A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Filters
A review of connectivity map and computational approaches in pharmacogenomics
2017
Briefings in Bioinformatics
Preserved Fulltext
He has been involved in development of computational tools and software for systems biology using advanced methods of signal processing and statistics. ...
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics ...
Acknowledgment For professional proof reading of the manuscript we would like to thank B arbara Mac ıas Sol ıs. ...
doi:10.1093/bib/bbw112
pmid:28069634
pmcid:PMC5952941
fatcat:7dpcxwe2obbmnpl6geslg4gzp4
Integrating adverse outcome pathways (AOPs) and high throughput in vitro assays for better risk evaluations, a study with drug-induced liver injury (DILI)_suppl
2019
ALTEX: Alternatives to Animal Experimentation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
On the other hand, mechanistic knowledge has always been critical for toxicological evaluations and should not be ignored even with the increasing availability of data. ...
AOPs were also used effectively to select a subset of assays from the Tox21 and L1000 projects as the predictors in predictive modeling of DILI risk. ...
Rui Xiong, Qiang Gu, and two anonymous reviewers for valuable comments. The authors also thank Joanne Berger, FDA Library, for manuscript editing assistance. ...
doi:10.14573/altex.1908151s
fatcat:ukgkouqrtfhathkaiterm3obhm
Systematic Quality Control Analysis of LINCS Data
2016
CPT: Pharmacometrics & Systems Pharmacology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
This work was supported by National Institutes of Health DK102694, GM10448301, and LM011945. ...
METHODS
Materials general In this study, level 3 data of the normalized profiles are used for the quality control data analysis. ...
Methods The flow of data processing and analysis is shown in Figure 1 . ...
doi:10.1002/psp4.12107
pmid:27796074
pmcid:PMC5192966
fatcat:2xjs27dtm5hptm7zy7ktc2q244
Signatures of cell death and proliferation in perturbation transcriptomics data - from confounding factor to effective prediction
[article]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
By linking perturbation transcriptomics data from the LINCS-L1000 project with cell viability phenotypic information upon genetic (from Achilles project) and chemical (from CTRP screen) perturbations for ...
AbstractTranscriptomics perturbation signatures are valuable data sources for functional genomic studies. ...
Small scale studies (comprehensively collected in (Wang et al., 2016) ), and the original Connectivity Map study (Lamb et al., 2006) provide rich perturbation signature data. ...
doi:10.1101/454348
fatcat:r7gd7tv6mfafjcvq7emr7tsily
Drug-induced adverse events prediction with the LINCS L1000 data
2016
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Using various benchmarking methods, we show that the integration of GE data with the CS of the drugs can significantly improve the predictability of ADRs. ...
Finally, we applied the classifier to all >20 000 small-molecules profiled, and developed a web portal for browsing and searching predictive small-molecule/ADR connections. ...
This classification method was selected after evaluating various alternatives including Random Forest (RF), Support Vector Machines (SVMs) and a few others (see Supplementary Methods). ...
doi:10.1093/bioinformatics/btw168
pmid:27153606
pmcid:PMC4965635
fatcat:sdtvuxsdgzg27k56oiudnahhvq
Integrating adverse outcome pathways (AOPs) and high throughput in vitro assays for better risk evaluations, a study with drug-induced liver injury (DILI)
2019
ALTEX: Alternatives to Animal Experimentation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
On the other hand, mechanistic knowledge has always been critical for toxicological evaluations and should not be ignored even with the increasing availability of data. ...
AOPs were also used effectively to select a subset of assays from the Tox21 and L1000 projects as the predictors in predictive modeling of DILI risk. ...
The authors also thank Joanne Berger, FDA Library, for manuscript editing assistance. ...
doi:10.14573/altex.1908151
pmid:31707421
fatcat:ows5kyjqr5frxpiourlm527m2m
SigCom LINCS: data and metadata search engine for a million gene expression signatures
2022
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up and down genes, a gene set, a single gene, or any search term. ...
When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO), connections between drugs, genes, pathways ...
All L1000 CRISPR knockdown signatures for a given TF were computed using the CD method, and then each of the three other methods, using the same perturbation and control profiles. ...
doi:10.1093/nar/gkac328
pmid:35524556
pmcid:PMC9252724
fatcat:7gjogoo6ijd3xki2ihmefprtye
Centralized scientific communities are less likely to generate replicable results
2019
eLife
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Here we identify a large sample of published drug-gene interaction claims curated in the Comparative Toxicogenomics Database (for example, benzo(a)pyrene decreases expression of SLC22A3) and evaluate these ...
claims by connecting them with high-throughput experiments from the LINCS L1000 program. ...
Library for Python (Pymnet); and T Natoli (Broad Institute) for advice on NIH LINCS L1000 data. ...
doi:10.7554/elife.43094
pmid:31264964
pmcid:PMC6606034
fatcat:tzqcodwqhbfzro2lulg6aaz7ra
Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction
2019
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Transcriptional perturbation signatures are valuable data sources for functional genomics. ...
We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 ...
B.S. would like to thank for the usage of MTA Cloud (https://cloud.mta.hu/) that significantly helped us achieving the results published in this paper. ...
doi:10.1093/nar/gkz805
pmid:31552418
pmcid:PMC6821211
fatcat:liq4rot2jbao5oop7ufybthi5a
Transforming L1000 profiles to RNA-seq-like profiles with deep learning
2022
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Such a dataset is invaluable for the discovery of drug and target candidates and for inferring mechanisms of action for small molecules. ...
The lack of full genome coverage limits knowledge discovery for half of the human protein coding genes, and the potential for integration with other transcriptomics profiling data. ...
Mark Keller from the University of Wisconsin at Madison for useful suggestions. ...
doi:10.1186/s12859-022-04895-5
pmid:36100892
pmcid:PMC9472394
fatcat:cgnytzeimfczdgvihsdehezfoa
Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates
2021
Human Molecular Genetics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
(L1000 Connectivity Map) that have inverse expression profiles compared to tissue-specific genetically regulated gene expression. ...
for drug development. ...
Acknowledgements We acknowledge the members of the COVID-19 Host Genetics Initiative for kindly releasing the GWAS summary statistics. ...
doi:10.1093/hmg/ddab049
pmid:33577681
pmcid:PMC7928862
fatcat:yjhi3uga3jc27i6uctish7wltm
A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles
[article]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs and disease states are connected by virtue of common gene-expression signatures. ...
Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high throughput reduced representation expression profiling method that ...
The characterization methods enable nuanced analyses of L1000 signatures in and of themselves, while the connectivity methods provide a framework by which external gene sets or L1000 signatures can be ...
doi:10.1101/136168
fatcat:lm5obdt2hjaj3kraonfe6fggoq
Chemical-induced Gene Expression Ranking and its Application to Pancreatic Cancer Drug Repurposing
[article]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
Several methods have been proposed to predict missing values in gene expression data. ...
Furthermore, a new drug screening pipeline based on CIGER is proposed to select approved or investigational drugs for the potential treatments of pancreatic cancer. ...
Second, due to the noisy issue in LINCS L1000 dataset, we can only utilize a small subset of this data for training thereby hindering the prediction performance of our method for de novo chemicals. ...
doi:10.1101/2021.12.13.472490
fatcat:ynhblaob45dt5hwuiu2kdmyzni
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles
2017
Cell
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We previously piloted the concept of a Connectivity Map (CMap), whereby genes, drugs and disease states are connected by virtue of common gene-expression signatures. ...
Here, we report more than a 1,000-fold scale-up of the CMap as part of the NIH LINCS Consortium, made possible by a new, low-cost, high throughput reduced representation expression profiling method that ...
Shapiro for helpful discussions. We thank Luminex Corporation for support with the FlexMap 3D system, and Qiagen for assistance with TurboCapture kits. ...
doi:10.1016/j.cell.2017.10.049
pmid:29195078
pmcid:PMC5990023
fatcat:yngteqimdjfcjk3asuitzddatm
Estimating Intraclonal Heterogeneity and Subpopulation Changes from Perturbational Bulk Gene Expression Profiles in LINCS L1000 CMap by Premnas
[article]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
The connectivity among signatures upon perturbations curated in the CMap library provides a valuable resource for understanding therapeutic pathways and biological processes associated with the drugs and ...
By recovering the information of subpopulation changes upon perturbation, the potentials of searching for drug cocktails and drug-resistant/susceptible subpopulations with CMap L1000 were further explored ...
Including as many single-cell transcriptomic data of the cell line of interest for a more comprehensive analysis should be taken for all further research applying Premnas. ...
doi:10.1101/2021.08.10.455781
fatcat:opvnpbnslbegri65ggvwqm7r6q
« Previous
Showing results 1 — 15 out of 391 results