Publications

Citation

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.
http://www.biomedcentral.com/1471-2105/14/128

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 Comput Biol 9: e1003198.
http://www.ploscompbiol.org/article/
info%3Adoi%2F10.1371%2Fjournal.pcbi.1003198

Data Integration (LINCS and other data types)

TREG

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)
http://www.nature.com/psp/journal/v2/n3/full/psp201311a.html

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

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. Nat Chem Biol. PMID: 24013279.
http://www.nature.com/nchembio/journal/
v9/n11/full/nchembio.1337.html

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
http://www.nature.com/nature/journal/
vaop/ncurrent/full/nature12688.html

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.
http://pubs.acs.org/doi/full/10.1021/ac400082e

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.
 http://stke.sciencemag.org/cgi/content/full/sigtrans;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.
http://bioinformatics.oxfordjournals.org/content/
29/21/2757.long

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.
http://www.sciencemag.org/content/341/6143/1238303.long

mRNA/

L1000

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
http://pubs.acs.org/doi/full/10.1021/ci300403k

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,
doi: 10.1371/journal.pone.0080832.

Kinase profiling & 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: 1872-8. PMID: 23749960
http://bioinformatics.oxfordjournals.org/content/29/15/1872.long

Multiple LINCS & 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. J Biomol Screen 18(9): 1062-1071. PMC3783590 PMID: 23788527.
http://jbx.sagepub.com/content/18/9/1062.long

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.
(http://dx.doi.org/10.1016/j.snb.2013.06.098).
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.
(http://dx.doi.org/10.1016/j.biomaterials.2013.09.031)
 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.
http://www.nature.com/nature/journal/
v483/n7391/full/nature11005.html
 

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. Nat Genet 44(2): 121-126. PMC3428019 PMID: 22281772.
http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html

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
http://www.plosone.org/article/
info%3Adoi%2F10.1371%2Fjournal.pone.0049198

Metadata & 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. Chem Biol 19(1): 140-154. PMC3270411 PMID: 22284361.
http://www.sciencedirect.com/science/article/
pii/S1074552111004613

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.
http://pubs.rsc.org/en/content/
articlehtml/2012/lc/c2lc40309a
 

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.
http://www.nature.com/nmeth/journal/
v8/n6/full/nmeth.1600.html

Data Format

SDCubes

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.
http://stke.sciencemag.org/cgi/content/
full/sigtrans;4/189/mr7

Phosphoproteomics

Public Challenge