Assay Development
Data Generation
Data Analysis
Data Integration
Signature Generation
Analytical Method Dev
Software Development
Data Standards
Links to Resources
Milani P, Escalante-Chong R, Shelley BC, Patel-Murray NL, Xin X, Adam M, Mandefro B, Sareen D, Svendsen CN, Fraenkel E (2016). Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells. Scientific Reports 6:25474.
PMID: 27146274 | PMCID: PMC4857123

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

Publication Summary

GR Browser

MATLAB/Python Scripts

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma’ayan A (2016). Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research pii: gkw377.
PMID: 27141961


Yu C, Mannan AM, Yvone GM, Ross KN, Zhang YL, et al. (2016). High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines. Nature Biotechnology 34(4):419-23.
PMID: 26928769

Wang Z, Clark NR, Ma’ayan A (2016). Drug induced adverse events prediction with the LINCS L1000 data. Bioinformatics pii: btw168.
PMID: 27153606


Young CW, Yeung KY, Raftery AE (2016). A posterior probability approach for gene regulatory network inference in genetic perturbation data. arXiv.

Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM (2016). Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Computational Biology 12(3):e1004790.
PMID: 26960204

Sokolov A, Paull EO, Stuart JM (2016). One-Class Detection of Cell States in Tumor Subtypes. Pacific Symposium on Biocomputing 21:405-14
PMID: 2776204

Abelin JG, Patel J, Lu X, Feeney CM, Fagbami L, et al. (2016). Reduced-representation phosphosignatures measured by quantitative targeted MS capture cellular states and enable large-scale comparison of drug-induced phenotypes. Molecular and Cellular Proteomics.
PMID: 26912667

LINCS PCCSE Panorama Repository

Fuller HR, Mandefro B, Shirran SL, Gross AR, Kaus AS, Botting CH, Morris GE, Sareen D (2016). Spinal muscular atrophy patient iPSC-derived motor neurons have reduced expression of proteins important in neuronal development. Frontiers in Cellular Neuroscience 9:506.
PMID: 26793058 | PMCID: PMC4707261

Shaby BA, Skibinski G, Ando M, LaDow ES, Finkbeiner S (2016). A three-groups model for high-throughput survival screens. Biometrics.
PMID: 26821783

Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma’ayan A (2015). Principal Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. Proceedings (IEEE Int Conf Bioinformatics Biomed) 256-262.
PMID: 26848405 | PMCID: PMC4737646

Principal Angle Enrichment Analysis (PAEA)

Allen BK, Mehta S, Ember SW, Schonbrunn E, Ayad N, Schurer SC (2015). Large-scale computational screening identifies first in class multitarget inhibitor of EGFR kinase and BRD4. Scientific Reports 5:16924.
PMID: 26596901 | PMCID: PMC4657038

Lin JR, Fallahi-Sichani M, Sorger PK (2015). Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nature Communications 6:8390.
PMID: 26399630 | PMCID: PMC4587398

Publication Summary

Project Explorer

ImageJ Macros and MATLAB Scripts

Rouillard AD, Wang Z, Ma’ayan A (2015). Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. Computational Biology and Chemistry 58:104-19.
PMID: 26101093 | PMCID: PMC4675694

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

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 | PMCID: PMC4607730

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

Publication Summary

Project Explorer

MATLAB Scripts

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

Publication Summary

Project Explorer

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


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

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

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

Olson DE, Udeshi ND, Wolfson NA, Pitcairn CA, et al. (2014). An unbiased approach to identify endogenous substrates of “histone” deacetylase 8. ACS Chemical Biology 9(10):2210-6.
PMID: 25089360 | PMCID: PMC4201337

Lincscloud P100 API

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

Review of CellNet (non-LINCS tool)

Tang Y (2014). A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. Current Protocols in Chemical Biology 6(1):1-5.
PMID: 24652619 | PMCID: PMC4016950

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


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


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

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


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

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


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


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

Publication Summary

Project Explorer

Vempati UD, Chung C, Mader C, Koleti A, et al. (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

LIFE and Data standards

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: 23788527 | PMCID: PMC3783590

Publication Summary

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

Publication Summary

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


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

UCSC Interaction Browser

Chen J, Hu Z, Phatak M, Reichard J, Freudenberg JM, Sivaganesan S, 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


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

Liu Q, Xu C, Kirubakaran S, Zhang X, et al. (2013). Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR. Cancer Research 73(8):2574-86.
PMID: 23436801 | PMCID: PMC3760004

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

Publication Summary

Project Explorer

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

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

Publication Summary

Project Explorer

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

Publication Summary


Santagata S, Mendillo ML, Tang YC, Subramanian A, et al. (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


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


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


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

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

Corcoran RB, Cheng KA, Hata AN, Faber AC, et al. (2013). Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models. Cancer Cell 23(1):121-8.
PMID: 23245996 | PMCID: PMC3667614

Jenkins SL, Ma’ayan A (2013). Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Pharmacogenomics 14(2):119-22.
PMID: 23327571 | PMCID: PMC3605723

Clark NR, Dannenfelser R, Tan CM, Komosinski ME, Ma’ayan A (2012). Sets2Networks: network inference from repeated observations of sets. BMC Systems Biology 6:89.
PMID: 22824380 | PMCID: PMC3443648


Liu Q, Ren T, Fresques T, Oppliger W, Niles BJ, Hur W, Sabatini DM, Hall MN, Powers T, Gray NS (2012). Selective ATP-competitive inhibitors of TOR suppress rapamycin-insensitive function of TORC2 in Saccharomyces cerevisiae. ACS Chemical Biology 7(6):982-7.
PMID: 22496512 | PMCID: PMC3376217

Ni J, Liu Q, Xie S, Carlson C, Von T, Vogel K, Riddle S, Benes C, Eck M, Roberts T, Gray N, Zhao J (2012). Functional characterization of an isoform-selective inhibitor of PI3K-p110β as a potential anticancer agent. Cancer Discovery 2(5):425-33.
PMID: 22588880 | PMCID: PMC3384541

Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK (2012). Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Systems Biology 6:29.
PMID: 22548703 | PMCID: PMC3436686

Garnett MJ, Edelman EJ, Heidorn SJ, Greenman CD, et al. (2012). Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483(7391):570-5.
PMID: 22460902PMCID: PMC3349233

Liu Q, Kirubakaran S, Hur W, Niepel M, et al. (2012). Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics. The Journal of Biological Chemistry 287(13):9742-52.
PMID: 22223645PMCID: PMC3322972

Sansone SA, Rocca-Serra P, Field D, Maguire E, et al. (2012). Toward interoperable bioscience data. Nature Genetics 44(2):121-6.
PMID: 22281772PMCID: PMC3428019

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


Zhang T, Inesta-Vaquera F, Niepel M, Zhang J, et al. (2012). Discovery of potent and selective covalent inhibitors of JNK. Chemistry and Biology 19(1):140-54.
PMID: 22284361PMCID: PMC3270411

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

Luckert K, Gujral, Chan M, Sevecka M, Joos TO, Sorger PK, Macbeath G, Potz O (2012). A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins. Science Signaling 5(206):pl1.
PMID: 22234610 | PMCID: PMC3465074

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


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