LINCS Resource Used

Readout/ Assay

Computational Tools

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.

Data Integration (LINCS and other data types)


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 Comput Biol 9: e1003198.

Data Integration (LINCS and other data types)


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

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
(99), doi: 10.1109/JBHI.2013.2281915.

Non-LINCS data


Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK (2013). Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat Chem Biol. PMID: 24013279.

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. DOI:10.1038/nature12688

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 DOI: 10.1021/ac400081e.

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. Sci Signal 6(294): ra84. NIHMS529254 PMID: 24065145.;6/294/ra84

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 PMC3799471 PMID: 23986566.

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. doi: 10.1126/science.1238303.



KS Query

Schürer SC, Muskal SM (2013). Kinome-wide activity modeling from diverse public high-quality data sets. J Chem Inf Model, doi:10.1021/ci300403k

Kinome profiling (LINCS and other data)


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,
doi: 10.1371/journal.pone.0080832.

Kinase profiling & Cue-Signal Response


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

Multiple LINCS & non-LINCS perturbation data


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. J Biomol Screen 18(9): 1062-1071. PMC3783590 PMID: 23788527.

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 188: 1-10, November 2013.
NIHMS manuscript (NIHMS504217).

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): 9779-9788.
 NIHMS manuscript (NIHMS526028).

Single-cell metabolism assay: Dual sensor for glucose & 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): 570-575. PMC3349233 PMID: 22460902.

Cell viability and other non-LINCS assays


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. Nat Genet 44(2): 121-126. PMC3428019 PMID: 22281772.

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, doi:10.1371/journal.pone.0049198

Metadata & Standards


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. Chem Biol 19(1): 140-154. PMC3270411 PMID: 22284361.

Multiple assays

Zhou J, Wu Y, Lee SK, Fan R (2012). High-content single cell analysis on chip using a laser microarray scanner. Lab Chip 12: 5025-5033.

Laser-scanning Cytometry

Millard BL, Niepel M, Menden MP, Muhlich JL, and Sorger PK (2011). Adaptive informatics for multifactorial and high-content biological data. Nat Methods 8(6): 487-492. PMC3105758 PMID: 21516115.

Data Format


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


Public Challenge