Shachaf Rofe

📢 SilicoScientia 𝐢𝐬 𝐏𝐫𝐞𝐬𝐞𝐧𝐭𝐢𝐧𝐠 𝐚𝐭 𝐭𝐡𝐞𝐃𝐫. 𝐃. 𝐘. 𝐏𝐚𝐭𝐢𝐥 𝐁𝐢𝐨𝐭𝐞𝐜𝐡𝐧𝐨𝐥𝐨𝐠𝐲 𝐚𝐧𝐝 𝐁𝐢𝐨𝐢𝐧𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐜𝐬 𝐈𝐧𝐬𝐭𝐢𝐭𝐮𝐭𝐞, 𝐏𝐮𝐧𝐞🎉 We are elated to announce that our team will be presenting at the 𝐈𝐧𝐭𝐞𝐫𝐧𝐚𝐭𝐢𝐨𝐧𝐚𝐥 𝐂𝐨𝐧𝐟𝐞𝐫𝐞𝐧𝐜𝐞 𝐨𝐧 𝐀𝐝𝐯𝐚𝐧𝐜𝐞𝐬 𝐢𝐧 𝐁𝐢𝐨𝐭𝐞𝐜𝐡𝐧𝐨𝐥𝐨𝐠𝐲 𝐚𝐧𝐝 𝐁𝐢𝐨𝐢𝐧𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐜𝐬 (𝐈𝐂𝐀𝐁𝐁 2024) on 27th of November This is an incredible opportunity to showcase our cutting-edge research and connect with global leaders in computational biology and drug discovery. 🔬 𝐎𝐮𝐫 𝐏𝐫𝐞𝐬𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧 𝐇𝐢𝐠𝐡𝐥𝐢𝐠𝐡𝐭𝐬: 𝐓𝐢𝐭𝐥𝐞: ToxAI: Revolutionizing Toxicity Prediction with Machine Learning We’re excited to share our expertise and foster collaboration with fellow innovators who are as passionate about accelerating advancements in bioinformatics as we are. 📅 𝐉𝐨𝐢𝐧 𝐔𝐬 Let’s discuss the future of bioinformatics and how we can shape it together. If you’re attending, come meet us and be part of this exciting journey! Link for the conference :- https://lnkd.in/dEcCijV2 #SilicoScientia #Bioinformatics #DYPatilUniversity #DrugDiscovery #AIinBiology #Collaboration #Innovation

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🔬 𝐍𝐞𝐰 𝐓𝐞𝐜𝐡𝐧𝐢𝐪𝐮𝐞 𝐟𝐨𝐫 𝐔𝐧𝐝𝐞𝐫𝐬𝐭𝐚𝐧𝐝𝐢𝐧𝐠 𝐨𝐟 𝐂𝐡𝐫𝐨𝐦𝐚𝐭𝐢𝐧 𝐎𝐫𝐠𝐚𝐧𝐢𝐳𝐚𝐭𝐢𝐨𝐧! 🧬 𝐈𝐧 𝐎𝐜𝐭𝐨𝐛𝐞𝐫 𝟐𝟎𝟐𝟒, Researchers at the UNIVERSITY OF CALIFORNIA, SAN DIEGO MEDICAL CENTER for #Epigenomics (C4E) have developed a new technique, called Droplet Hi-C, that allows #scientists to rapidly determine chromatin organization, the arrangement of genetic material within #cells. Chromatin organization influences how genes are activated in cells and, in turn, how those cells function The researchers have already deployed the technique, which works by capturing individual cells in tiny droplets, to study chromatin organization in mouse brain cells and in human tumors. In the long term, Droplet Hi-C could drive the discovery of new drug targets and help explain how cancer evolves to resist treatment. The technique may also have applications in #clinical settings, where it could provide personalized insights into disease progression and #treatment options. 𝗕𝗿𝗼𝘄𝘀𝗲 𝗮𝘁 𝗼𝘂𝗿 𝗥𝗲𝗹𝗮𝘁𝗲𝗱 𝗥𝗲𝗽𝗼𝗿𝘁 👉 https://lnkd.in/gGeN6Kcn #ChromaticOrganization #Epigenomics #NewTechnique #GeneticMaterial #ComplexDisease

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🚀 𝐔𝐧𝐥𝐨𝐜𝐤 30% 𝐎𝐟𝐟 𝐘𝐨𝐮𝐫 𝐍𝐞𝐱𝐭 𝐓𝐫𝐚𝐧𝐬𝐜𝐫𝐢𝐩𝐭𝐨𝐦𝐢𝐜𝐬 𝐒𝐞𝐪𝐮𝐞𝐧𝐜𝐢𝐧𝐠 𝐏𝐫𝐨𝐣𝐞𝐜𝐭! 🚀 𝘌𝘯𝘥 𝘵𝘩𝘦 𝘺𝘦𝘢𝘳 𝘴𝘵𝘳𝘰𝘯𝘨 𝘸𝘪𝘵𝘩 𝘦𝘹𝘤𝘭𝘶𝘴𝘪𝘷𝘦 𝘴𝘢𝘷𝘪𝘯𝘨𝘴 𝘰𝘯 𝘤𝘶𝘵𝘵𝘪𝘯𝘨-𝘦𝘥𝘨𝘦 𝘵𝘳𝘢𝘯𝘴𝘤𝘳𝘪𝘱𝘵𝘰𝘮𝘪𝘤𝘴 𝘴𝘰𝘭𝘶𝘵𝘪𝘰𝘯𝘴. 𝘚𝘶𝘱𝘦𝘳𝘤𝘩𝘢𝘳𝘨𝘦 𝘺𝘰𝘶𝘳 𝘳𝘦𝘴𝘦𝘢𝘳𝘤𝘩 𝘸𝘪𝘵𝘩 𝘵𝘩𝘪𝘴 𝘭𝘪𝘮𝘪𝘵𝘦𝘥-𝘵𝘪𝘮𝘦 𝘰𝘧𝘧𝘦𝘳 — 𝘢𝘷𝘢𝘪𝘭𝘢𝘣𝘭𝘦 𝘶𝘯𝘵𝘪𝘭 𝘋𝘦𝘤𝘦𝘮𝘣𝘦𝘳 30𝘵𝘩, 2024. 𝘋𝘰𝘯’𝘵 𝘮𝘪𝘴𝘴 𝘰𝘶𝘵! In genomics, capturing a complete view of gene expression is vital for accurate biological insights. But when it comes to RNA sequencing, two approaches often stand out: Whole-Transcriptome Sequencing (WTS) and mRNA Sequencing (RNA-seq). While both have unique strengths, there are key differences that make WTS invaluable in research and diagnostics. Let's dive in! 🔬 1️⃣ 𝐂𝐨𝐦𝐩𝐫𝐞𝐡𝐞𝐧𝐬𝐢𝐯𝐞 𝐂𝐨𝐯𝐞𝐫𝐚𝐠𝐞 𝐨𝐟 𝐭𝐡𝐞 𝐓𝐫𝐚𝐧𝐬𝐜𝐫𝐢𝐩𝐭𝐨𝐦𝐞 RNA-seq focuses specifically on mRNA, giving insights into protein-coding genes by analyzing exons. This is excellent for studying gene expression at the coding level. WTS, on the other hand, captures ALL RNA types—including non-coding RNA, long non-coding RNA (lncRNA), small RNA, microRNA (miRNA) and circular RNA. This gives a complete view of the transcriptome, unlocking data that RNA-seq can't access, which is essential for understanding complex regulatory networks. 2️⃣ 𝐍𝐨𝐧-𝐂𝐨𝐝𝐢𝐧𝐠 𝐑𝐍𝐀𝐬 𝐚𝐧𝐝 𝐓𝐡𝐞𝐢𝐫 𝐑𝐨𝐥𝐞 𝐢𝐧 𝐃𝐢𝐬𝐞𝐚𝐬𝐞 With the broader coverage of WTS, researchers can detect non-coding RNAs, which play crucial roles in gene regulation, disease mechanisms, and cancer pathways. These RNA species often remain underexplored with RNA-seq, limiting the depth of insights for diseases with regulatory complexity. 3️⃣ 𝐃𝐞𝐭𝐞𝐜𝐭𝐢𝐧𝐠 𝐆𝐞𝐧𝐞 𝐅𝐮𝐬𝐢𝐨𝐧𝐬 𝐚𝐧𝐝 𝐈𝐬𝐨𝐟𝐨𝐫𝐦𝐬 Unlike mRNA sequencing, WTS allows for the discovery of gene fusions, alternative splicing events, and transcript isoforms that contribute to cellular diversity. These details can be pivotal in cancer research, where fusion genes and isoform diversity often drive disease progression and drug resistance. 4️⃣ 𝐁𝐢𝐨𝐦𝐚𝐫𝐤𝐞𝐫 𝐃𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐲 𝐚𝐧𝐝 𝐃𝐢𝐚𝐠𝐧𝐨𝐬𝐭𝐢𝐜𝐬 𝐏𝐨𝐭𝐞𝐧𝐭𝐢𝐚𝐥 WTS’s ability to capture the entire RNA landscape opens doors to more comprehensive biomarker discovery. Non-coding RNAs, fusion genes, and novel transcripts offer new diagnostic markers that RNA-seq would miss, broadening potential applications in personalized medicine. In essence, while mRNA sequencing remains a powerful tool for understanding gene expression, Whole-Transcriptome Sequencing offers a 360-degree view that is unmatched. For researchers and clinicians aiming to unravel complex diseases, WTS provides the full transcriptomic picture needed to make breakthrough discoveries. 🌐💡 Let’s continue advancing our genomic toolbox and leverage these innovations to drive impactful insights!

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🚀 Exciting Research Update! 🚀 We are thrilled to share that Dmytro Pastukh from Diagnostics @Fraunhofer IMM is embarking on a 3-month research stay at INTERFIBIO under the supervision of Dr. Ciara O' Sullivan and Dr. Vasoula Skouridou. Dmytro’s research focuses on the dynamic and increasingly crucial field of on-chip recombinase polymerase amplification for point-of-care settings. As at INTERFIBIO, the current research goal of the cancer and infection diagnostics group at Fraunhofer IMM is to address the emerging and future paradigm of personalised medicine in which the detection of multiple biomarkers plays a pivotal role #cfDNA. During his time at INTERFIBIO, Dmytro will concentrate on developing solid-phase amplification systems to facilitate multiplexed detection, pushing the boundaries of diagnostic capabilities. INTERFIBIO has a long-standing collaboration with Fraunhofer-IMM, having worked together on over 10 EU-financed projects since 2003 and publishing in high-impact factor peer-reviewed journals. Currently, Interfibio and Fraunhofer-IMM are collaborating on three EU-financed projects. Interfibio is developing solid-phase amplification strategies for detecting SNPs, genes, and aptamer-based protein detection, while Fraunhofer-IMM is creating the prototype microsystem to house all reagents and detection devices. This partnership highlights the excellent complementarity between our teams. Stay tuned for more updates as we continue to innovate and drive forward the future of diagnostics! #Research #Innovation #Diagnostics #PersonalizedMedicine #Collaboration #Biomarkers

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Dr. Hans Binder took part in a two-day symposium, "Advances in Epigenetics and Biotechnology," held at Russian - Armenian University (RAU) from December 16 to 17, 2024. He shared his expertise in bioinformatics. His presentation focused on how combining different -omics data modalities can help improve our understanding of diseases. 🧬💻 The symposium gathered participants from a variety of top universities and institutions across several countries, including Russia, Armenia, Germany, and the United States. These participants, including researchers from Leipzig University, Southern Federal University, Saarland University, and more, shared their work on epigenetics, cancer therapies, gene editing, and more.🌍

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An Optimized Protocol of Electroporation of Hepatocyte Nuclear Factor 1 Alpha (Hnf-1α) in Mesenchymal Stem Cells https://lnkd.in/egG2zmPW #Alamarblue #G418 #pulse #stemcells #transfectionefficiency #viability #voltage Abstract The objective of this study was to investigate the optimization of electroporation of hepatocyte nuclear factor 1 alpha (Hnf-1α) in murine mesenchymal stem cells (mBM-MSCs). mBM-MSCs were phenotypically observed and confirmed by positive expression of stemness markers with differentiation capacity into osteocytes. Hnf-1α plasmid DNA was transfected via Neon electroporation system into the mBM-MSCs. The cells were maintained in a complete DMEM medium. Following single 0.5 μg Hnf-1α electroporation the differences in viability of mBM-MSCs were statistically insignificant at 24 h, 72 h, and post-21 days. Fluorescence imaging of turbo green fluorescence protein (tGFP) was detected for the efficiency of transfection. The transfection efficiency was detected at parameters of 1000 pulse voltage (V), 10 pulse width (ms), and at 3 pulse number at 24 h (***p-value < 0.001, 66.5 ± 12.2%) in mBM-MSCs. The efficiency of transfected 0.5 μg Hnf-1α was decreased at 72 h (40.2 ± 10.9%) and 21 days (31.7 ± 5%). 250 μg/mL G418 Sulfate was used for the selection of Hnf-1α transfected positive cells. TaqMan-qRT-PCR results of independent experiments revealed significant fold differences in Hnf-1α expression with above mentioned defined parameters. Therefore, 0.5 μg Hnf-1α plasmid into 2.5 × 105 mBM-MSCs with a pulse voltage of 1000 V, pulse width of 10 ms, and pulse number of 3, was optimized, which was not reported before. These parameters can be considered for transfection with cell viability of 65–96% from 24 h to 21 days and 60–70% transfection efficiency after 24 h. Hence, this optimized procedure with efficient transfection rates can be applied for further gene functions and differentiation studies in the liver, pancreas, kidney, intestine, and for other tissues in specialized niches. Keywords:  Alamar blue G418 pulse stem cells transfection efficiency viability voltage

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I am delighted to share my recent contributions to the collaborative posters presented by Ilya Volodyaev at the 14th biennial ALPHA Scientists In Reproductive Medicine meeting. One of our projects, titled “Some tips and tricks after over 1,000 nuclear transfers in mice”, encapsulates our practical experience in mouse embryo pronuclear transfers. Furthermore, our second poster, named “Chromosomal abnormalities in embryo development: what do we really know about them and what have we made up?", meticulously examines the current understanding of chromosomal abnormalities in early human embryos, deciphering the evidence from non-evidence. For more details on our work, you can access the full abstracts at the link below: https://lnkd.in/e_HK6iJN #ALPHAconference #embryology #mosaicism #nucleartransfer

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Recent research at Sheba Medical Center is uncovering the microbiome’s significant role in cancer treatment. Ben Boursi, a doctor in the Gastrointestinal Cancer Department, and his team are exploring how the bacteria, viruses, and fungi within our bodies influence cancer progression and treatment responses. Their study suggests that unique microbial signatures may predict how patients respond to therapies, including immunotherapy. In a recent clinical trial, metastatic melanoma patients who hadn’t responded to conventional treatments showed promising results with fecal microbiome transplantation (FMT). This innovative approach is paving the way for personalized cancer care, offering new hope for treatment-resistant cancers. Read the full article here: https://lnkd.in/dHqTUb5B 

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#SCIENCENEWS 🔬🧬 Exciting breakthrough in mRNA regulation research from Hebrew University! This study sheds light on how genes are activated in specific cells at precise times, revolutionising our understanding of embryonic development. This advancement in gene regulation unfolds potential applications in medicine and biology. Curious to learn more🧐🤔? Read the full article at: https://lnkd.in/geBxQxUh 🔍 Take a deeper look into our profile as well to explore the depth of the cutting-edge projects we're working on, pushing the boundaries of what’s possible. 🌟Together, we embark on a meaningful journey, united by a common purpose: to create a better tomorrow for all. 📧📫Contact us: sharehuj.sg@gmail.com Join SHARE - Where Every Idea Counts, Innovation takes Center Stage, together we celebrate the spirit of collaboration!  ---------------------- SHARE- The Singapore-Hebrew University Alliance for Research and Enterprise ✔️Website: https://lnkd.in/gtd6JZ5V ✔️FB Page: https://lnkd.in/eGAnnCmM ✔️Instagram: https://lnkd.in/gnmK_84A ✔️LinkedIn: https://lnkd.in/gMrj9apd ✔️YouTube Channel: www.youtube.com/@SHARESG 📌Address: CREATE TOWER, SINGAPORE #SHAREResearch #ResearchSG #ResearchSingapore #ShareHUJ  #InnovationHub  #ResearchExcellence  #ResearchPartnerships #AcademicAlliance #SGResearchHub    #CareerAdvancement #Opportunities #ProfessionalGrowth #ResearchOpportunities #JoinOurTeam #Joinshare #HebrewUniversity #HUJ #Science #Technology #Molecular #Molecules #Biology #Zebrafish #Embryo #Development #RNA #mRNA #FutureTech

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Bacterial Memory: A New Frontier in #Probiotic #Engineering: Beneficial bacteria's memory paves the way for improved agricultural and industrial applications, thanks to groundbreaking research from Reichman University. https://lnkd.in/gfEmjkXA #probiotics #synbio

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𝐁𝐞𝐭𝐭𝐞𝐫 𝐥𝐚𝐭𝐞 𝐭𝐡𝐚𝐧 𝐧𝐞𝐯𝐞𝐫, 𝐫𝐢𝐠𝐡𝐭? I am very glad that my Master's degree main article is out and published in BMC Genomics! Title: "𝗘𝘃𝗼𝗹𝘂𝘁𝗶𝗼𝗻 𝗼𝗳 𝗺𝘆𝘅𝗼𝘇𝗼𝗮𝗻 𝗺𝗶𝘁𝗼𝗰𝗵𝗼𝗻𝗱𝗿𝗶𝗮𝗹 𝗴𝗲𝗻𝗼𝗺𝗲𝘀: 𝗶𝗻𝘀𝗶𝗴𝗵𝘁𝘀 𝗳𝗿𝗼𝗺 𝗺𝘆𝘅𝗼𝗯𝗼𝗹𝗶𝗱𝘀." 𝗬𝗼𝘂 𝗰𝗮𝗻 𝗰𝗵𝗲𝗰𝗸 𝘁𝗵𝗲 𝗽𝗱𝗳 𝗼𝗳 𝘁𝗵𝗲 𝗳𝘂𝗹𝗹 𝗮𝗿𝘁𝗶𝗰𝗹𝗲 𝗳𝗼𝗿 𝗳𝗿𝗲𝗲 𝗶𝗻 𝗺𝘆 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵𝗚𝗮𝘁𝗲 𝗽𝗮𝗴𝗲. We fully assembled 5 mitochondrial genomes of myzoxoan species, from a clade that was lacking enough representativity in the genomics databases. Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.

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🌊🦪Dive into the wonders of DUI (Doubly Uniparental Inheritance). We often think mitochondrial DNA is solely inherited from the mother, but clams like Ruditapes philippinarum (Manila clam) and more bivalve species teach us that fathers play a crucial role too! 🦪🔬 This unique genetic inheritance and bottlenecks leads to a mind-blowing scenario: DUI clams of different species can be more genetically similar to each other than to the opposite gender of their own species! It’s a reminder of how much more there is to explore and discover in the world of marine biology. 🌊✨ In short, the presentation of the poster was very experiential and fun thanks to the amazing team members and our supervisor Professor Yaron Tikochinski Stay curious and keep exploring! #MarineBiology #Genetics #DUI #ScienceExploration

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