LINCS Resource Used

Readout / Assay

Computational Tools

Wang Z, Clark NC, Ma’ayan A (2015). Dynamics of the discovery process of protein-protein interactions from low content studies. BMC Systems Biology 9(1):26.
PMID: 26048415 | PMCID: PMC4456804

Data integration

Custom code

Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma’ayan A (2015). GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinformatics pii:btv297.
PMID: 25971742

Data integration

GEO2Enrichr and Enrichr

Roux J, Hafner M, Bandara S, Sims JJ, Hudson H, Chai D, Sorger PK (2015). Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold. Molecular Systems Biology 11(5):803.
PMID: 25953765 | PMCID: PMC4461398

Imaging assays

Data exploration website

Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK (2015). Systematic analysis of BRAFV600E melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis. Molecular Systems Biology 11(3):797.
PMID: 25814555 | PMCID: PMC4380931

Imaging assays, RPPA assays

Data exploration website

Hornbeck PV, Zhang B, Murray B, Kornhauser JM, Latham V, Skrzypek E (2015). PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Research 43:D512-20.
PMID: 25514926 | PMCID: PMC4383998

Data integration


Jain S, Gitter A, Bar-Joseph Z (2014). Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Computational Biology 10(12):e1003943.
PMID: 25522349 | PMCID: PMC4270428

Modeling signaling networks

Custom code

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

Gujral TS, Chan M, Peshkin L, Sorger PK, Kirschner MW, MacBeath G (2014). A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell 159(4):844-56.
PMID: 25417160 | PMCID: PMC4243058

Cignal 45-Pathway Reporter Array assays, imaging assays, RPPA assays

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

P100, targeted mass spectrometry proteomics, epigenetics

Lincscloud P100 API

Ma’ayan A, Duan Q (2014). A blueprint of cell identity. Nature Biotechnology 32(10):1007-8.
PMID: 25299921 | PMCID: PMC4274604

Data integration, stem cells, cell engineering

Review of CellNet (non-LINCS tool)

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


Sharma V, Eckels J, Taylor GK, Shulman NJ, Stergachis AB, Joyner SA, Yan P, Whiteaker JR, Halusa GN, Schilling B, Gibson BW, Colangelo CM, Paulovich AG, Carr SA, Jaffe JD, MacCoss MJ, MacLean B (2014). Panorama: a targeted proteomics knowledge base. Journal of Proteome Research 13(9):4205-10.
PMID: 25102069 | PMCID: PMC4156235

P100, targeted mass spectrometry proteomics, phosphoproteomics

Lincscloud P100 API

Ma’ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y (2014). Lean Big Data integration in systems biology and systems pharmacology. Trends in Pharmacological Sciences 35(9):450-60.
PMID: 25109570 | PMCID: PMC4153537

Data integration

Review of multiple tools and databases

Clark AM, Bunin BA, Litterman NK, Schürer SC, Visser U (2014). Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation. PeerJ e524.
PMID: 25165633  | PMCID: PMC4137659

Ontologies, search engine, metadata


Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma’ayan A (2014). LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Research 42:W449-60.
PMID: 24906883 | PMCID: PMC4086130

L1000 data, visualization tools, enrichment analysis, LINCS data search engine, cross LINCS centers collaboration

LINCS Canvas Browser

Abeyruwan S, Vempati UD, Küçük-McGinty H, Visser U, Koleti A, Mir A, Sakurai K, Chung C, Bittker JA, Clemons PA, Brudz S, Siripala A, Morales AJ, Romacker M, Twomey D, Bureeva S, Lemmon V, Schürer SC (2014). Evolving BioAssay Ontology (BAO): modularization, integration and applications. Journal of Biomedical Semantics 5:S5.
PMID: 25093074 | PMCID: PMC4108877

Ontologies, metadata


Guo D, van de Ven AL, Zhou X (2014). 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


Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Muhlich JL, Schoeberl B, Sorger PK (2014). Analysis of growth factor signaling in genetically diverse breast cancer lines. BMC Biology 12:20.
PMID: 24655548 | PMCID: PMC4234128

ELISA assays

Data exploration website

Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC (2014). Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). Journal of Biomolecular Screening 19(5):803-816.
PMID: 24518066

Data integration, ontologies, metadata


McAllister FE, Niepel M, Haas W, Huttlin E, Sorger PK, Gygi SP (2013). Mass spectrometry based method to increase throughput for kinome analyses using ATP probes. Analytical Chemistry 85(9):4666-74.
PMID: 23607489 | PMCID: PMC3771683

Proteomics, KAYAK assays

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


Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM (2013). The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Research 41:W218-24.
PMID: 23748957 | PMCID: PMC3692096

Data integration

UCSC Interaction Browser

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


Benes CH (2013). Functionalizing genomic data for personalization of medicine. Clinical Pharmacology and Therapeutics 93(4):309-11.
PMID: 23321554 | PMCID: PMC3609407


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

Data integration

Liu Q, Xu C, Kirubakaran S, Zhang X, Hur W, Liu Y, Kwiatkowski NP, Wang J, Westover KD, Gao P, Ercan D, Niepel M, Thoreen CC, Kang SA, Patricelli MP, Wang Y, Tupper T, Altabef A, Kawamura H, Held KD, Chou DM, Elledge SJ, Janne PA, Wong KK, Sabatini DM, Gray NS. (2013). Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR. Cancer Research 73(8):2574-86.
PMID: 23436801 | PMCID:PMC3760004

Various cell profiling assays

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

Imaging assays

Data exploration website

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


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

ELISA assays, imaging assays

Data exploration website

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

Data integration


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


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)


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


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

Data integration


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

Imaging assays

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


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


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 formatting standards


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

DREAM Challange