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A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.
Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. Cesana M, et al. Among authors: califano a. Cell Stem Cell. 2018 Apr 5;22(4):575-588.e7. doi: 10.1016/j.stem.2018.03.012. Cell Stem Cell. 2018. PMID: 29625070 Free PMC article.
Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis.
Westphalen CB, Takemoto Y, Tanaka T, Macchini M, Jiang Z, Renz BW, Chen X, Ormanns S, Nagar K, Tailor Y, May R, Cho Y, Asfaha S, Worthley DL, Hayakawa Y, Urbanska AM, Quante M, Reichert M, Broyde J, Subramaniam PS, Remotti H, Su GH, Rustgi AK, Friedman RA, Honig B, Califano A, Houchen CW, Olive KP, Wang TC. Westphalen CB, et al. Among authors: califano a. Cell Stem Cell. 2016 Apr 7;18(4):441-55. doi: 10.1016/j.stem.2016.03.016. Cell Stem Cell. 2016. PMID: 27058937 Free PMC article.
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information.
Lachmann A, Giorgi FM, Lopez G, Califano A. Lachmann A, et al. Among authors: califano a. Bioinformatics. 2016 Jul 15;32(14):2233-5. doi: 10.1093/bioinformatics/btw216. Epub 2016 Apr 23. Bioinformatics. 2016. PMID: 27153652 Free PMC article.
Given that the previous version of ARACNe is extremely demanding, the new version of the algorithm will allow even researchers with modest computational resources to build complex regulatory networks from hundreds of gene expression profiles. AVAILABILITY AND IMPLEMENTATION: A …
Given that the previous version of ARACNe is extremely demanding, the new version of the algorithm will allow even researchers with modest c …
Detection and removal of spatial bias in multiwell assays.
Lachmann A, Giorgi FM, Alvarez MJ, Califano A. Lachmann A, et al. Among authors: califano a. Bioinformatics. 2016 Jul 1;32(13):1959-65. doi: 10.1093/bioinformatics/btw092. Epub 2016 Feb 28. Bioinformatics. 2016. PMID: 27153732
Bone Marrow Myeloid Cells Regulate Myeloid-Biased Hematopoietic Stem Cells via a Histamine-Dependent Feedback Loop.
Chen X, Deng H, Churchill MJ, Luchsinger LL, Du X, Chu TH, Friedman RA, Middelhoff M, Ding H, Tailor YH, Wang ALE, Liu H, Niu Z, Wang H, Jiang Z, Renders S, Ho SH, Shah SV, Tishchenko P, Chang W, Swayne TC, Munteanu L, Califano A, Takahashi R, Nagar KK, Renz BW, Worthley DL, Westphalen CB, Hayakawa Y, Asfaha S, Borot F, Lin CS, Snoeck HW, Mukherjee S, Wang TC. Chen X, et al. Among authors: califano a. Cell Stem Cell. 2017 Dec 7;21(6):747-760.e7. doi: 10.1016/j.stem.2017.11.003. Epub 2017 Nov 30. Cell Stem Cell. 2017. PMID: 29198940 Free PMC article.
Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.
Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A. Rajbhandari P, et al. Among authors: califano a. Cancer Discov. 2018 May;8(5):582-599. doi: 10.1158/2159-8290.CD-16-0861. Epub 2018 Mar 6. Cancer Discov. 2018. PMID: 29510988 Free PMC article.
Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.
Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Broyde J, et al. Among authors: califano a. Nat Biotechnol. 2021 Feb;39(2):215-224. doi: 10.1038/s41587-020-0652-7. Epub 2020 Sep 14. Nat Biotechnol. 2021. PMID: 32929263 Free PMC article.
342 results