Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON
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DOI: 10.1038/s41467-023-44103-3
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- Edroaldo Lummertz da Rocha & R. Grant Rowe & Vanessa Lundin & Mohan Malleshaiah & Deepak Kumar Jha & Carlos R. Rambo & Hu Li & Trista E. North & James J. Collins & George Q. Daley, 2018. "Reconstruction of complex single-cell trajectories using CellRouter," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
- Mubeen Goolam & Maria-Eleni Xypolita & Ita Costello & John P. Lydon & Francesco J. DeMayo & Elizabeth K. Bikoff & Elizabeth J. Robertson & Arne W. Mould, 2020. "The transcriptional repressor Blimp1/PRDM1 regulates the maternal decidual response in mice," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
- Kenji Kamimoto & Blerta Stringa & Christy M. Hoffmann & Kunal Jindal & Lilianna Solnica-Krezel & Samantha A. Morris, 2023. "Dissecting cell identity via network inference and in silico gene perturbation," Nature, Nature, vol. 614(7949), pages 742-751, February.
- Amos Tanay & Aviv Regev, 2017. "Scaling single-cell genomics from phenomenology to mechanism," Nature, Nature, vol. 541(7637), pages 331-338, January.
- Alex K. Shalek & Rahul Satija & Joe Shuga & John J. Trombetta & Dave Gennert & Diana Lu & Peilin Chen & Rona S. Gertner & Jellert T. Gaublomme & Nir Yosef & Schraga Schwartz & Brian Fowler & Suzanne W, 2014. "Single-cell RNA-seq reveals dynamic paracrine control of cellular variation," Nature, Nature, vol. 510(7505), pages 363-369, June.
- Sascha Jung & Evan Appleton & Muhammad Ali & George M. Church & Antonio del Sol, 2021. "A computer-guided design tool to increase the efficiency of cellular conversions," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- J. Gray Camp & Keisuke Sekine & Tobias Gerber & Henry Loeffler-Wirth & Hans Binder & Malgorzata Gac & Sabina Kanton & Jorge Kageyama & Georg Damm & Daniel Seehofer & Lenka Belicova & Marc Bickle & Ric, 2017. "Multilineage communication regulates human liver bud development from pluripotency," Nature, Nature, vol. 546(7659), pages 533-538, June.
- Hongxu Ding & Eugene F. Douglass & Adam M. Sonabend & Angeliki Mela & Sayantan Bose & Christian Gonzalez & Peter D. Canoll & Peter A. Sims & Mariano J. Alvarez & Andrea Califano, 2018. "Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
- Peijie Zhou & Shuxiong Wang & Tiejun Li & Qing Nie, 2021. "Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
- Tetsutaro Hayashi & Haruka Ozaki & Yohei Sasagawa & Mana Umeda & Hiroki Danno & Itoshi Nikaido, 2018. "Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
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