Editorial in Science Translational Medicine

Posted on: May 23rd, 2016 by Sherry Jenkins No Comments

Reproducibility will only come with data liberation

In a recent editorial in Science Translational Medicine, Mohammed AlQuraishi and Peter Sorger from the HMS LINCS Center make the case for improving accessibility and usability of published experimental data of all data types.

Citation: AlQuraishi M, Sorger PK. Reproducibility will only come with data liberation. Sci Transl Med. 2016 May 18;8(339):339ed7. PMID: 27194726

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SEP-L1000

Posted on: May 20th, 2016 by Sherry Jenkins No Comments

Side effect prediction based on L1000 data

A web portal for browsing and searching predictive small-molecule/ADR connections

logo-sepSEP-L1000 serves the results of the predicted ADRs for the drugs and small-molecule compounds profiled in the LINCS L1000 project. A network of predictive ADRs was constructed based on their drug similarity and visualized using a stacked bubble chart. Each drug and ADR has a dedicated page with a list of the relevant predictions and external links.

Citation: Wang Z, Clark NR, Ma’ayan A. Drug-induced adverse events prediction with the LINCS L1000 dataBioinformatics 2016 PMID: 27153606

GR Metrics Calculator and Browser

Posted on: May 20th, 2016 by Sherry Jenkins No Comments

Drug-response studies play an important role in both preclinical and clinical research, but such studies are complicated by differences in cell growth rates across samples and conditions. To improve the value and reliability of such studies, new metrics for parameterizing drug response were developed and published in Nature Methods by the HMS LINCS Center. The online GR tools were developed by the BD2K-LINCS Data Coordination and Integration Center.

Citation: Hafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugsNature Methods 2016. PMID: 27135972

GR Metrics Calculator and Browser

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HMS LINCS Center: Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs

Posted on: May 17th, 2016 by Sherry Jenkins No Comments

hafner-natmethods-2016The HMS LINCS Center’s most recent study (Hafner, Niepel et al (2016)) which describes new “GR” metrics that account for variation in cell growth when quantifying cellular dose response to perturbagens, was published in Nature Methods. Explore the publication in more detail, or, through the online GR Browser developed in collaboration with the BD2K-LINCS DCIC, calculate GR metrics from your own data and browse several available LINCS dose-response datasets.

Hafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods. 2016 May 2. doi: 10.1038/nmeth.3853. PMID: 27135972

Cover of Molecular and Cellular Proteomics: Phosphosignatures from the P100 Sentinel Assay

Posted on: May 2nd, 2016 by Sherry Jenkins No Comments

A publication from the LINCS Proteomic Characterization Center for Signaling and Epigenetics was highlighted on the cover of the May 2016, 15 (5) issue of Molecular and Cellular Proteomics.

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A set of kinase inhibitors directed at known pathways (top) were introduced to cells. Phosphosignatures from the novel P100 sentinel assay are shown after 3, 6, or 24 hours of treatment (middle). Correlation of all samples demonstrates strong signals in the assay, and off-diagonal correlation reinforces the hypothesized modularity of the pathway into MAPK, PI3K/mTOR, and Cell Cycling modules (bottom).

For more details, see the article: Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, Creech AL, Hu R, Lam D, Davison D, Pino L, Qiao JW, Kuhn E, Officer A, Li J, Abbatiello S, Subramanian A, Sidman R, Snyder EY, Carr SA, Jaffe JD. Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes. PMID: 26912667

NIH LINCS Program on Social Media

Posted on: April 25th, 2016 by Sherry Jenkins No Comments

nih lincs ytPlease follow the NIH LINCS Program on social media for information on the consortium’s latest news and data releases! NIH LINCS Program YouTube channel

 

 

 

 

 

 

 

HMS LINCS Center Updates

Posted on: April 6th, 2016 by Sherry Jenkins No Comments

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Dose response metrics were released for the drug combinations tested in the LINCS Pilot Phase Joint Project and analyzed by imaging by the HMS LINCS Center and by L1000 by the Broad LINCS Center.

Three datasets were released that assess the effects of cell plating density on the calculation of dose-response metrics for 6 breast cancer cell lines treated with 12 different kinase inhibitors. See HMS LINCS Dataset #20258 for a comparison of metrics based on standard, cell count-based calculations and metrics based on using newly-derived, growth rate-independent calculations.

New Feature for LINCS Tools: ‘Quick Start with LINCS’

Posted on: March 28th, 2016 by Sherry Jenkins No Comments

 

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The ‘Quick Start with LINCS‘ analysis tool feature enables users to search signatures (L1000CDS2), access data (LINCS Data Portal), analyze data (iLINCS), search transcriptomics (Slicr) and visualize proteomics (piLINCS).

NeuroLINCS Center Releases New Tool: AChroMap

Posted on: March 28th, 2016 by Sherry Jenkins No Comments

4H5rsFt3_400x400AChroMap (accessible chromatin mapper of transcriptional regulators) is a data integration tool for transcriptomic and epigenomic data. This tool generates a list of enriched motifs in open chromatin regions (as assayed by ATAC-seq or DNAseH) for a given set genes. The foreground list of genes are differentially expressed or highly expressed genes and the background list of genes are the rest of the genes in the transcriptomic experiment.

 

LINCS Outreach Meeting 2016 – Video Archive

Posted on: March 23rd, 2016 by Sherry Jenkins No Comments

Molecular Medicine Tri-Conference 2016

Posted on: February 5th, 2016 by Sherry Jenkins No Comments

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On March 8, 2016, as part of the BD2K-LINCS DCIC’s community outreach efforts, Avi Ma’ayan PhD and Stephan Schurer PhD will present in the Informatics channel at the Molecular Medicine Tri-Conference 2016 in San Francisco, CA.

Bioinformatics for Big Data
L1000CDS2: LINCS L1000 Characteristic Direction Signature Search Engine Predicts Kenpaullone as a Potential Therapeutic for Ebola
Avi Ma’ayan, PhD, Icahn School of Medicine at Mount Sinai

Integrated Informatics Driving Translational Research and Precision Medicine
Rational Data-Driven Development of Novel Poly-Pharmacology Small Molecules
Stephan Schurer, PhD, Miller School of Medicine, University of Miami

LINCS Outreach Meeting 2016

Posted on: February 4th, 2016 by Sherry Jenkins No Comments

March 10-11, 2016 | University of California, Irvine

General Info | Agenda | Registration | Meeting Flyer

neuro_outreachThe Library of Integrated Network-based Cellular Signatures (LINCS) program aims to create a network-based understanding of biology by cataloging changes induced by exogenous perturbations on cellular processes through the lens of molecular and morphological profiling signatures. By generating, integrating, and publicly releasing data and tools that indicate how cells respond to various genetic and environmental stressors, the LINCS project will help us gain a more detailed understanding of cell pathways and aid efforts to develop therapies that might restore perturbed pathways and networks to their normal states. Come join us at our first ever Outreach Meeting to see examples of LINCS in action and learn how to effectively work with these unprecedented datasets.

Confirmed Speakers:

  • Walter Koroshetz, NINDS
  • Zak Kohane, Harvard Medical School
  • Henry Rodriguez, NCI
  • Jane Roskams, Allen Institute for Brain Science
  • Fred Gage, The Salk Institute
  • Gustavo Stolovitzky, IBM
  • Phil Nelson, Google
  • Trey Ideker, UCSD

Meet investigators from the LINCS Data and Signature Generation Centers and the BD2K-LINCS Data Coordination and Integration Center to establish collaborations!

Present your work at our poster session! A limited number of travel fellowships are available.

 

The BD2K-LINCS DCIC’s Systems Biology Data Science Symposium 2016

Posted on: January 25th, 2016 by Sherry Jenkins No Comments

On January 19-20, 2016, the first annual Systems Biology Data Science Symposium (SBDSS 2016) at the University of Miami brought together the BD2K-LINCS Data Coordination and Integration Center, local researchers, and outside experts who apply or develop computational systems biology resources. In presentations, a poster reception and several working sessions, the DCIC showcased tools/resources and scientific projects, connected developers with users, and initiated new collaborations.

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Systems Biology Data Science Symposium, Day 1 Presentations:

Keynote Address: Overcoming Cancer Cell Heterogeneity through Epigenetic Therapies
Speaker: Stephen D. Nimer MD, University of Miami

The NIH BD2K Initiative: How it Hopes to Impact Biomedical Research
Ajay Pillai, PhD, Program Director – National Human Genome Research Institute (NHGRI), NIH Program

From Big Data to Knowledge – Experiences in Rare Disease Genomics
Stephan Zuchner, MD, PhD, University of Miami

LINCS Computational Pipelines for Drug Discovery
Avi Ma’ayan, PhD, Icahn School of Medicine at Mount Sinai | BD2K-LINCS DCIC

Uncovering Perturbation Mode of Action with LINCS Data and Tools
Mario Medvedovic, PhD, University of Cincinnati | BD2K-LINCS DCIC

L1K++: Fast and Accurate Pipeline for Processing L1000 Gene Expression Data
Ka Yee Yeung, PhD, University of Washington

Target Predictions using LINCS Perturbation Data
Ziv Bar-Joseph, PhD, Carnegie Mellon University

Disease and Perturbagen Posttranslational Signatures across Multiple Signaling Pathways in Lung Cancer Cell Lines: Analysis of TMT Data Published in PhosphoSitePlus (PSP)
Peter Hornbeck, PhD, Cell Signaling Technology

Building a Culture of Model-driven Drug Discovery at Merck
Chris Waller, PhD, Merck & Co.

Modeling Spinal Cord Injury using Knowledge-Based and Data Driven Approaches
Vance Lemmon, PhD, University of Miami

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles
Aravind Subramanian, PhD, Broad Institute of MIT & Harvard

Systematic Discovery of Drug Targets and Disease Indications using Genetics and Connectivity Map
Pankaj Agarwal, PhD, GlaxoSmithKline

For more information about the SBDSS 2016 and the full agenda, click here.

New LINCS L1000 Tool and updated release of LINCS Data Portal

Posted on: December 22nd, 2015 by Sherry Jenkins No Comments

slicr_L1000

 

 

The BD2K-LINCS DCIC recently released a new tool called Slicr which is a metadata search engine that searches for LINCS L1000 gene expression profiles and signatures matching user’s input parameters. It features download of selected search results as csv files in a zipped folder and visualization of selected results in a 3D scatter plot using PCA or MDS.

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The BD2K-LINCS DCIC recently released an updated version of the LINCS Data Portal which provides a unified interface for searching LINCS dataset packages and reagents

New Release of Enrichr

Posted on: November 19th, 2015 by Sherry Jenkins No Comments

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Updated ChEA library, new LINCS L1000 libraries and Harmonizome Mobile App

In this new release of Enrichr, the BD2K-LINCS DCIC updated their ChIP-X Enrichment Analysis (ChEA) database with gene sets extracted from forty new studies. The previous version is now in the ‘Legacy’ category for provenance.

They also added a new gene set library created from the database of Genotypes and Phenotypes (dbGaP), as well as two new libraries with the up- and down-regulated genes from the L1000 Connectivity Map chemical perturbation profiles from the LINCS Center for Transcriptomics. The previous version of the Connectivity Map Affymetrix data was renamed to Old CMAP.

Please visit the ‘What’s New?‘ section of the Enrichr website for more details about the new release.

Enrichr | BD2K-LINCS DCIC Resources

LINCS In the News

Posted on: November 19th, 2015 by Sherry Jenkins No Comments

nature_outlook_coverGenetics: Big Hopes for Big Data

Jill U. Adam

Nature 527, S108–S109 (19 November 2015) doi:10.1038/527S108a
Published online 18 November 2015

Learn more: http://www.nature.com/nature/journal/v527/n7578_supp/full/527S108a.html

 

BD2K-LINCS DCIC | Accepting applications for 2016 summer research training program

Posted on: November 5th, 2015 by Sherry Jenkins No Comments

dcic_summer_version_nov2

The BD2K-LINCS DCIC Summer Research Training Program in Biomedical Big Data Science is a research intensive ten-week training program for undergraduate and graduate students interested in participating in cutting edge research projects aimed at solving data-intensive biomedical problems. Summer fellows conduct faculty-mentored independent research projects within laboratories affiliated with the Center in the following areas: data integration, dynamic data visualization, machine learning, data harmonization, computational drug discovery, metadata and APIs, knowledge modeling, Bayesian networks and statistical mining.

In summer session 2016, our research training program will be offered at the three sites affiliated with our NIH-funded Center:

Ma’ayan Laboratory of Computational Systems Biology | Icahn School of Medicine at Mount Sinai
Medvedovic Laboratory for Statistical Genomics and Systems Biology | University of Cincinnati
Schurer Laboratory in the Center for Computational Science | University of Miami

Application Deadline: March 4, 2016 at 11:00 PM ET

Program Description | How to Apply

BD2K-LINCS DCIC | Systems Biology Data Science Symposium | January 19-20, 2016

Posted on: September 23rd, 2015 by Sherry Jenkins No Comments

dcic500x375The BD2K-LINCS Data Coordination and Integration Center and the University of Miami will host a two-day Systems Biology Data Science Symposium on January 19-20, 2016 at the University of Miami.

This first Systems Biology Data Science Symposium at the University of Miami will bring together the BD2K-LINCS DCIC, local researchers, and outside experts who apply or develop computational systems biology resources. In presentations of local experts, invited guests and our Center, a poster reception and several working sessions we want to show the tools/resources and scientific projects at the DCIC, connect developers with users, initiate new collaborations and to obtain feedback from expert and casual users of computational systems biology resources. Another important goal of our Center is outreach and education and we invite undergraduate/graduate students and postdoctoral researchers to participate in the symposium.

Detailshttp://lincs-dcic.org/#/2016-data-science-symposium

New Course: Big Data Science with the BD2K-LINCS Data Coordination and Integration Center

Posted on: September 17th, 2015 by Sherry Jenkins No Comments

The BD2K-LINCS Data Coordination and Integration Center (DCIC) launched this MOOC on Coursera on September 15, 2015 which covers various methods of analysis including: unsupervised clustering, gene-set enrichment analyses, data visualization, and supervised machine learning applications to LINCS data.

Go to Coursehttps://www.coursera.org/course/bd2klincs

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Course Summary

The BD2K-LINCS Data Coordination and Integration Center (DCIC) is commissioned to organize, analyze, visualize and integrate this data with other publicly available relevant resources. In this course we will introduce the various Centers that collect data for LINCS, describing the experimental data procedures and the various data types. We will then cover the design and collection of metadata and how metadata is linked to ontologies. We will then cover basic data processing and data normalization methods to clean and harmonize LINCS data. This will follow with a discussion about how the data is served as RESTful APIs and JSON, and for this we will cover concepts from client-server computing. Most importantly, the course will focus on various methods of analysis including: unsupervised clustering, gene-set enrichment analyses, data visualization, and supervised machine learning applications to LINCS data and other relevant Big Data from molecular biomedicine.

New Resource: L1000 Characteristic Direction Signature Search Engine (L1000CDS2)

Posted on: August 17th, 2015 by Sherry Jenkins No Comments

L1000CDS2, developed by Ma’ayan Laboratory for the BD2K-LINCS DCIC, queries gene expression signatures against the LINCS L1000 to identify and prioritize small molecules that can reverse or mimic the observed input expression pattern.

BD2K-LINCS DCIC Resources

Data Standards Update

Posted on: August 17th, 2015 by Sherry Jenkins No Comments

The Data Standards page has been updated to reflect the most recent standards releases in LINCS Production Phase 2.

Data Releases: DToxS, HMS LINCS, LINCS Center for Transcriptomics, LINCS PCCSE, and NeuroLINCS

Posted on: August 13th, 2015 by Sherry Jenkins No Comments

LINCS centers recently released the first wave of data which includes RNA-seq, L1000, P100, SWATH, Cell Viability and Growth, KinomeScan, and RPPA profiling human cell lines treated with many drugs and small molecules.

The data releases and milestones page describes the collections of data released and planned to be released to the public by the LINCS consortium.

Workshop: Interdisciplinary Approaches to Biomedical Data Science Challenges: SAMSI Innovations Lab | July 20-24, 2015

Posted on: August 6th, 2015 by Sherry Jenkins No Comments

Stephan Schurer PhD, BD2K-LINCS Data Coordination and Integration Center, served as a mentor in this workshop to guide scientists in the formation of interdisciplinary projects aimed at developing models, methods, and approaches to overcome biomedical data science challenges. During the course of the workshop, participants were exposed to LINCS resources.  The workshop took place from July 20 to 24, 2015 at the Hamner Conference Center at the NC Biotechnology Center, 15 TW Alexander Drive in Research Triangle Park, North Carolina.

Workshop Summary | Detailed Description

Workshop: Genomic and Computational Approaches for Biomarker and Drug Discovery | June 19, 2015

Posted on: April 13th, 2015 by Sherry Jenkins No Comments

Purpose of this workshop is to bring together (Library of Integrated Network-based Cellular Signatures) LINCS scientists and scientists from the alcohol research community to explore how LINCS resources can facilitate identification of druggable targets and novel and/or repurposed compounds for the treatment of alcohol dependence.

Date | Time | Location

  • Friday, June 19, 2015 from 2-5 PM
  • Grand Hyatt (Room: Travis C/D), San Antonio, TX

Register

  • Please RSVP by May 1, 2015 to Matthew Reilly at reillymt@mail.nih.gov
  • Space is limited to 50 participants

Agenda

Welcome and Opening Remarks
Matthew Reilly PhD and Ajay Pillai PhD, NIH

Hands-on Session: Web Apps and Tools
Session Leaders: Avi Ma’ayan PhD, BD2K-LINCS Data Coordination and Integration Center and Aravind Subramanian PhD, LINCS Center for Transcriptomics

This session will consist of a hands on demonstration of currently available web apps and tools from the LINCS Common Fund program. Participants will learn how to apply these tools to their own research programs. Please bring your laptop computer and gene expression or other genomic data to analyze.

Additional Information

  • Please register and create a lincscloud.org account before the workshop.
  • Your genomics datasets you bring to analyze should be formatted either as (1) official gene symbols or (2) Affymetrix U133A probe IDs. Some of the web tools require a list of both up-regulated and down-regulated gene lists and some of the tools only accept gene symbols.
  • Because the majority of the LINCS datasets use human cell lines, gene sets should be annotated for mammalian species.
  • When you RSVP for the workshop, please indicate your area of expertise: genomics, computational or other.
  • Also, if you already have experience with working with any of the LINCS tools, you are welcome to submit questions/concerns, suggestions or other feedback in advance of the workshop. You can submit your questions etc., to the workshop organizer: Matthew Reilly at reillymt@mail.nih.gov.

Administrative Supplements to Extend the Scope and Reach of LINCS Datasets

Posted on: February 28th, 2015 by Sherry Jenkins No Comments

This notice (NOT-RM-15-102) announces an opportunity to request administrative supplements to existing NIH research grants, to support generation of new data that will also advance the goals of the LINCS program. Please view the funding opportunities page for more details.

Call for External Collaborations with the BD2K-LINCS Data Coordination and Integration Center

Posted on: February 24th, 2015 by Avi Maayan No Comments

The BD2K-LINCS DCIC announces a call for applications for the next round of external data science research projects. The call is for two year projects that would leverage LINCS generated data through application of novel computational methods. For more information, please visit: http://www.lincs-dcic.org/#/edsr. Please visit the funding opportunities page for more details.

LINCS Cell Line Data Integrated into ChEMBL

Posted on: February 20th, 2015 by Sherry Jenkins No Comments

CHEMBL now provides CHEMBL IDs for all cell lines stored in their database and also cross references to the LINCS project.

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LINCS Investigators Present at the AACR Special Conference on Computational and Systems Biology of Cancer

Posted on: February 8th, 2015 by Sherry Jenkins No Comments

February 8-11, 2015
The Fairmont San Francisco
San Francisco, California

Conference Co-Chairpersons
Andrea Califano, Columbia University, New York, New York
Brenda J. Andrews, University of Toronto, Toronto, Ontario, Canada
Peter K. Jackson, Stanford University, Stanford, California

View Program

Spatial Systems Biology and Cancer
Joe W. Gray, MEP LINCS Center

Using Single-cell Pharmacology to Improve Drug Design
Peter K. Sorger, HMS LINCS Center

Lean Data Integration Strategy in Cancer Systems Biology and Systems Pharmacology
Avi Ma’ayan, BD2K-LINCS Data Coordination and Integration Center

Transcriptional Landscape of Drug Response Guides the Design of Specific and Potent Drug Combinations
Marc Hafner, HMS LINCS Center

Spotlight on LINCS Information FramEwork (LIFE)

Posted on: January 28th, 2015 by Sherry Jenkins No Comments

BioGPS Spotlight on the LINCS Information FramEwork (LIFE) which is a novel knowledge-based, extensible information system of interconnected components that leverages semantic-web technologies and domain level ontologies.

The full article is posted here.

NIH Launches a United Ecosystem for Big Data

Posted on: January 8th, 2015 by Sherry Jenkins No Comments

12 Big Data to Knowledge Centers of Excellence Funded

Article about the recently funded Big Data to Knowledge Centers of Excellence was published in Biomedical Computation Review. The Data Integration and Cellular Signaling section of the article describes the BD2K-LINCS Data Coordination and Integration Center’s efforts.

The full article is posted here.

NIH invests almost $32 million to increase utility of biomedical research data

Posted on: October 9th, 2014 by Sherry Jenkins No Comments

News release published by the National Institutes of Health about the Big Data to Knowledge (BD2K) initiative. The BD2K-LINCS Data Coordination and Integration Center is one of the components of the new BD2K awards.

The BD2K-LINCS Data Coordination and Integration Center will be a data coordination center for the NIH Common Fund’s Library of Integrated Network-based Cellular Signatures (LINCS) program, which aims to characterize how a variety of types of cells, tissues and networks respond to disruption by drugs and other factors. The center will support data science research focusing on interpreting and integrating LINCS-generated data from different data types and databases in the LINCS-funded projects. This center is co-funded by BD2K and the NIH Common Fund.

http://www.nih.gov/news/health/oct2014/od-09.htm

NIH awards aim to improve understanding of cell pathways, development of new therapies

Posted on: September 11th, 2014 by Sherry Jenkins No Comments

News release published by the National Institutes of Health about the funding of six Data and Signature Generating Centers for the Library of Integrated Network-based Cellular Signatures (LINCS) program.

The LINCS program aims to catalog and analyze cellular function and molecular activity in response to perturbing agents — such as drugs and genetic factors — that are potentially disruptive to cells. LINCS researchers then will measure the cells’ tiniest molecular and biochemical responses, and use computer analyses to uncover common patterns in these responses — called “signatures.” LINCS data will be freely available to any scientist.

http://www.nih.gov/news/health/sep2014/nhgri-11.htm