Ryan is a Ph.D. candidate studying translational human genomics in the Bioinformatics and Integrative Genomics program at Harvard Medical School. He is supported by an award from the Graduate Research Fellowship Program (GRFP) through the National Science Foundation (NSF).
- @EricTopol @nature @WeizmannScience @LenPennacchio @SHEBA_ Very interesting paper—good example of trouble with the reference sequence: “Transcriptome analysis revealed that an unannotated open reading frame (Percc1) flanks the regulatory sequence…” Amazingly, this work was originally submitted in September of 2014! Tenacity! t.co/Qd6ycO0bC2
- @Jack_Kosmicki Yeah, I was thinking along the same lines My 2c: deletion of a TSS, even if protein-coding seq is not impacted, seems like a direct effect on transcript encoded by the gene. Not "noncoding" in the cis-regulatory (e.g. distal enhancer) sense Either way, still a great example
- Just published in @NatureProtocols: a step-by-step guide for using DNA spike-ins ('sequins') in human genome sequencing, including both wet-lab and bioinformatics. t.co/1OFGXDW3qE
- Final thought: 👏 to authors for very thorough workup: 1. mapped clustered deletions 2. reporter assay validated function of critical element 3. characterized locus in relevant tissue & found unannotated gene 4. knockout of gene in mouse -> phenotype 5. rescue via transgene Wow!