cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1604900
title: Supplementary Table 2.1.xls

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604901
title: Supplementary Table 2.2.xls

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604898
title: Supplementary Table 3.9.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604900.v1
title: Supplementary Table 2.1.xls

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604898.v1
title: Supplementary Table 3.9.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604901.v1
title: Supplementary Table 2.2.xls

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604896
title: Supplementary Table 3.5.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604897
title: Supplementary Table 3.10.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604893
title: De novo genes in chimpanzee - Origins of de novo genes in human and chimpanzee

description: GTF with the exonic coordinates of de novo genes in chimpanzee
DOI: 10.6084/m9.figshare.1604895
title: Supplementary Table 3.6.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604899.v1
title: Supplementary Table 3.7.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604897.v1
title: Supplementary Table 3.10.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604892
title: De novo genes in human - Origins of de novo genes in human and chimpanzee

description: GTF with the exonic coordinates of de novo genes in human
DOI: 10.6084/m9.figshare.1604896.v1
title: Supplementary Table 3.5.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604890
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis.<br>All rights reserved<br>© 2015 Pallab Bhowmick<br>Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604891
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604895.v1
title: Supplementary Table 3.6.xlsx

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604890.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis.<br>All rights reserved<br>© 2015 Pallab Bhowmick<br>Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604891.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604893.v1
title: Origins of de novo genes in human and chimpanzee

description: GTF with the exonic coordinates of de novo genes in chimpanzee
DOI: 10.6084/m9.figshare.1604889
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604886
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604887
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604888
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604885
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604889.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604885.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604887.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604888.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604886.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604879
title: Increased DUX4 expression during muscle differentiation correlates with decreased SMCHD1 protein levels at D4Z4

description: Facioscapulohumeral muscular dystrophy is caused by incomplete epigenetic repression of the transcription factor DUX4 in skeletal muscle. A copy of <i>DUX4</i> is located within each unit of the D4Z4 macrosatellite repeat array and its derepression in somatic cells is caused by either repeat array contraction (FSHD1) or by mutations in the chromatin repressor SMCHD1 (FSHD2). While DUX4 expression has thus far only been detected in FSHD muscle and muscle cell cultures, and increases with <i>in vitro</i> myogenic differentiation, the D4Z4 chromatin structure has only been studied in proliferating myoblasts or non-myogenic cells. We here show that SMCHD1 protein levels at D4Z4 decline during muscle cell differentiation and correlate with DUX4 derepression. In FSHD2, but not FSHD1, the loss of SMCHD1 repressor activity is partially compensated by increased Polycomb Repressive Complex 2 (PRC2)–mediated H3K27 trimethylation at D4Z4, a situation that can be mimicked by SMCHD1 knockdown in control myotubes. In contrast, moderate overexpression of SMCHD1 results in DUX4 silencing in FSHD1 and FSHD2 myotubes demonstrating that DUX4 derepression in FSHD is reversible. Together, we show that in FSHD1 and FSHD2 the decline in SMCHD1 protein levels during muscle cell differentiation renders skeletal muscle sensitive to DUX4.
DOI: 10.6084/m9.figshare.1604879.v1
title: Increased DUX4 expression during muscle differentiation correlates with decreased SMCHD1 protein levels at D4Z4

description: Facioscapulohumeral muscular dystrophy is caused by incomplete epigenetic repression of the transcription factor DUX4 in skeletal muscle. A copy of <i>DUX4</i> is located within each unit of the D4Z4 macrosatellite repeat array and its derepression in somatic cells is caused by either repeat array contraction (FSHD1) or by mutations in the chromatin repressor SMCHD1 (FSHD2). While DUX4 expression has thus far only been detected in FSHD muscle and muscle cell cultures, and increases with <i>in vitro</i> myogenic differentiation, the D4Z4 chromatin structure has only been studied in proliferating myoblasts or non-myogenic cells. We here show that SMCHD1 protein levels at D4Z4 decline during muscle cell differentiation and correlate with DUX4 derepression. In FSHD2, but not FSHD1, the loss of SMCHD1 repressor activity is partially compensated by increased Polycomb Repressive Complex 2 (PRC2)–mediated H3K27 trimethylation at D4Z4, a situation that can be mimicked by SMCHD1 knockdown in control myotubes. In contrast, moderate overexpression of SMCHD1 results in DUX4 silencing in FSHD1 and FSHD2 myotubes demonstrating that DUX4 derepression in FSHD is reversible. Together, we show that in FSHD1 and FSHD2 the decline in SMCHD1 protein levels during muscle cell differentiation renders skeletal muscle sensitive to DUX4.
DOI: 10.6084/m9.figshare.1604873
title: Gaussian Job Archive for C6H20O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604869
title: H-reflex gain during postural loaded locomotion

description: This file comprises the data presented according to the results of a paper published in PLoS One (Liang and Brown, 2015).
DOI: 10.6084/m9.figshare.1604870
title: Data from Zimmerman and Vitousek 2012

description: Processed fungal endophyte community and environmental metadata from Zimmerman and Vitousek 2012.
DOI: 10.6084/m9.figshare.1604869.v1
title: H-reflex gain during postural loaded locomotion

description: This file comprises the data presented according to the results of a paper published in PLoS One (Liang and Brown, 2015).
DOI: 10.6084/m9.figshare.1604873.v1
title: Gaussian Job Archive for C6H20O8

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1604870.v1
title: Data from Zimmerman and Vitousek 2012

description: Processed fungal endophyte community and environmental metadata from Zimmerman and Vitousek 2012.
DOI: 10.6084/m9.figshare.1604827
title: Semi-supervised Multi-View Learning for Gene Network Reconstruction

description: Semi-supervised Multi-View Learning for Gene Network Reconstruction SynTReN Data: E.coli and Yeast sub-networks, generated expression data and gold standards (Input_Datasets.zip) Interactions predicted by base methods (Base_Method_Predictions.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK.zip) Dream5 Data: Expression data and gold standards provided by Marbach et al. 2012 [1] (Input_Datasets_D5.zip) Interactions predicted by the considered DREAM5 base methods provided by Marbach et al. 2012 [1] (Base_Method_Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with PCA (Predictions_D5.zip) Interactions predicted by our approach - Clustering performed with K-means (PredictionsK_D5.zip) <em>[1] Marbach, D., Costello, J. C., Kuffner, R., Vega, N. M., Prill, R. J., Camacho, D. M., Allison, K. R., Kellis, M., Collins, J. J., and Stolovitzky, G., Wisdom of crowds for robust gene network inference, Nature Methods, 9, 796-804, 2012.</em>
DOI: 10.6084/m9.figshare.1604854
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.
DOI: 10.6084/m9.figshare.1604826
title: miR-155 targets Caspase-3 mRNA in activated macrophages

description: To secure the functionality of activated macrophages in the innate immune response, efficient life span control is required. Recognition of bacterial lipopolysaccharides (LPS) by toll-like receptor 4 (TLR4) induces downstream signaling pathways, which merge to induce the expression of cytokine genes and anti-apoptotic genes. MicroRNAs (miRNAs) have emerged as important inflammatory response modulators, but information about their functional impact on apoptosis is scarce. To identify miRNAs differentially expressed in response to LPS, cDNA libraries from untreated and LPS-activated murine macrophages were analyzed by deep sequencing and regulated miRNA expression was verified by Northern blotting and qPCR. Employing TargetScan<sup>TM</sup> we identified CASPASE-3 (CASP-3) mRNA that encodes a key player in apoptosis as potential target of LPS-induced miR-155. LPS-dependent primary macrophage activation revealed TLR4-mediated enhancement of miR-155 expression and CASP-3 mRNA reduction. Endogenous CASP-3 and cleaved CASP-3 protein declined in LPS-activated macrophages. Accumulation of miR-155 and CASP-3 mRNA in miRNA-induced silencing complexes (miRISC) was demonstrated by ARGONAUTE 2 (AGO2) immunoprecipitation. Importantly, specific antagomir transfection effectively reduced mature miR-155 and resulted in significantly elevated CASP-3 mRNA levels in activated macrophages. <i>In vitro</i> translation assays demonstrated that the target site in the CASP-3 mRNA 3'UTR mediates miR-155-dependent Luciferase reporter mRNA destabilization. Strikingly, Annexin V staining of macrophages transfected with antagomir-155 and stimulated with LPS prior to staurosporine (SSP) treatment implied that LPS-induced miR-155 prevents apoptosis through CASP-3 mRNA down-regulation. In conclusion, we report that miR-155-mediated CASP-3 mRNA destabilization in LPS-activated RAW 264.7 macrophages suppresses apoptosis, as a prerequisite to maintain their crucial function in inflammation.
DOI: 10.6084/m9.figshare.1604854.v1
title: The role of structural disorder in the degradation signal in the ubiquitin-proteasome pathway

description: These are supporting information related to PhD thesis. All rights reserved © 2015 Pallab Bhowmick Apart from any fair dealing for the purposes of research, private study, criticism or review, this publication may not be reproduced, stored in a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording, scanning, or otherwise), without prior written permission of the author.