Publications

2014
Wählby C, Lee Conery A, Bray MA, Kamentsky L, Larkins-Ford J, Sokolnicki KL, Veneskey M, Michaels K, Carpenter AE, O'Rourke EJ. High- and low-throughput scoring of fat mass and body fat distribution in C. elegans [Internet]. Methods 68(3):492-499 2014; Publisher's Version
Nieland TJF, Logan DJ, Saulnier J, Lam D, Johnson C, Root DE, Carpenter AE, Sabatini BL. High Content Image Analysis Identifies Novel Regulators of Synaptogenesis in a High-Throughput RNAi Screen of Primary Neurons. [Internet]. PLoS ONE 9(3):e91744 2014; Publisher's Version
Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Siddiqi N, Rubin EJ, Hung DT. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth [Internet]. PLoS Pathogens 10(2):e1003946 2014; Publisher's Version
Chudnovsky Y, Kim D, Zheng S, Whyt WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Mitalipova M, Muffat J, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. ZFHX4 is a master regulator of NuRD core member CHD4 and regulates the glioblastoma tumor initiating cell state. [Internet]. Cell Reports 6(2):313-324 2014; Publisher's Version
Singh S, Carpenter AE, Genovesio A. Increasing the content of high-content screening: an overview [Internet]. Journal of Biomolecular Screening 19(5):640-650 2014; Publisher's Version
Majithia AR, Flannick J, Shahinian P, Guo M, Bray MA, Fontanillas P, Gabriel SE, Consortium GT2D, Pr NHGRI/FHSAS. Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes [Internet]. PNAS 2014; 111(36):13127-13132. Publisher's Version
PMID: 1410428111 PMCID: PMC25157153
2013
Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, Shamji AF. Multiplex cytological profiling assay to measure diverse cellular states. [Internet]. PLoS One 2013;8(12):e80999. Publisher's Version

[**Authors Gustafsdottir, SM and Ljosa, V contributed equally.]
[*Authors Clemons, PA, Carpenter, AE, and Shamji, AF contributed equally.]

Ljosa V, Caie PD, ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE. Comparison of Methods for Image-Based Profiling of Cellular Morphological Responses to Small-Molecule Treatment. [Internet]. Journal of Biomolecular Screening 18:1321-1329 2013; Publisher's Version
Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MAS, Scadden DT, Schreiber SL, Ebert BL, Golub TR. Niche-based screening identifies small-molecule inhibitors of leukemia stem cells [Internet]. Nature Chemical Biology 2013;9(12):840-848. Publisher's Version
March S, Ng S, Velmurugan S, Galstian A, Shan J, Logan DJ, Carpenter AE, Thomas D, Sim BK, Mota MM, Hoffman SL, Bhatia SN. A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax. [Internet]. Cell Host & Microbe 2013;14(1):104–15. Publisher's Version
Shan J, Schwartz RE, Ross NT, Logan DJ, Thomas D, Duncan SA, North TE, Goessling W, Carpenter AE, Bhatia SN. Identification of small molecules for human hepatocyte expansion and iPS differentiation. [Internet]. Nature Chemical Biology 2013;9(8):514–520. Publisher's Version
Floyd SR, Pacold ME, Huang Q, Clarke SM, Lam FC, Cannell IG, Bryson BD, Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC, Maffa A, Del Rosario AM, Root DE, Carpenter AE, Hahn WC, Sabatini DM, Chen CC, White FM, Bradner JE, Yaffe MB. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling [Internet]. Nature 2013;498(7453):246–250. Publisher's Version
Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM. Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death. [Internet]. Cell Host Microbe, 13(4):406-16 2013; Publisher's Version
Pardo-Martin C, Allalou A, Medina J, Eimon PM, Wählby C, Faith Yanik M. High-throughput hyperdimensional vertebrate phenotyping [Internet]. Nat. Commun., 4:1467 2013; Publisher's Version
Ishaq O, Negri J, Bray MA, Pacureanu A, Peterson RT, Wählby C. Automated quanitification of zebrafish tail deformation for high-throughput drug screening. [Internet]. Protoc Int Symp Biomed Imaging: 902-905 2013; Publisher's Version
2012
Bray MA, Carpenter AE. Advanced Assay Development Guidelines for Image-Based High Content Screening and Analysis. In: Sittampalam GS et al., eds. Assay Guidance Manual. 2012;
Wen Q, Goldenson B, Silver SJ, Schenone M, Dancik V, Huang Z, Wang LZ, Lewis TA, An WF, Li X, Bray MA, Thiollier C, Diebold L, Gilles L, Vokes MS, Moore CB, Bliss-Moreau M, Verplank L, Tolliday NJ, Mishra R, Vemula S, Shi J, Wei L, Kapur R, Lopez CK, Gerbek B, Ballerini P, Pflumio F, Gilliland DG, Goldberg L, Birger Y, Izraeli S, Gamis AS, Smith FO, Woods WG, Taub J, Scherer CA, Bradner JE, Goh BC, Mercher T, Carpenter AE, Gould RJ, Clemons PA, Carr SA, Root DE, Schreiber SL, Stern AM, Crispino JD. Identification of Regulators of Polyploidization Presents Therapeutic Targets for Treatment of AMKL [Internet]. Cell 150(3):575-89 2012; Publisher's Version
Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. [Internet]. Nature Methods 9(7):697-710 2012; Publisher's Version
Carpenter AE, Kamentsky L, Eliceiri KW. A call for bioimaging software usability. [Internet]. Nature Methods 9(7):666-70 2012; Publisher's Version
Ljosa V, Sokolnicki KL, Carpenter AE. Annotated high-throughput microscopy image sets for validation [Internet]. Nature Methods 9(7):637 2012; Publisher's Version

Pages