function of ciliopathy protein complexes
inferred← citeshttps://doi.org/10.1016/j.jbc.2022.101964openalex-snapshot
Intersubunit and intrasubunit interactions driving the MukBEF ATPase
inferred← citeshttps://doi.org/10.1016/j.mcpro.2023.100600openalex-snapshot
Cross-Linking Mass Spectrometry Uncovers Interactions Between High-Density Lipoproteins and the SARS-CoV-2 Spike Glycoprotein
inferred← citeshttps://doi.org/10.1016/j.molcel.2022.10.017openalex-snapshot
ATG9A and ATG2A form a heteromeric complex essential for autophagosome formation
inferred← citeshttps://doi.org/10.1016/j.molcel.2024.06.002openalex-snapshot
Mechanism of chaperone coordination during cotranslational protein folding in bacteria
inferred← citeshttps://doi.org/10.1016/j.molcel.2024.07.003openalex-snapshot
The V-ATPase/ATG16L1 axis is controlled by the V1H subunit
inferred← citeshttps://doi.org/10.1016/j.molcel.2026.05.020openalex-snapshot
Distinct associations of pioneer factor Ascl1-E12a with nucleosomes drive changes in cell fate
inferred← citeshttps://doi.org/10.1016/j.molp.2023.03.013openalex-snapshot
Capturing the hierarchically assorted modules of protein–protein interactions in the organized nucleome
inferred← citeshttps://doi.org/10.1016/j.sbi.2024.102872openalex-snapshot
Chemical cross-linking and mass spectrometry enabled systems-level structural biology
inferred← citeshttps://doi.org/10.1016/j.str.2020.08.012openalex-snapshot
Molecular Mechanism of LEDGF/p75 Dimerization
inferred← citeshttps://doi.org/10.1016/j.str.2020.09.011openalex-snapshot
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry
inferred← citeshttps://doi.org/10.1016/j.str.2021.08.002openalex-snapshot
Assembly principles of the human R2TP chaperone complex reveal the presence of R2T and R2P complexes
inferred← citeshttps://doi.org/10.1016/j.str.2023.01.011openalex-snapshot
Structural and dynamic insights into α-synuclein dimer conformations
inferred← citeshttps://doi.org/10.1016/j.str.2024.10.031openalex-snapshot
The kinetoplastid kinetochore protein KKT23 acetyltransferase is a structural homolog of GCN5 that acetylates the histone H2A C-terminal tail
inferred← citeshttps://doi.org/10.1016/j.str.2024.11.010openalex-snapshot
Assembly of the Xrn2/Rat1–Rai1–Rtt103 termination complexes in mesophilic and thermophilic organisms
inferred← citeshttps://doi.org/10.1016/j.str.2024.12.017openalex-snapshot
Structural insights into the role of the proline rich region in tau function
inferred← citeshttps://doi.org/10.1021/acs.analchem.3c01369openalex-snapshot
Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo
inferred← citeshttps://doi.org/10.1021/acs.analchem.3c02824openalex-snapshot
4D-diaXLMS: Proteome-wide Four-Dimensional Data-Independent Acquisition Workflow for Cross-Linking Mass Spectrometry
inferred← citeshttps://doi.org/10.1021/acs.biochem.2c00151openalex-snapshot
Mechanistic Insights into the Functioning of a Two-Subunit GMP Synthetase, an Allosterically Regulated, Ammonia Channeling Enzyme
inferred← citeshttps://doi.org/10.1021/acs.biochem.4c00157openalex-snapshot
Mapping the Intersubunit Interdomain FMN-Heme Interactions in Neuronal Nitric Oxide Synthase by Targeted Quantitative Cross-Linking Mass Spectrometry
inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c00786openalex-snapshot
Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein–Protein Interactions─A Method for All Seasons
inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00583openalex-snapshot
Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein–Protein Interaction Networks in Vivo
inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c01000openalex-snapshot
MS Annika: A New Cross-Linking Search Engine
inferred← citeshttps://doi.org/10.1021/acs.jproteome.1c00025openalex-snapshot
Identification of Native Cross-Links in Bacillus subtilis Spore Coat Proteins
inferred← citeshttps://doi.org/10.1021/acs.jproteome.3c00325openalex-snapshot
MS Annika 2.0 Identifies Cross-Linked Peptides in MS2–MS3-Based Workflows at High Sensitivity and Specificity
inferred← citeshttps://doi.org/10.1021/acs.jproteome.4c00567openalex-snapshot
PhoXplex: Combining Phospho-enrichable Cross-Linking with Isobaric Labeling for Quantitative Proteome-Wide Mapping of Protein Interfaces
inferred← citeshttps://doi.org/10.1038/s41421-022-00516-wopenalex-snapshot
Structural insights into DNA N6-adenine methylation by the MTA1 complex
inferred← citeshttps://doi.org/10.1038/s41467-021-23441-0openalex-snapshot
Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry
inferred← citeshttps://doi.org/10.1038/s41467-021-23589-9openalex-snapshot
Structural insight on assembly-line catalysis in terpene biosynthesis
inferred← citeshttps://doi.org/10.1038/s41467-022-31396-zopenalex-snapshot
Hsp multichaperone complex buffers pathologically modified Tau
inferred← citeshttps://doi.org/10.1038/s41467-022-35444-6openalex-snapshot
Functional crosstalk between the cohesin loader and chromatin remodelers
inferred← citeshttps://doi.org/10.1038/s41467-024-46760-4openalex-snapshot
VCF1 is a p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates
inferred← citeshttps://doi.org/10.1038/s41467-024-47732-4openalex-snapshot
Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions
inferred← citeshttps://doi.org/10.1038/s41467-024-52844-yopenalex-snapshot
Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure
inferred← citeshttps://doi.org/10.1038/s41467-025-64968-wopenalex-snapshot
GroEL/ES chaperonin unfolds then encapsulates a nascent protein on the ribosome
inferred← citeshttps://doi.org/10.1038/s41467-025-65315-9openalex-snapshot
Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15
inferred← citeshttps://doi.org/10.1038/s41467-025-66824-3openalex-snapshot
Chromosome compartment assembly is essential for subtelomeric gene silencing in trypanosomes
inferred← citeshttps://doi.org/10.1038/s41586-022-05303-xopenalex-snapshot
Structure of the NuA4 acetyltransferase complex bound to the nucleosome
inferred← citeshttps://doi.org/10.1038/s41589-021-00831-5openalex-snapshot
HUWE1 employs a giant substrate-binding ring to feed and regulate its HECT E3 domain
inferred← citeshttps://doi.org/10.1038/s41592-024-02478-1openalex-snapshot
Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics
inferred← citeshttps://doi.org/10.1038/s41594-023-01075-8openalex-snapshot
Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4–NOT
inferred← citeshttps://doi.org/10.1038/s41594-024-01250-5openalex-snapshot
Structure of the human 20S U5 snRNP
inferred← citeshttps://doi.org/10.1038/s41594-024-01281-yopenalex-snapshot
Structure of the native γ-tubulin ring complex capping spindle microtubules
inferred← citeshttps://doi.org/10.1038/s41594-025-01619-0openalex-snapshot
Conformational plasticity of a BiP–GRP94 chaperone complex
inferred← citeshttps://doi.org/10.1038/s41594-025-01676-5openalex-snapshot
The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking
inferred← citeshttps://doi.org/10.1038/s42003-023-04773-7openalex-snapshot
Does AlphaFold2 model proteins’ intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins
inferred← citeshttps://doi.org/10.1038/s42003-023-04885-0openalex-snapshot
Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon
inferred← citeshttps://doi.org/10.1038/s42003-023-05373-1openalex-snapshot
Structure of the human ATAD2 AAA+ histone chaperone reveals mechanism of regulation and inter-subunit communication
inferred← citeshttps://doi.org/10.1038/s44318-024-00128-yopenalex-snapshot
Higher-order structure and proteoforms of co-occurring C4b-binding protein assemblies in human serum
inferred← citeshttps://doi.org/10.1042/bcj20253431openalex-snapshot
Unconventional binding of calmodulin to CHK2 kinase inhibits catalytic activity
inferred← citeshttps://doi.org/10.1042/ebc20220168openalex-snapshot
Cross-linking mass spectrometry for mapping protein complex topologies in situ
inferred← citeshttps://doi.org/10.1073/pnas.1917635117openalex-snapshot
A precisely positioned MED12 activation helix stimulates CDK8 kinase activity
inferred← citeshttps://doi.org/10.1073/pnas.2107277118openalex-snapshot
Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling
inferred← citeshttps://doi.org/10.1073/pnas.2318601121openalex-snapshot
An integrated structural model of the DNA damage-responsive H3K4me3 binding WDR76:SPIN1 complex with the nucleosome
inferred← citeshttps://doi.org/10.1073/pnas.2420961122openalex-snapshot
PSKH1 kinase activity is differentially modulated via allosteric binding of Ca 2+ sensor proteins
inferred← citeshttps://doi.org/10.1074/mcp.ra119.001839openalex-snapshot
Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker
inferred← citeshttps://doi.org/10.1083/jcb.202206131openalex-snapshot
Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa1043openalex-snapshot
crisscrosslinkeR: identification and visualization of protein–RNA and protein–protein interactions from crosslinking mass spectrometry
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad077openalex-snapshot
ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry
inferred← citeshttps://doi.org/10.1093/nar/gkaa569openalex-snapshot
3-Dimensional architecture of the human multi-tRNA synthetase complex
inferred← citeshttps://doi.org/10.1093/nar/gkae584openalex-snapshot
Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation
inferred← citeshttps://doi.org/10.1101/2021.02.04.429764openalex-snapshot
Perturbation of BRMS1 interactome reveals pathways that impact cell migration
inferred← citeshttps://doi.org/10.1101/2021.11.02.466878openalex-snapshot
Reconstitution of 3’-processing of mammalian pre-mRNA reveals a central role of RBBP6
inferred← citeshttps://doi.org/10.1101/2022.02.10.479924openalex-snapshot
SARS-CoV-2 Nsp1 N-terminal and linker regions as a platform for host translational shutoff
inferred← citeshttps://doi.org/10.1101/2022.02.27.481963openalex-snapshot
Mechanistic insights into the functioning of GMP synthetase: a two-subunit, allosterically regulated, ammonia tunnelling enzyme
inferred← citeshttps://doi.org/10.1101/2022.03.18.484853openalex-snapshot
Hsp multichaperone complex buffers pathologically modified Tau
inferred← citeshttps://doi.org/10.1101/2022.04.21.489026openalex-snapshot
Xlink Mapping and AnalySis (XMAS) - Smooth Integrative Modeling in ChimeraX
inferred← citeshttps://doi.org/10.1101/2022.07.24.501325openalex-snapshot
Specific recognition and ubiquitination of slow-moving ribosomes by human CCR4-NOT
inferred← citeshttps://doi.org/10.1101/2022.08.14.503837openalex-snapshot
Capturing the Hierarchically Assorted Modules of Protein Interaction in the Organized Nucleome
inferred← citeshttps://doi.org/10.1101/2022.09.20.508727openalex-snapshot
Proteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo
inferred← citeshttps://doi.org/10.1101/2022.10.08.511438openalex-snapshot
AI-guided cryo-EM probes a thermophilic cell-free system with succinyl-coA manufacturing capability
inferred← citeshttps://doi.org/10.1101/2023.01.26.525761openalex-snapshot
Autoinhibited kinesin-1 adopts a hierarchical folding pattern
inferred← citeshttps://doi.org/10.1101/2023.07.09.548259openalex-snapshot
An Amino Acid-Resolution Interactome for Motile Cilia Illuminates the Structure and Function of Ciliopathy Protein Complexes
inferred← citeshttps://doi.org/10.1101/2023.07.25.550448openalex-snapshot
VCF1 is an unconventional p97/VCP cofactor promoting recognition of ubiquitylated p97-UFD1-NPL4 substrates
inferred← citeshttps://doi.org/10.1101/2023.10.11.561882openalex-snapshot
Dynamic localization of the chromosomal passenger complex is controlled by the orphan kinesins KIN-A and KIN-B in the kinetoplastid parasite Trypanosoma brucei
inferred← citeshttps://doi.org/10.1101/2024.01.22.576655openalex-snapshot
Mechanism of chaperone coordination during cotranslational protein folding in bacteria
inferred← citeshttps://doi.org/10.1101/2024.04.19.590270openalex-snapshot
Phase separation of a microtubule plus-end tracking protein into a fluid fractal network
inferred← citeshttps://doi.org/10.1101/2024.06.17.599268openalex-snapshot
Biochemical and structural insights into the auto-inhibited state of Mical1 and its activation by Rab8
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.17160.1openalex-snapshot
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.17160.2openalex-snapshot
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry
inferred← citeshttps://doi.org/10.1371/journal.pone.0259128openalex-snapshot
Perturbation of BRMS1 interactome reveals pathways that impact metastasis
inferred← citeshttps://doi.org/10.15252/embj.2022112504openalex-snapshot
Stable kinetochore‐microtubule attachment requires loop‐dependent Ndc80‐Ndc80 binding
inferred← citeshttps://doi.org/10.3390/plants13121632openalex-snapshot
Chemical Protein Crosslinking-Coupled Mass Spectrometry Reveals Interaction of LHCI with LHCII and LHCSR3 in Chlamydomonas reinhardtii
inferred← citeshttps://doi.org/10.70675/a5d4eb6fz69fdz4101z9552zed56bd1806b4openalex-snapshot
Spectrométrie de masse native et pontage chimique pour l'analyse structurale de complexe protéique
inferred← citeshttps://doi.org/10.7554/elife.81977openalex-snapshot
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex
inferred← citeshttps://doi.org/10.7554/elife.86776openalex-snapshot
Autoinhibited kinesin-1 adopts a hierarchical folding pattern
inferred← citeshttps://doi.org/10.7554/elife.86776.1openalex-snapshot
Autoinhibited kinesin-1 adopts a hierarchical folding pattern
inferred← citeshttps://doi.org/10.7554/elife.86776.1.sa1openalex-snapshot
Reviewer #1 (Public Review): Autoinhibited kinesin-1 adopts a hierarchical folding pattern
inferred← citeshttps://doi.org/10.7554/elife.86776.2openalex-snapshot
Autoinhibited kinesin-1 adopts a hierarchical folding pattern
inferred← citeshttps://doi.org/10.7554/elife.86776.3openalex-snapshot
Autoinhibited kinesin-1 adopts a hierarchical folding pattern
inferred← citeshttps://doi.org/10.7554/elife.90762openalex-snapshot
Secreted dengue virus NS1 from infection is predominantly dimeric and in complex with high-density lipoprotein
inferred← citeshttps://doi.org/10.7554/elife.90762.3openalex-snapshot
Secreted dengue virus NS1 from infection is predominantly dimeric and in complex with high-density lipoprotein
inferred← citeshttps://doi.org/10.7554/elife.93522openalex-snapshot
Dynamic localization of the chromosomal passenger complex in trypanosomes is controlled by the orphan kinesins KIN-A and KIN-B
inferred← citeshttps://doi.org/10.7554/elife.93522.1openalex-snapshot
Dynamic localization of the chromosomal passenger complex is controlled by the orphan kinesin KIN-A in the kinetoplastid parasite Trypanosoma brucei
inferred← citeshttps://doi.org/10.7554/elife.93522.2openalex-snapshot
Dynamic localization of the chromosomal passenger complex is controlled by the orphan kinesins KIN-A and KIN-B in the kinetoplastid parasite Trypanosoma brucei
inferred← citeshttps://doi.org/10.7554/elife.93522.3openalex-snapshot
Dynamic localization of the chromosomal passenger complex in trypanosomes is controlled by the orphan kinesins KIN-A and KIN-B
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.