Top 10 Biorxiv Papers Today


2.062 Mikeys
#1. A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions
Michael Goetze, Claudio Iacobucci, Christian Ihling, Andrea Sinz
We present a cross-linking/mass spectrometry (XLMS) workflow for performing proteome-wide cross-linking analyses within one week. The workflow is based on the commercially available MS-cleavable cross-linker disuccinimidyl dibutyric urea (DSBU) and can be employed by every lab having access to a mass spectrometer with tandem MS capabilities. We provide an updated version 2.0 of the freeware software tool MeroX, available at www.StavroX.com, that allows conducting fully automated and reliable studies delivering insights into protein-protein interaction networks and protein conformations at the proteome level. We exemplify our optimized workflow for mapping protein-protein interaction networks in Drosophila melanogaster embryos on a system-wide level. From cross-linked Drosophila embryo extracts, we detected 18,037 cross-link spectrum matches corresponding to 5,129 unique cross-linked residues in biological triplicate experiments at 5% FDR (3,098 at 1% FDR). Among these, 1,237 inter-protein cross-linking sites were identified that...
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SinzAndrea: Our latest paper on a proteome-wide cross-linking workflow with the cross-linker DSBU and our MeroX software is now available at https://t.co/yOnJDN5sF0 Thank you, Michael and Claudio, for the hard work!
ClaudioIacobuc2: Happy to share the link of our latest study on system-wide cross-linking mass spectrometry and our new MeroX 2.0 software (https://t.co/U4puQn3eIM): https://t.co/ZbkWNNqqSA https://t.co/uQJae8FTuK
realBioMassSpec: RT @biorxivpreprint: A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions https://t.co/eMj5dYiQef #…
jsteward2930: RT @biorxivpreprint: A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions https://t.co/eMj5dYiQef #…
dhiraj_d_bhatia: RT @biorxivpreprint: A Simple Cross-Linking/Mass Spectrometry Workflow to Study System-Wide Protein Interactions https://t.co/eMj5dYiQef #…
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Total Words: 6974
Unqiue Words: 2668

2.05 Mikeys
#2. Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation
Bryan A Gibson, Lynda K Doolittle, Liv E Jensen, Nathan Gamarra, Sy Redding, Michael K Rosen
Genomic DNA is highly compacted in the nucleus of eukaryotic cells as a nucleoprotein assembly called chromatin. The basic unit of chromatin is the nucleosome, where ~146 base pair increments of the genome are wrapped and compacted around the core histone proteins. Further genomic organization and compaction occur through higher order assembly of nucleosomes. This organization regulates many nuclear processes, and is controlled in part by histone post-transtranslational modifications and chromatin-binding proteins. Mechanisms that regulate the assembly and compaction of the genome remain unclear. Here we show that in the presence of physiologic concentrations of mono- and divalent salts, histone tail-driven interactions drive liquid-liquid phase separation (LLPS) of nucleosome arrays, resulting in substantial condensation. Phase separation of nucleosomal arrays is inhibited by histone acetylation, whereas histone H1 promotes phase separation, further compaction, and decreased dynamics within droplets, mirroring the relationship...
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biorxivpreprint: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/r3CBulIYs9 #bioRxiv
Alexis_Verger: #365papers 1⃣7⃣ Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/WXFfUeJCqu https://t.co/VEvuLRi6SO
ShorterLab: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation, very exciting work from Mike Rosen et al.!: https://t.co/v1LC8mwi8r
YSPTSPS: This paper from the lab of Michael "Oh My Goodness" Rosen is as exciting and simple and elegant and impactful as you can read. A monument to the continued utility of biochemistry even the age of omics and super-scopes (which I also love, obviously). https://t.co/QmP9tAvjM9
biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
ReddingLab: Preprint from our collab with Michael Rosen UTSW and @bryangibsonphd is now live! Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/wpUfLyw0CB
Castaneda_lab: And the transcription/gene regulation/phase separation story gets even more interesting. See the preprint linked below from Rosen's lab. https://t.co/rt4TGg5g4K
YSPTSPS: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/QmP9tAvjM9
PromPreprint: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/bNtVjpXWat
rassobar: https://t.co/ZH7EIFmqCW
bryangibsonphd: Check it interwebs!, up on @biorxivpreprint now is our collab with the @ReddingLab on liquid-liquid phase separation of the #chromatin fiber. Dynamic and reversible compaction and material properties modulation through #phaseseparation. https://t.co/cUzQJOzAhL
skurukuti: https://t.co/BZMeND3Jpi
Alexis_Lomakin: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
meter: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
rraadd88: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
Parikki: RT @YSPTSPS: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/QmP9tAvjM9
Ryan_Cupo: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
PeterLyLab: RT @biorxivpreprint: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/r3CBulIYs9 #bioRxiv
lab_zhang: RT @YSPTSPS: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/QmP9tAvjM9
biofiziksmama: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
oz__gur: RT @biorxivpreprint: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/r3CBulIYs9 #bioRxiv
LabZhu: RT @YSPTSPS: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/QmP9tAvjM9
AlZuko1: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
krishna92: RT @biorxiv_biophys: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/owlLq4rYBT #biorxiv_biophys
NZthRzXeiplAQA6: RT @biorxivpreprint: Organization and Regulation of Chromatin by Liquid-Liquid Phase Separation https://t.co/r3CBulIYs9 #bioRxiv
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Total Words: 5350
Unqiue Words: 1835

2.05 Mikeys
#3. A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity
Hélène Ruffieux, Jérôme Carayol, Mary Ellen Harper, Robert Dent, Wim Saris, Arne Astrup, Anthony Davison, Jorg Hager, Armand Valsesia
The genetic contribution to obesity has been widely studied, yet the functional mechanisms underlying metabolic states remain elusive. This has prompted analysis of endophenotypes via quantitative trait locus studies, which assess how genetic variants affect intermediate gene (eQTL) or protein (pQTL) expression phenotypes. To leverage shared regulatory patterns, we present the first integrative multivariate pQTL analysis, performed with our scalable Bayesian framework LOCUS on plasma mass-spectrometry and aptamer-based proteomic datasets. We identify 136 pQTL associations in the Ottawa obesity clinical practice, of which > 80% replicate in the DiOGenes obesity cohort and show significant functional enrichments; 16% of the validated hits would be missed by standard univariate methods. By also exploiting extensive clinical data, our methods and results reveal the implication of proteins under genetic control in low-grade inflammation, insulin resistance, and dyslipidemia, thereby opening new perspectives for diagnosing and treating...
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biorxivpreprint: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/97E8mUsQLB #bioRxiv
biorxiv_genetic: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/ndzgziRk9v #biorxiv_genetic
jessicabakerphd: RT @biorxiv_genetic: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/ndzgziRk9v #bio…
CamronBryantPhD: RT @biorxiv_genetic: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/ndzgziRk9v #bio…
gtimblin: RT @biorxivpreprint: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/97E8mUsQLB #bio…
Armand_v1: RT @biorxivpreprint: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/97E8mUsQLB #bio…
evogen_p: RT @biorxiv_genetic: A large-scale multivariate pQTL study sheds light on the genetic architecture of obesity https://t.co/ndzgziRk9v #bio…
Github

locus R package - Large-scale variational inference for combined covariate and response selection in sparse regression models

Repository: locus
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Language: R
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2.045 Mikeys
#4. In vivo structure of the Legionella type II secretion system by electron cryotomography
Debnath Ghosal, Ki Woo Kim, Huaixin Zheng, Mohammed Kaplan, Joseph P. Vogel, Nicholas P. Cianciotto, Grant J Jensen
The type II secretion system (T2SS) is a multi-protein envelope-spanning assembly that translocates a wide range of virulence factors, enzymes and effectors through the outer membrane (OM) of many Gram-negative bacteria. Here, using electron cryotomography and subtomogram averaging methods, we present the first in situ structure of an intact T2SS, imaged within the human pathogen Legionella pneumophila. Although the T2SS has only limited sequence and component homology with the evolutionarily-related Type IV pilus (T4P) system, we show that their overall architectures are remarkably similar. Despite similarities, there are also differences, including for instance that the T2SS-ATPase complex is usually present but disengaged from the inner membrane, the T2SS has a much longer periplasmic vestibule, and it has a short-lived flexible pseudopilus. Placing atomic models of the components into our ECT map produced a complete architectural model of the intact T2SS that provides new insights into the structure and function of its...
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biorxivpreprint: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/yXs60DBBA6 #bioRxiv
biorxiv_micrbio: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/PlzIsGdQMS #biorxiv_micrbio
cryoEM_Papers: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/pNfBja6zu4
PromPreprint: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/wjawHfHAf1
jsteward2930: RT @biorxiv_micrbio: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/PlzIsGdQMS #bior…
t2438: RT @cryoEM_Papers: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/pNfBja6zu4
genolib_19: RT @biorxivpreprint: In vivo structure of the Legionella type II secretion system by electron cryotomography https://t.co/yXs60DBBA6 #bioR…
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Total Words: 10064
Unqiue Words: 3234

2.042 Mikeys
#5. Transcriptomic correlates of electrophysiological and morphological diversity within and across neuron types
Claire Bomkamp, Shreejoy Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling Leffler, Ann Marie Craig, Paul Pavlidis
In order to further our understanding of how gene expression contributes to key functional properties of neurons, we combined publicly accessible gene expression, electrophysiology, and morphology measurements to identify cross-cell type correlations between these data modalities. Building on our previous work using a similar approach, we distinguished between correlations which were "class-driven," meaning those that could be explained by differences between excitatory and inhibitory cell classes, and those that reflected graded phenotypic differences within classes. Taking cell class identity into account increased the degree to which our results replicated in an independent dataset as well as their correspondence with known modes of ion channel function based on the literature. We also found a smaller set of genes whose relationships to electrophysiological or morphological properties appear to be specific to either excitatory or inhibitory cell types. Next, using data from Patch-seq experiments, allowing simultaneous...
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biorxivpreprint: Transcriptomic correlates of electrophysiological and morphological diversity within and across neuron types https://t.co/iGgYrYV2po #bioRxiv
biorxiv_neursci: Transcriptomic correlates of electrophysiological and morphological diversity within and across neuron types https://t.co/FSND7nqSay #biorxiv_neursci
CyrilPedia: 'In summary, we have identified a number of relationships between gene expression, electrophysiology, and morphology that provide testable hypotheses for future studies.' https://t.co/DMShh4W4Eg
Claire_Bomkamp: Hey so @neuronJoy and I and some other people did a thing? We got to play with a couple of really cool (and publicly accessible!) datasets from @AllenInstitute https://t.co/tSFkQiCe0o
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Repository: transcriptomic_correlates
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2.036 Mikeys
#6. Individual differences in the effects of priors on perception: a multi-paradigm approach
Kadi Tulver, Jaan Aru, Renate Rutiku, Talis Bachmann
The present study investigated individual differences in how much subjects rely on prior information, such as expectations or knowledge, when faced with perceptual ambiguity. The behavioural performance of forty-four participants was measured on four different visual paradigms (Mooney face recognition, illusory contours, blur detection and representational momentum) in which priors have been shown to affect perception. In addition, questionnaires were used to measure autistic and schizotypal traits in the non-clinical population. We hypothesized that someone who in the face of ambiguous or noisy perceptual input relies heavily on priors, would exhibit this tendency across a variety of tasks. This general pattern would then be reflected in high pairwise correlations between the behavioural measures and an emerging common factor. On the contrary, our results imply that there is no single factor that explains the individual differences present in the aforementioned tasks, as further evidenced by the overall lack of robust...
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biorxivpreprint: Individual differences in the effects of priors on perception: a multi-paradigm approach https://t.co/aFhn3G69me #bioRxiv
biorxiv_neursci: Individual differences in the effects of priors on perception: a multi-paradigm approach https://t.co/Nv1btCyOzx #biorxiv_neursci
PavelProsselkov: "...the effects of priors likely originate from several independent sources and it is important to consider the role of specific tasks and stimuli more carefully when reporting effects of priors on perception" https://t.co/AaIF92kZyN
jaaanaru: Which priors do you mean? We found that there is no general factor of "relying on priors" in different visual tasks: priors depend on the task. Hence, making general claims about a particular (patient) population having strong/weak priors seems unwarranted https://t.co/iP0JZmGWfg
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2.035 Mikeys
#7. Transposable elements drive reorganisation of 3D chromatin during early embryogenesis
Kai Kruse, Noelia Diaz, Rocio Enriquez-Gasca, Xavier Gaume, Maria-Elena Torres-Padilla, Juan M Vaquerizas
Transposable elements are abundant genetic components of eukaryotic genomes with important regulatory features affecting transcription, splicing, and recombination, among others. Here we demonstrate that the Murine Endogenous Retroviral Element (MuERV-L/MERVL) family of transposable elements drives the 3D reorganisation of the genome in the early mouse embryo. By generating Hi-C data in 2-cell-like cells, we show that MERLV elements promote the formation of insulating domain boundaries throughout the genome in vivo and in vitro. The formation of these boundaries is coupled to the upregulation of directional transcription from MERVL, which results in the activation of a subset of the gene expression programme of the 2-cell stage embryo. Domain boundaries in the 2-cell stage embryo are transient and can be remodelled without undergoing cell division. Remarkably, we find extensive inter-strain MERVL variation, suggesting multiple non-overlapping rounds of recent genome invasion and a high regulatory plasticity of genome organisation....
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generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine Endogenous Retroviral Element (MuERV-L/MERVL) promote formation of insulating domain boundaries coupled to upregulation of directional MERVL transcription https://t.co/VXwNJcrrSg
vaquerizasjm: 1/ Excited to announce our latest work looking at the role of transposable elements in regulating 3D chromatin during early mammalian development, out now in @biorxivpreprint @vaquerizas_lab #3DGenome #transposons #early_mouse_development https://t.co/M67x4vZu7D
vaquerizasjm: 1/ Excited to announce out latest work looking at the role of transposable elements in regulating 3D chromatin during early mammalian development, out now in @biorxivpreprint @vaquerizas_lab #3DGenome #transposons #early_mouse_development https://t.co/M67x4vZu7D
vaquerizas_lab: Our latest @vaquerizas_Lab results are out in @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis. Work led by Kai Kruse (@kaukrise) in collaboration with the Torres-Padilla lab. https://t.co/Gi02JnSCJA Summary below: (1/n) https://t.co/nOch6X7JYK
vaquerizas_lab: Really nice work from Kai Kruse (@kaukrise), Noelia Díaz (@NoeliaDiaz27), and Rocio Enriquez-Gasca, and a fun collaboration with the Torres-Padilla lab (@epigeneticsHMGU) (8/8) https://t.co/Gi02JnSCJA
mirimiam: “MERLV [transposable] elements promote the formation of insulating domain boundaries throughout the genome in vivo and in vitro. The formation of these boundaries is coupled to the upregulation of directional transcription from MERVL” https://t.co/uu8QtnaBbg
Dariloops: Transposable elements promoting the formation of chromatin boundaries!!! Well done @vaquerizas_lab https://t.co/CF9yeDUGcK
LlewellynGreen: A lot of interesting stuff to process in this one: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis (mouse) https://t.co/gt09mPt2aV (4)
kwartiov: Evidence for the functions of "junk DNA". Are the ancient viruses responsible for development? Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/uX1PJBwj3B
etrompouki: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis | bioRxiv https://t.co/wxYSmtu685
arianelismer: MERVL transposable elements regulate 3D chromatin conformation in the 2-cell embryo by transiently forming insulating domain boundaries. Really cool functional insight on the role of TEs during early embryogenesis!! https://t.co/O68y1zdgj2
minjaf: Really fascinating story from @vaquerizas_lab! MERVL transposable elements shape 3D genome architecture in mouse blastomeres. Waiting follow-up about how exactly Dux1 and/or MERVL induce insulation, and most important, what is it's functional meaning? https://t.co/zQomApwx4i https://t.co/FGci48h46w
PromPreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/kpcoVpWdSK
vaschetto_luis: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/Ggmd8q1yZS
BioRxivCurator: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/Yv4NOoPLhr
Julie_B92: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Alfons_Valencia: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
NatureSMB: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
3D_Genome: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
CedricFeschotte: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Team_Thomma: RT @biorxiv_genomic: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/sOKybIlfeQ #biorxi…
grawoig: RT @PromPreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/kpcoVpWdSK
grawoig: RT @etrompouki: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis | bioRxiv https://t.co/wxYSmtu685
Noncodarnia: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
timtriche: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
DonnellyCentre: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
EpigeneticsGuy: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
elenagomezdiaz: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
tylervkent: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
vaquerizasjm: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
ameliacervera: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
JuliaHorsfield: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Finnsense: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
tsubu2an: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
jsteward2930: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
laloizquierdo90: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
lambros_f: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
mirimiam: RT @Dariloops: Transposable elements promoting the formation of chromatin boundaries!!! Well done @vaquerizas_lab https://t.co/CF9yeDUGcK
PablixSil: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
marcotrizzino: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
RobKlose: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Elsie_youlater: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
StanInScience: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
GJCVeenstra: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
mate_palfy: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
nzradu: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
i_jerko: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
_diegobalboa_: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
BioGibberish: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
drosoigmm: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
drosoigmm: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
PgpMartin: RT @Dariloops: Transposable elements promoting the formation of chromatin boundaries!!! Well done @vaquerizas_lab https://t.co/CF9yeDUGcK
sudhirthakurela: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
PrecursorCell: RT @etrompouki: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis | bioRxiv https://t.co/wxYSmtu685
a_z_usa__: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
tsagakis_bio: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
awuebersohn: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Nina_CabezasW: RT @etrompouki: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis | bioRxiv https://t.co/wxYSmtu685
Moreno_AA: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
AGuleren: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
quirze92: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Milana_FM: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
CantoneIrene: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
ilyavkirov: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
the_beckhamin: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
AntoineZalc: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
Qenvio: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Chris_G_Smith1: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
cjy8709: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
ChingHua_Shih: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
psaima: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
MO_BAUDEMENT: RT @Dariloops: Transposable elements promoting the formation of chromatin boundaries!!! Well done @vaquerizas_lab https://t.co/CF9yeDUGcK
AlejoFraticelli: RT @etrompouki: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis | bioRxiv https://t.co/wxYSmtu685
Circe777: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
lunazere9: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
SaraMaciasRNA: RT @biorxivpreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/3MagNlIBUG #bioRxiv
drjaydutt: RT @biorxiv_genomic: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/sOKybIlfeQ #biorxi…
Adamu56106323: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
rozesshr: RT @PromPreprint: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/kpcoVpWdSK
Feli_Bas: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
bgbrink: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Can_mi_lan_o: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
alexia_grasso: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
ChongjingX: RT @biorxiv_genomic: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/sOKybIlfeQ #biorxi…
StephaneBoissi1: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
WeltnerJ: RT @generegulation: Transposable elements drive reorganisation of 3D chromatin during early embryogenesis https://t.co/OxOcNccoVG Murine En…
Github
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Sample Sizes : [15, 30, 1050000]
Authors: 6
Total Words: 13629
Unqiue Words: 3754

2.031 Mikeys
#8. Managing genomic variant calling workflows with Swift/T
Azza Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal Fadlelmola, Daniel Katz, Katherine Kendig, Matthew Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew Weber, Jennie Zermeno, Justin Wozniak, Liudmila Sergeevna Mainzer
Genomic variant discovery is frequently performed using the GATK Best Practices variant calling pipeline, a complex workflow with multiple steps, fans/merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Here we describe a wrapper for the GATK-based variant calling workflow using the Swift/T parallel scripting language. Standard built-in features include the flexibility to split by chromosome before variant calling, optionally permitting the analysis to continue when faulty samples are detected, and allowing users to analyze multiple samples in parallel within each cluster node. The use of Swift/T conveys two key advantages: (1) Thanks to the embedded ability of Swift/T to transparently operate in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.,) a single workflow is trivially portable across numerous clusters; (2) The leaf...
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biorxivpreprint: Managing genomic variant calling workflows with Swift/T https://t.co/PyQZMZ8RFN #bioRxiv
biorxiv_bioinfo: Managing genomic variant calling workflows with Swift/T https://t.co/sutP7skG8U #biorxiv_bioinfo
razoralign: Managing genomic variant calling workflows with Swift/T: https://t.co/ipNgxhVEQY https://t.co/TEwPa9VaMi
MrsLaviniaG: RT @biorxiv_bioinfo: Managing genomic variant calling workflows with Swift/T https://t.co/sutP7skG8U #biorxiv_bioinfo
francois_sabot: RT @biorxiv_bioinfo: Managing genomic variant calling workflows with Swift/T https://t.co/sutP7skG8U #biorxiv_bioinfo
ChongjingX: RT @biorxiv_bioinfo: Managing genomic variant calling workflows with Swift/T https://t.co/sutP7skG8U #biorxiv_bioinfo
Github
Repository: Swift-T-Variant-Calling
User: ncsa
Language: Swift
Stargazers: 2
Subscribers: 6
Forks: 1
Open Issues: 6
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Sample Sizes : None.
Authors: 14
Total Words: 10258
Unqiue Words: 3918

2.029 Mikeys
#9. Structural Insights into GluK3-kainate Receptor Desensitization and Recovery
Jyoti Kumari, Rajesh Vinnakota, Janesh Kumar
GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play key role in regulation of synaptic transmission. For better understanding of structural changes that underlie receptor recovery from desensitized state, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. We show that receptor recovery from desensitization requires major rearrangements of the ligand binding domains (LBD) while the amino terminal (ATD) and transmembrane domains remain virtually unaltered. While, the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a partially recovered state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using these structures as guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating...
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emeKato: Structural Insights into GluK3-kainate Receptor Desensitization and Recovery https://t.co/0fU0S5xxi3 インド国内からの膜タンパクcryoEM構造論文って初めて見た気がする。acknowledgmentを見る限り、データはここで取った模様(https://t.co/gJe6XUX63I)。なおlastの人はMark Mayer研出身。
tokarev331: RT @emeKato: Structural Insights into GluK3-kainate Receptor Desensitization and Recovery https://t.co/0fU0S5xxi3 インド国内からの膜タンパクcryoEM構造論文っ…
JonnyWalker0806: RT @emeKato: Structural Insights into GluK3-kainate Receptor Desensitization and Recovery https://t.co/0fU0S5xxi3 インド国内からの膜タンパクcryoEM構造論文っ…
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Sample Sizes : None.
Authors: 3
Total Words: 12670
Unqiue Words: 3454

2.028 Mikeys
#10. Cysteine modification can gate non-equilibrium conformational dynamics during enzyme catalysis
Medhanjali DasGupta, Dominik Budday, Peter Madzelan, Javier Seravalli, Brandon Hayes, Raymond G. Sierra, Roberto Alonso-Mori, Aaron S. Brewster, Nicholas K. Sauter, Gregory A. Applegate, Virendra Tiwari, David B. Berkowitz, Michael C. Thompson, James S. Fraser, Michael E. Wall, Henry van den Bedem, Mark A. Wilson
Post-translational modification of cysteine residues can regulate protein function and is essential for catalysis by cysteine-dependent enzymes. Covalent modifications neutralize charge on the reactive cysteine thiolate anion and thus alter the active site electrostatic environment. Although a vast number of enzymes rely on cysteine modification for function, precisely how altered structural and electrostatic states of cysteine affect protein dynamics remains poorly understood. Here we use X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent modification of the active site cysteine residue in isocyanide hydratase (ICH) affects the protein conformational ensemble. ICH exhibits a concerted helical displacement upon cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained residue Ile152. The mobile helix samples alternative conformations in crystals exposed to synchrotron X-ray radiation due to the...
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Tweets
LivingMatterLab: Check out this new preprint https://t.co/MauC4zgiPz by Henry, James, and Mark on #enzyme dynamics! https://t.co/QZem9zdIir
HvandenBedem: New preprint https://t.co/X3RiZ6sbwP w/ Mark Wilson & @fraser_lab! We use (serial) X-ray crystallography, computation, and enzyme kinetics to characterize isocyanide hydratase (ICH). ICH samples an extraordinarily wide-spread and well-resolved conformational ensemble in xtals https://t.co/8YRAAtKXcd
fraser_lab: RT @HvandenBedem: New preprint https://t.co/X3RiZ6sbwP w/ Mark Wilson & @fraser_lab! We use (serial) X-ray crystallography, computation, an…
MattChallacombe: RT @HvandenBedem: New preprint https://t.co/X3RiZ6sbwP w/ Mark Wilson & @fraser_lab! We use (serial) X-ray crystallography, computation, an…
Jackson_Lab: RT @HvandenBedem: New preprint https://t.co/X3RiZ6sbwP w/ Mark Wilson & @fraser_lab! We use (serial) X-ray crystallography, computation, an…
_amelie_rocks: RT @HvandenBedem: New preprint https://t.co/X3RiZ6sbwP w/ Mark Wilson & @fraser_lab! We use (serial) X-ray crystallography, computation, an…
DominikBudday: RT @HvandenBedem: New preprint https://t.co/X3RiZ6sbwP w/ Mark Wilson & @fraser_lab! We use (serial) X-ray crystallography, computation, an…
Github
None.
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None.
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Sample Sizes : None.
Authors: 17
Total Words: 11070
Unqiue Words: 3317

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