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Mashup Score: 59PIVOT: an open-source tool for multi-omic spatial data registration - 11 hour(s) ago
Advances in spatial profiling have resulted in the generation of multi-omic atlases that span biological scales. In general, multiple workflows are required for image registration, coordinate registration, and spot deconvolution to integrate modalities. To improve the throughput of registration of multi-omic cohorts, we introduce PIVOT, a user-friendly and open-source interface for streamlined nonlinear registration. We demonstrate PIVOT’s strengths through registration of three multi-omic datasets and show comparison of its performance to existing workflows. ### Competing Interest Statement AM is listed as an inventor on a patent that has been licensed from Johns Hopkins University to Exact Sciences Ltd. BreakThrough Cancer Data Science BreakThrough Cancer Demystifying Pancreatic Cancer Therapies the Johns Hopkins University Data Science and Artificial Intelligence Institute (DSAI) National Institutes of Health, U54CA268083, U54CA274371, U24CA274274, U2CCA233280 Lustgarten Foundation-
Source: www.biorxiv.orgCategories: General Medicine NewsTweet
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Mashup Score: 0
A spatial functional genomics platform termed Perturb-map combines CRISPR pools, multiplex imaging, and spatial transcriptomics to enable the identification of genetic determinants of tumor composition, organization, and immunity.
Source: www.cell.comCategories: General Medicine NewsTweet-
Original PerturbMap paper from Brown lab @IcahnMountSinai https://t.co/UXLLwMMk6d
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Mashup Score: 1The Neuroscience of Cancer - 2 day(s) ago
Of the many tumor slides William Hwang, MD ’15 PhD ’13, has seen, there’s one in particular that is seared into his memory. He encountered it as a medical student while on a rotation caring for an elderly patient with pancreatic cancer. “What struck me as the most horrible part of the experience for them was the pain,” he recalls. Hwang wanted to understand where that intractable pain was coming from. So, he asked Mari Mino-Kenudson, an HMS professor of pathology at Massachusetts General Hospital, to
Source: magazine.hms.harvard.eduCategories: General Medicine NewsTweet-
RT @DrWilliamHwang: https://t.co/jojjT0ccfP
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Mashup Score: 15Private equity firm will finance Harvard research lab, in possible template for future - 3 day(s) ago
A private equity firm will finance a Harvard University research lab, a possible template for the future as schools nationwide absorb federal funding cuts.
Source: www.statnews.comCategories: General Medicine NewsTweet-
Adding private equity to alternative sources of funding. The caveat is PE is likely to fund research with unequivocal translational potential (typically therapeutic) - not the fundamental mechanistic science that NIH has supported. Via @statnews: https://t.co/6zpDQoDwa4 https://t.co/SIRubc6614
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Mashup Score: 15Private equity firm will finance Harvard research lab, in possible template for future - 3 day(s) ago
A private equity firm will finance a Harvard University research lab, a possible template for the future as schools nationwide absorb federal funding cuts.
Source: www.statnews.comCategories: General Medicine NewsTweet-
Adding private equity to alternative sources of funding. The caveat is PE is likely to fund research with unequivocal translational potential (typically therapeutic) - not the fundamental mechanistic science that NIH has supported. Via @statnews: https://t.co/6zpDQoDwa4 https://t.co/SIRubc6614
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Mashup Score: 13Private equity firm will finance Harvard research lab, in possible template for future - 3 day(s) ago
A private equity firm will finance a Harvard University research lab, a possible template for the future as schools nationwide absorb federal funding cuts.
Source: www.statnews.comCategories: General Medicine NewsTweet-
Adding private equity to alternative sources of funding. The caveat is PE is likely to fund research with unequivocal translational potential (typically therapeutic) - not the fundamental mechanistic science that NIH has supported. Via @statnews: https://t.co/6zpDQoDwa4 https://t.co/SIRubc6614
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Mashup Score: 5Spatial Total RNA Sequencing of Formalin-Fixed Paraffin Embedded Tissues by spRandom-seq - 8 day(s) ago
Current sequencing-based spatial transcriptomic methods have been widely used to resolve gene expression; however, these methods are limited to fresh or fresh-frozen samples due to the low efficiency of oligo(dT) primers in capturing RNA transcripts in degraded samples. Here, we have developed a random primer-based spatial total RNA sequencing (spRandom-seq) technology for capturing full-length total RNAs in partially degraded (low RIN values) formalin-fixed paraffin-embedded (FFPE) tissues. Our spRandom-seq approach exhibited no discernible biases at the 3’- or 5’-ends within gene bodies and could be integrated with the commercially available 10X Visium and other well-established sequencing-based spatial transcriptomic platforms. Our spRandom-seq approach outperformed oligo(dT)-based 10X Visium with an 8-fold higher capturing rate for long-non-coding RNA (lncRNA) and other non-polyadenylated RNA biotypes, including miRNA, snRNA, and miscRNA. The unsupervised clustering with solely non
Source: www.biorxiv.orgCategories: General Medicine NewsTweet-
RT @LukasValihrach: Spatial Total RNA Sequencing of Formalin-Fixed Paraffin Embedded Tissues by spRandom-seq https://t.co/qMUGI4at5w
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Mashup Score: 14
Login with your AGA username and password. Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN, United States Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, United States Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan Department of Gastroenterology and Hepatology
Source: www.gastrojournal.orgCategories: General Medicine NewsTweet-
Pharmacological inhibition of the RAS pathway in PRECANCERS for cancer interception enters the clinic. In @AGA_Gastro Safety and efficacy of MEK inhibitor treatment for gastric pre-cancerous lesions (intestinal metaplasia) https://t.co/zJDpNGfH4e https://t.co/TkC3osKtzO
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Mashup Score: 19Cancer statistics, 2025 - 19 day(s) ago
Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths in the United States and compiles the most recent data on population-based cancer occurrence and outcomes u…
Categories: General Medicine NewsTweet-
Major challenges: - Cancer disparities remain widespread - Cancer incidence in women continues to rise surpassing men in Gen X already - Challenges of recalcitrant cancers like #PancreaticCancer persist Link to the #OpenAccess paper https://t.co/UtlS5vt3bT
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Mashup Score: 11He Was Bleeding Internally. Then Doctors Found the Real Danger. - 20 day(s) ago
After weeks of discomfort, the 25-year-old man got a shocking explanation for his abdominal pain.
Source: www.nytimes.comCategories: General Medicine NewsTweet-
25 year old man with #PancreaticCancer arising in association with a pancreatic pseudocyst (presenting symptoms). Strange case. Cannot tell if the lesion is an adenocarcinoma or a variant histology. At 25y, I hope they looked for germline mutations. https://t.co/64dEn2R9rM
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PIVOT is a very useful open source tool from @AshleyKiemen @andreforjaz @deniswirtz and colleagues at @hopkinskimmel that allows for co-registration and integration of multi-omic spatial data (eg, Visium, cyclicIF, imaging mass cytometry). Preprint: https://t.co/WkwNJSyger https://t.co/aI8V8wZ5M8