Publications

Sep 30, 2020 Genome Biol.

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation.

Roayaei Ardakany A, Gezer HT, Lonardi S, Ay F.

Sep 21, 2020 J Immunol

TL1A Promotes Lung Tissue Fibrosis and Airway Remodeling

Herro R, Miki H, Sethi GS, Mills D, Mehta AK, Nguyen XX, Feghali-Bostwick C, Miller M, Broide DH, Soloff R, Croft M

Jul 1, 2020 SSRN

Single-Cell Transcriptomic Analysis of SARS-CoV-2 Reactive CD4 + T Cells

Meckiff BJ, Ramírez-Suástegui C, Fajardo V, Chee SJ, Kusnadi A, Simon H, Grifoni A, Pelosi E, Weiskopf D, Sette A, Ay F, Seumois G, Ottensmeier C, Vijayanand P.

Mar 24, 2020 Lancet Infect Dis

Safety and immunogenicity of th tetravalent, live-attenuated dengue vaccine Butantan-DV in adults in Brazil: a two-step, double-blind, randomized placebo-controlled phase 2 trial

Kallas EG, Precioso AR, Palacios R, Thome B, Braga PE, Vanni T, Campos LMA, Ferrari L, Mondini G, da Graca Salomao M, da Silva A, Espinola HM, do Prado Santos J, Santos CLS, Timenetsky MDCST, Miraglia JL, Gallina NMF, Weiskopf D, Sette A, Goulart R, Salles RT, Maestri A, Sallum AME, Farhat SCL, Sakita NK, Ferreira JCOA, Silverira CGT, Casta PR, Raw I, Whitehead SS, Durbin AP, Kalil J

Mar 15, 2020 Nat Protoc.

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

Kaul A, Bhattacharyya S, Ay F

Sep 29, 2019 Genome Res

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control

Rivera-Mulia JC, Kim S, Gabr H, Chakraborty A, Ay F, Kahveci T, Gilbert DM

Jul 17, 2019 Genome Res

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing

Zhang S, Wang Y, Jia L, Wen X, Zhonghua D, Wang C, Hao Y, Yu D, Zhou L, Chen N, Chen J, Chen H, Zhang H, Celik I, Gulsoy G, Luo J, Qin B, Cui X, Liu Z, Zhang S, Esteban MA, Ay F, Li W, Xu W, Chen R, Hoffman AR, Hu J, Cui J

Jul 15, 2019 Bioinformatics

Selfish: discovery of differential chromatin interactions via a self-similarity measure

Ardakany AR, Ay F, Lonardi S

Jul 15, 2019 J Immunol

Human eosinophils express a distinct gene expression program in response to IL-3 compared with common β-chain cytokines IL-5 and GM-CSF

Nelson RK, Brickner H, Panwar B, Ramírez-Suástegui C, Herrera-de la Mata S, Liu N, Diaz D, Alexander LEC, Ay F, Vijayanand P, Seumois G, Akuthota P

Jun 21, 2019 J Exp Med

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

Clarke J, Panwar B, Madrigal A, Singh D, Gujar R, Wood O, Chee SJ, Eschweiler S, King EV, Awad AS, Hanley CJ, McCann KJ, Bhattacharyya S, Woo E, Alzetani A, Seumois G, Thomas GJ, Ganesan AP, Friedmann PS, Sanchez-Elsner T, Ay F, Ottensmeier CH, Vijayanand P

Jun 1, 2019 Semin Cell Dev Biol

The role of 3D genome organization in disease: From compartments to single nucleotides

Chakraborty A, Ay F

Mar 19, 2019 Genome Biol

Measuring the reproducibility and quality of Hi-C data

Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, Taylor J, Yue F, Dekker J, Noble WS