Publications

Citation

LINCS Resource Used

Readout/ Assay

Computational Tools

Duan Q, Wang Z, Fernandez NF, Rouillard AD, Tan CM, Benes CH, Ma’ayan A (2014). Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. Bioinformatics 30(22):3289-90.
PMID: 25100688 | PMCID: PMC4221125

Visualization tools, cancer cell line drug response, cross LINCS centers collaboration

LINCS Drug/Cell-line Browser

Olson DE, Udeshi ND, Wolfson NA, Pitcairn CA, Sullivan ED, Jaffe JD, Svinkina T, Natoli T, Lu X, Paulk J, McCarren P, Wagner FF, Barker D, Howe E, Lazzaro F, Gale JP, Zhang YL, Subramanian A, Fierke CA, Carr SA, Holson EB (2014). An unbiased approach to identify endogenous substrates of “histone” deacetylase 8. ACS Chemical Biology 9(10):2210-6.
PMID: 25089360 | PMCID: PMC4201337
Vidović D, Koleti A, Schürer SC (2014). Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action. Frontiers in Genetics 5:342.
PMID: 25324859 | PMCID: PMC4179751

Analysis of LINCS data, data integration

LIFE

Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Vaz Meirelles G, Clark NR, Ma’ayan A (2013). Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14:128.
PMID: 23586463PMCID: PMC3637064

Data integration (LINCS and other data types)

Enrichr

Chen J, Hu Z, Phatak M, Reichard J, Freudenberg JM, Sivaganesan S, and Medvedovic M (2013). Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules. PLoS Computational Biology 9(9): e1003198.
PMID:24039560PMCID: PMC3764016

Data integration (LINCS and other data types)

TREG

Duan Q, Kou Y, Clark NR, Gordonov S, Ma’ayan A (2013). Metasignatures identify two major subtypes of breast cancer. CPT: Pharmacometrics and Systems Pharmacology 2:e35.
PMID: 23836026PMCID: PMC3615534

Non-LINCS data

Data integration method

Guo D, van de Ven AL, Zhou X (2013). Red blood cells tracking using optical flow methods. IEEE Journal of Biomedical and Health Informatics 18(3):991-8.
PMID: 24058034PMCID: PMC3990667

Non-LINCS data

CellIA

Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK (2013). Metrics other than potency reveal systematic variation in responses to cancer drugs. Nature Chemical Biology 9(11):708-14.
PMID: 24013279PMCID: PMC3947796

Cell survival assays, single cell imaging, western blots, and non-LINCS data

Johannessen CM, Johnson LA, Piccioni F, Townes A, Frederick DT, Donahue MK, Narayan R, Flaherty KT, Wargo JA, Root DE, Garraway LA (2013). A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. Nature 504(7478):138-42.
PMID: 24185007 | PMCID: PMC4098832

mRNA/L1000

KS Query and GSEA

Lu Y, Chen JJ, Mu L, Xue Q, Wu Y, Wu PH, Li J, Vortmeyer AO, Miller-Jensen K, Wirtz D, Fan R (2013). High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity. Analytical Chemistry 85(4):2548-56.
PMID: 23339603PMCID: PMC3589817

Secreted proteins (single cell)

MATLAB scripts

Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Schoeberl B, Sorger PK (2013). Profiles of basal and stimulated receptor signaling networks predict drug response in breast cancer lines. Science Signaling 6(294):ra84.
PMID: 24065145PMCID: PMC3845839

ELISAs and imaging

ImageRail and other analysis pipelines

Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM (2013). Discovering causal pathways linking genomic events to transcriptional states using tied diffusion through interacting events (Tiedie). Bioinformatics 29(21):2757-64.
PMID: 23986566PMCID: PMC3799471

Non-LINCS data

TieDIE (pathway models)

Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr, Whitesell L, Lindquist S (2013). Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science 341(6134):1238303.
PMID: 23869022PMCID: PMC3959726

mRNA/L1000

KS Query

Schürer SC, Muskal SM (2013). Kinome-wide activity modeling from diverse public high-quality data sets. Journal of Chemical Information Modeling 53(1):27-38.
PMID: 23259810PMCID: PMC3569091

Kinome profiling (LINCS and other data)

LIFE

Shao H, Peng T, Ji Z, Su J, Zhou X (2013). Systematically studying kinase inhibitor induced signaling network signature by integrating both therapeutic and side effects. PLoS One 8(12):e80832.
PMID: 24339888PMCID: PMC3855094

Kinase profiling and cue-signal response

KIEP

Tan CM, Chen EY, Dannenfelser R, Clark NR, Ma’ayan A (2013). Network2Canvas: Network visualization on a canvas with enrichment analysis. Bioinformatics 29(15):1872-8.
PMID: 23749960PMCID: PMC3712222

Multiple LINCS and non-LINCS perturbation data

N2C

Tang Y, Xie T, Florian S, Moerke N, Shamu C, Benes C, Mitchison TJ (2013). Differential determinants of cancer cell insensitivity to antimitotic drugs discriminated by a one-step cell imaging assay. Journal of Biomolecular Screening 18(9):1062-71.
PMID: 23788527PMCID: PMC3783590

New imaging assay

MATLAB scripts

Tian Y, Fuller E, Klug S, Lee F, Su F, Zhang L, Chao S, Meldrum D (2013). A fluorescent colorimetric pH sensor and the influences of matrices on sensing performances. Sensors and Actuators B, Chemical 188:1-10.
PMID: 24078772 | PMCID: PMC3782379

Single-cell metabolism assay: pH sensor

Zhang L, Su F, Buizer S, Lu H, Gao W, Tian Y, Meldrum D (2013). A dual sensor for real-time monitoring of glucose and oxygen. Biomaterials 34(38):9779-88.
PMID: 24090834 | PMCID: PMC3878311

Single-cell metabolism assay: dual sensor for glucose and oxygen

Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, Dastur A, Lau KW, Greninger P, Thompson IR, Luo X, Soares J, Liu Q, Iorio F, Surdez D, Chen L, Milano RJ, Bignell GR, Tam AT, Davies H, Stevenson JA, Barthorpe S, Lutz SR, Kogera F, Lawrence K, McLaren-Douglas A, Mitropoulos X, Mironenko T, Thi H, Richardson L, Zhou W, Jewitt F, Zhang T, O’Brien P, Boisvert JL, Price S, Hur W, Yang W, Deng X, Butler A, Choi HG, Chang JW, Baselga J, Stamenkovic I, Engelman JA, Sharma SV, Delattre O, Saez-Rodriguez J, Gray NS, Settleman J, Futreal PA, Haber DA, Stratton MR, Ramaswamy S, McDermott U, Benes CH (2012). Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483(7391):570-5.
PMID: 22460902PMCID: PMC3349233

Cell viability and other non-LINCS assays

Multiple

Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, Kleinjans J, Harland L, Haug K, Hermjakob H, Ho Sui SJ, Laederach A, Liang S, Marshall S, McGrath A, Merrill E, Reilly D, Roux M, Shamu CE, Shang CA, Steinbeck C, Trefethen A, Williams-Jones B, Wolstencroft K, Xenarios I, Hide W (2012). Toward interoperable bioscience data. Nature Genetics 44(2):121-6.
PMID: 22281772PMCID: PMC3428019

Metadata and standards

Vempati, UD, Przydzial MJ, Chung C, Abeyruwan S, Mir A, Sakurai K, Visser U, Lemmon VP, Schürer SC (2012). Formalization, annotation and analysis of diverse drug and probe screening assay datasets using the BioAssay Ontology (BAO). PLoS One 7(11):e49198.
PMID: 23155465 | PMCID: PMC3498356

Metadata and standards

BAO

Zhang T, Inesta-Vaquera F, Niepel M, Zhang J, Ficarro SB, Machleidt T, Xie T, Marto JA, Kim N, Sim T, Laughlin JD, Park H, Lograsso PV, Patricelli M, Nomanbhoy TK, Sorger PK, Alessi DR, Gray NS (2012). Discovery of potent and selective covalent inhibitors of JNK. Chemistry and Biology 19(1):140-54.
PMID: 22284361PMCID: PMC3270411

Multiple assays

Zhou J, Wu Y, Lee SK, Fan R (2012). High-content single cell analysis on chip using a laser microarray scanner. Lab on a Chip 12(23):5025-33.
PMID: 22991099

Laser-scanning cytometry

Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK (2011). Adaptive informatics for multifactorial and high-content biological data. Nature Methods 8(6):487-93.
PMID: 21516115 | PMCID: PMC3105758

Data format

SDCubes

Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G (2011). Crowdsourcing network inference: the dream predictive signaling network challenge. Science Signaling 4(189):mr7.
PMID: 21900204PMCID: PMC3465072

Phosphoproteomics

Public Challenge