Will Hooper

bioinformatics scientist @nygenome — all opinions my own

[Dr. Bishoy M. Faltas @FaltasLab]

Excited to be part of this huge #teamscience effort to generate next-generation patient-derived models for diverse cancers with @ElementoLab
@WCMEnglanderIPM
https://t.co/NXVvDYcS1p

[Giuseppe Narzisi @gnarzisi]

Excited to see this work published. Lancet2 comes with many improvements in genotyping, variant scoring, visualization, and runtime. Outstanding work of @omicsnut. Great collab. with Benedict Paten group. Work supported by @theNCI under #NCIITCR. Article: https://t.co/iGNJR766mM

[Dr. Bishoy M. Faltas @FaltasLab]

This is the result of several years of dedicated work by many people.
Spearheaded by @AbhishekBose @Weisi_liu in my lab. Important contributions from Paul yoo, Alina Sami @MichalBoniecki @madhuratweets @MHosmanMD @DuyDNguyen2 @UrkodC @GiannakakouEvi @BhavneetBhinder @willbfx @ElementoLab @notSoJunkDNA Milaid G. Rodriguez @Gerhardtlab. Great collaboration with @mouwlab @DanaFarber @LChelico13828 @usask #teamscience

[New York Focus @nysfocus]

NEW: Hotels and motels have quietly become New York’s most common solution for emergency shelter for homeless people outside NYC.

Many stay in dilapidated rooms without the social services that shelters are required to provide.
https://t.co/YdEHZn2157

[Dr. Bishoy M. Faltas @FaltasLab]

Grateful for the opportunity to present our CLONEVO investigator-initiated trial (IIT) in bladder cancer at @ASCO #ASCO2025. Here are some lessons I learned along the way:

Investigator-initiated trials (IITs) are essential. IITs are clinical trials independently designed and led by physician-scientists. These trials usually start from scientific observations in the lab. They are driven by unmet clinical needs, making them uniquely powerful for testing new therapeutic hypotheses!

Investigator-initiated trials are hard! Taking something from the laboratory to the bedside 🔬➡️ 🛏️ takes years of sustained effort.

It takes a team. This truly takes a huge team of brilliant and dedicated colleagues, including clinicians such as oncologists, pathologists, urologists, research nurses, laboratory scientists, computational biologists, regulatory staff, and many more! @MHosmanMD
@cnsternberg @DoctorMargolis @DrJonesNauseef
@DrAnaMolina @DrDavidNanus @rohitjainMD
@scientistatlrge @DrMhidalgo @notSoJunkDNA
@willbfx @ElementoLab @SuzanneColeMD @scherr_doug #clinicaltrials #teamscience

🤝 This is a model of successful industry-academia collaboration. We made the initial discoveries @WeillCornell @FaltasLab designed and conducted the trial. @EliLillyandCo supported the trial, and @CarisLS supported whole-exome (WES), ctDNA WES, and RNAseq—and shared the raw data so we could do our deep computational analyses in-house and with our collaborators. We were supported by @WCM_MeyerCancer @nyphospital

🪟 The window-of-opportunity design is a powerful platform to directly test on-target 🎯 activity in vivo, understand how therapies affect disease biology, and measure the effect directly in clinical samples. In our study of #bladdercancer patients, we collected pre/post-treatment tissues, ctDNA, and urine cfDNA. We worked with @WCMEnglanderIPM to establish patient-derived organoids and xenografts and performed spatial imaging mass cytometry of 630,000 single cells.

💡 Encouraging to see an efficacy signal — and even better when we can understand the underlying biology at the same time!

🙏 Immense gratitude to the patients and families who made this possible. You inspire us every day.

Funding for science and cancer research is essential. Without it, we wouldn’t be able to do this work, to take new therapeutic ideas from bench to bedside and bring hope to patients with cancer. @ASCOPost @JCO_ASCO @OncoAlert @OncBrothers @medicalwatchBC
@PGrivasMDPhD @TwoOncDocs @OncBrothers
@Larvol @TiansterZhang @GlopesMd
@HammersMD @sonpavde @drenriquegrande
@scserendipity1 @BraunMDPhD @Uromigos
@AminNassarMD @ZiadBakouny @DrRanaMcKay
@NazliDizman @urotoday @Uromigos @DrChoueiri

[Dan Landau @landau_lab]

Excited to share our exploration @naturemethods into new horizons opening up in the era of low cost sequencing!

🔥 Deeper sequencing at WGS scale for PPM sensitivity of tumor informed MRD
🔥Duplex sequencing at WGS scale for plasma only exploration of ctDNA

Check out thread 👇

[bioRxiv Bioinfo @biorxiv_bioinfo]

Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graph https://t.co/9wzvlfJgC5 #biorxiv_bioinfo

[Dr. Bishoy M. Faltas @FaltasLab]

Good time to read our Tweetorial/ X-planation of our https://t.co/sU6uF9rfGa paper now featured on the cover of @Nature!

[Dr. Bishoy M. Faltas @FaltasLab]

🚀Big News! Excited to share our work “The Interplay of Mutagenesis and ecDNA Shapes Urothelial Cancer Evolution” published in @Nature! https://t.co/sU6uF9rNvI

[Nicolas Robine @notSoJunkDNA]

Special nugget for my genomics friends in today's paper: Read everything but don't miss Extended Data Fig. 8, where @willbfx assembled a CCND1-ecDNA from @nanopore reads!

[Will Hooper @willbfx]

@AlexandrePCheng @CRCHUM @etsmtl Congrats! 🎉🥳🍾

[Dan Landau @landau_lab]

"Did you know that you don't need targeted panels for ultra-sensitive MRD?"

🥳 Down right ebullient to share our latest 🥳@NatureMedicine !

MRD-EDGE leverages advanced #ML for #WGS #ctDNA detection across clinical context

https://t.co/drJasWVwoE

#DeepLearning

🪡

[Kentsis Research Group @KentsisResearch]

Human cancer is a disease of somatic mutations. As we age, tissues accumulate errors in DNA, but what causes mutations in young healthy cells? Read our new paper “Childhood cancer mutagenesis caused by transposase-derived PGBD5” https://t.co/B3RKAtYIWd 1/n

[Nicolas Robine @notSoJunkDNA]

We (@nygenome cancer compbio group) are very fortunate to work closely with @WCMEnglanderIPM and have several papers in preparation. Here is one focused on brain metastases in prostate cancer with @FKhaniPath @willbfx @mishabeltran
https://t.co/v7rT6XQV3v

[Toni Choueiri, MD @DrChoueiri]

I like very much this work from @FaltasLab in bladder cancer. It is innovative and an example of tumor evolution. It builds on what we know from #TracerX with @CharlesSwanton’ group. Bravo Bishoy! @OncoAlert @Cornell @DanaFarber_GU @OncoBellmunt @CharleneMantia @bergsa83 @BradMcG04 @sonpavde

[Dr. Bishoy M. Faltas @FaltasLab]

Pre-print alert 🚨Excited to share our new preprint “The interplay between mutagenesis and extrachromosomal DNA shapes urothelial cancer evolution” 🧬🔬#bladdercancer https://t.co/lDZf36CpB9 @OncoAlert

[Nicolas Robine @notSoJunkDNA]

[job] Join my group! Bioinformatics Analyst, Computational Biology @nygenome. https://t.co/xM0lnJQoc6

[GenomeWeb @GenomeWeb]

NY Genome Center Team Harnesses Ultima Genomics Platform for High-Sensitivity ctDNA Sequencing. Taking advantage of the new platform’s low sequencing cost, the researchers sequenced cell-free circulating DNA (ccfDNA) in plasma at high depth for... https://t.co/EdHALvo6H5

[Dan Landau @landau_lab]

🔥Extra-hot pre-print before this hellsite goes up in smoke 🔥

New horizons open up when sequencing costs go ↘️ @UltimaGenomics

Interested in deep cfDNA WGS for ultra-sensitive cancer detection? Duplex sequencing at genome scale?

https://t.co/DJeCo86ok8
Check out 🪡👇

[Kentsis Research Group @KentsisResearch]

Read our latest on the causes of oncogenic DNA rearrangements in medulloblastomas, a common childhood brain tumor: Childhood cancer mutagenesis caused by a domesticated DNA transposase https://t.co/4h37LJEoSv