Elated to share our latest paper, "System-wide transcriptome damage and tissue identity loss in COVID-19 patients," led by @JIWOONPARK_ @jfoox in our lab & @RobSchwartzLab @RiceLaboratory @cemmeydan @RockefellerUniv @WCMCPathology @nygenome cell.com/cell-reports-m… 🧵 /1 We used spatial protein and expression profiling on @nanostringtech GeoMx on 357 tissue sections from 16 patient lung samples and RNA-seq on 646 clinical NP swabs, plus 39 patient autopsies to define body-wide transcriptome changes in response to COVID-19. /2

I'm elated to release four @metasub papers today, with new species, data interfaces, & online resources. The first is in @CellCellPress, "A global metagenomic map of urban microbiomes and antimicrobial resistance" led by @dcdanko @Daniela_Bezdan cell.com/cell/fulltext/…" a 🧵 /1 Our metagenome atlas spans ~5,000 samples from mass-transit systems in 60 cities over 3 years, showing thousands of species, antimicrobial resistance (AMR) markers & novel biology everywhere: 10,928 new viruses, 1,302 new bacteria, 2 new archaea, and 838,532 new CRISPR arrays /2

Announcing the "COVIDgenes" data portal: covidgenes.weill.cornell.edu, an open site for all to mine the RNA-seq expression results from our @WeillCornell|@nyphospital COVID-19 patient data. This site (v1.0) hosts various visualization, statistics, & normalization options including: /1 Single-gene plots for expression changes with infection status, comparison to other respiratory infections’ expression changes, absolute expression or z-score, & a differentially expressed gene (DEG) q-value sorting tab based on a variety of patient group comparisons /2

Our new @biorxivpreprint is up! "Host, Viral, and Environmental Transcriptome Profiles of SARS-CoV-2." COVID-19 patients (n=338) examined w/ qRT-PCR, RT-LAMP, & total RNA-seq, host responses (e.g. ACE2) & new diagnostic methods. biorxiv.org/content/10.110… Some highlights: /1 Viral evolution maps can be built directly from the total RNA-seq data, with likely origin of NYC viruses from Europe, and less commonly from Asia, plus we think an NYC-specific clade and some novel mutations, also now posted in @nextstrain and @GISAID of course. /2