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Arnau Montagud

@arnaumontagud.bsky.social
387 followers 913 following 36 posts

Tenured Researcher on Computational Systems Biology Institute for Integrative Systems Biology (@i2sysbio.bsky.social), @csic.es visitor at @bsc-cns.bsky.social, @alfonsovalencia.bsky.social team also at @arnaumontagud@fediscience.org

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Reposted by Arnau Montagud
Emily R. Trunnell, Ph.D. @ertrunnell.bsky.social · 09/10/2025
An international team of immunologists, clinicians, experimentalists, computational biologists, and engineers is building an Immune Digital Twin to transform human healthcare for immune-mediated diseases. #ImmunoSky #DigitalTwin 🧪
Figure two from the paper linked below: The BIDT WG and connected Systems Biology communities.
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Emily R. Trunnell, Ph.D. @ertrunnell.bsky.social · 09/10/2025
By Niarakis et al., including: @athinacp.bsky.social @eirini-tsirvouli.bsky.social @hasanbalci.bsky.social @ozanozisik.bsky.social @arnaumontagud.bsky.social @subbannayya.bsky.social @mkutmon.bsky.social Learn about their 5-year plan: www.immunoinformaticsjournal.com/article/S266...
immunoinformaticsjournal.com
Building Immune Digital Twins: An International and Transdisciplinary Community Effort
Digital twins, initially developed for industrial applications, are set to make significant advancements in medicine and healthcare. They have demonstrated promising potential for drug development and...
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Reposted by Arnau Montagud
Beatriz Urda @beatrizurda.bsky.social · 02/09/2025
🚨 New in PNAS! 🧬 64% of disease co-occurrences can be explained by transcriptomic similarities. Comorbidities aren’t random—they have a molecular basis. Here’s how we found it 👇 (1/n) 🔗 doi.org/10.1073/pnas.2421060122 @alfonsovalencia.bsky.social
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Beatriz Urda @beatrizurda.bsky.social · 02/09/2025
8/ Science already takes time, I hope to help make it worth it. Finally, terrified, we sent it to PNAS @pnas.org. After one round of review, reports came back: supportive. Positive. Accepted 🎉 🎉
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Beatriz Urda @beatrizurda.bsky.social · 02/09/2025
1/ Everything that could go wrong in paper publishing… did. A story of patience, absurdity, and persistence 🌀 <1min From Alfonso Valencia’s lab and a very stubborn PhD student (me).
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I2SysBio @i2sysbio.es · 29/07/2025
📢🔬 Abierto el plazo de inscripción para la II Jornada de Colaboración Público-Privada sobre Biología Computacional del #I2SysBio (@csic.es - @uv.es). 🗓 2 de septiembre www.i2sysbio.es/communicatio... ✍ Asistencia gratuita bajo previa inscripción. @moldrug.bsky.social @protoqsar.bsky.social
i2sysbio.es
Registration is now open for the 2nd Public-Private Collaboration Workshop on Computational Biology at I2SysBio
<p><strong>The I2SysBio (CSIC-UV) will hold its second Public-Private Collaboration Workshop, a meeting that will bring together researchers, companies and organisations from the sector to discuss eme...
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Arnau Montagud @arnaumontagud.bsky.social · 01/08/2025
Great opportunity to learn about computational systems biology modelling at the Wellcome Genome Campus in December. If you are interested in signing up, do so as soon as possible as the deadline is August 25!
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Alfonso Valencia @alfonsovalencia.bsky.social · 31/07/2025
>> My conclusion: we do not have to demonstrate anything they have to change and adapt to the evolution of science / biology<< And computational biology is an essential component of biology. (It is ridiculous to have to say this in 2025)
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Reposted by Arnau Montagud
Schneier on Security @schneier.com · 07/07/2025
Hiding Prompt Injections in Academic Papers Academic papers were found to contain hidden instructions to LLMs: It discovered such prompts in 17 articles, whose lead authors are affiliated with 14 institutions including Japan's Waseda University, South Korea's KAIST, China's Peking University and…
schneier.com
Hiding Prompt Injections in Academic Papers
Academic papers were found to contain hidden instructions to LLMs: It discovered such prompts in 17 articles, whose lead authors are affiliated with 14 institutions including Japan's Waseda University, South Korea's KAIST, China's Peking University and the National University of Singapore, as well as the University of Washington and Columbia University in the U.S. Most of the papers involve the field of computer science.
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Reposted by Arnau Montagud
I2SysBio @i2sysbio.es · 09/05/2025
Original article: www.nature.com/articles/s41... 🧬🖥️ 👩‍🔬 🧪 The article explains how long-read transcriptomics enables the study of isoform expression, discovery of novel RNAs, gene annotation in understudied species, and differential expression between paternal and maternal chromosomes, etc.
nature.com
Transcriptomics in the era of long-read sequencing - Nature Reviews Genetics
Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read RNA sequencing, including expe...
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Reposted by Arnau Montagud
I2SysBio @i2sysbio.es · 13/05/2025
🦑🧪 I2SysBio researchers participate in Catalan Initiative for the Earth Biogenome Project @catbiogenoma.bsky.social of the Institut d'Estudis Catalans @iec.cat. Recently, Maria Dzunkova's @dzunkovam.bsky.social team published a paper in Ecology and Evolution 🌐 www.i2sysbio.es/communicatio... ⬇️
i2sysbio.es
A more effective extraction method has been identified for obtaining high-quality DNA in less than ideal conditions
<p><strong>The &lsquo;<a href="https://i2sysbio.es/groups/19/">Microbial Single-Cell Genomics</a>&#39; research group at the Institute for Integrative Systems Biology I2SysBio (University of Valencia-...
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Vincent Noël @vincent-noel.fr · 12/05/2025
Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.
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Arnau Montagud @arnaumontagud.bsky.social · 08/05/2025
... it's dissolving humanity and culture and science... Without pause and time to think and reflect, and dedication to reach deeper into a problem, we only have the appearance of science. The incentives are all in the wrong side.
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Reposted by Arnau Montagud
I2SysBio @i2sysbio.es · 06/05/2025
🚨 Two PhD positions available in the lab of @arnaumontagud.bsky.social in I2SysBio 🇪🇸. Both are related to simulations of biological tissues
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Arnau Montagud @arnaumontagud.bsky.social · 06/05/2025
📢 Exciting news! We will soon open two PhD positions at @i2sysbio.bsky.social @csic.es, in research projects in collaboration with the @bsc-cns.bsky.social. Both are related to tools to simulate biological tissues. Here’s the description of the open positions. #PhDpositions #PhDOpportunities 👇
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Laura Cantini @cantinilab.bsky.social · 16/04/2025
Excited to see scPRINT published in @natcomms.nature.com ! scPRINT is a large cell model for the inference of gene networks pre-trained on 50Mcells with innovative pretraining tasks inspired from biology. Work led by @jkobject.com
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I2SysBio @i2sysbio.es · 04/04/2025
Alfred Fillol @alfredfisa.bsky.social, Arnau Montagud @arnaumontagud.bsky.social and Guillem Salazar @guillemsalazar.bsky.social are the three scientists who joined the Faculty of our institute I2SysBio last year. Follow them on Bluesky! More info on our website www.i2sysbio.es/communicatio... 🧪🦠💻🧬
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Clémence Frioux @cfrioux.bsky.social · 08/04/2025
⭐️We are hiring! ⭐️ We have 2 open postdoctoral positions in systems biology in Bordeaux, France. - 1️⃣ 2 years (+ 2) in metabolic modelling for cultivating uncultured bacteria. - 2️⃣ 18 months (+ 14 mo) in metabolic modelling of the rumen microbiome for methane reduction More info: cfrioux.github.io ⬇️
cfrioux.github.xn--io-ix0a
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PathoGenOmics Lab @pathogenomics.bsky.social · 25/03/2025
HubBCB-01 @CSIC.es. Impacto del microbioma respiratorio humano en la introducción de un nuevo patógeno. IP Mireia Coscolla (I2SYSBIO, Valencia) Cinco meses, cinco mensualidades de 600€, 20 horas/semana. Nota media de grado al menos 7. Si grado terminado, matriculado master bioinformática o similar.
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Christina Toft @christinatoft.bsky.social · 25/03/2025
Beca JAE-Intro ICU 2025 para realización TFM en bioinformática (HubBCB-14), bajo la dirección de @christinatoft.bsky.social en el @i2sysbio.bsky.social 5 meses, 20h/semana, 600euros/mes Solicitudes hasta 16 Abril '25 más información en: sede.csic.gob.es/tramites/pro... DM si interesado/a
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Arnau Montagud @arnaumontagud.bsky.social · 18/03/2025
Convocatoria JAE Intro @csic.es abierta! El @i2sysbio.bsky.social oferta 5 plazas para personas que tengan un grado en Ciencias durante 5 meses a media jornada. Ideales para estudiantes de máster en busca de un proyecto de iniciación a la investigación. Más info: sede.csic.gob.es/tramites/pro...
sede.csic.gob.es
Convocatoria JAE Intro ICU 2025 | Sede CSIC
Becas de introducción a la investigación para estudiantes universitarios.
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Ana Conesa @anaconesa.bsky.social · 14/03/2025
Tercer día de la #2AsambleaBCBHub. Tenemos el honor de contar con Elena Cartea de @csic-vaact.bsky.social abriendo la jornada contandonos las iniciativas de @csic.es en Conexiones y PTIs.
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Ⓙⓐⓥⓘⓔⓡ🇵🇸🍉 Ⓑⓤⓒⓔⓣⓐ🇺🇦🇪🇺 @javierbuceta.bsky.social · 08/03/2025
🚨El I2SysBio participa en los eventos internacionales celebrando la 'Biophysics Week' con el ya tradicional BIOPHYZZA 🍕🍻 *El evento es gratuito pero hay que inscribirse!* research.uv.es/biophyzza/ @i2sysbio.bsky.social @ucciuv.bsky.social @biophysicalsoc.bsky.social Ayudanos a difundir ↩️🙏
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BSC-CNS @bsc-cns.bsky.social · 07/03/2025
🌐Europe takes a major step towards digital autonomy in supercomputing and #AI with the launch of the DARE project 💻Based on #RISCV , this EuroHPC project coordinated by BSC will deliver high-performance & energy-efficient supercomputing for research & industry. 🔗 www.bsc.es/ZyZ
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Vera Pancaldi @verapancaldi.bsky.social · 10/03/2025
Really excited that Anna Niarakis will give the next CRCT #bioinformatics seminar on Friday 14th March at 11 in salle Cazaux!
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Ana Conesa @anaconesa.bsky.social · 13/03/2025
Next, Ana Martinez and Carmen Gil from @cib-csic.bsky.social presenting how to use a consortium of AI tools for drug design, with múltiple applicatons in the clínic @bcbhubcsic.bsky.social @csic-vaact.bsky.social #2AsambleaBCBHub
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Ana Conesa @anaconesa.bsky.social · 13/03/2025
Kickking off the second day our @bcbhubcsic.bsky.social meeting with scientific sesions with Victor Sánchez Gaya, presenting POSTRE, a tool to predict the funcional impact of pstructural variants @hitseq.bsky.social @ibv-csic.bsky.social @csic-vaact.bsky.social
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Arnau Montagud @arnaumontagud.bsky.social · 12/03/2025
@anaconesa.bsky.social opening the Second General Assembly of the @bcbhubcsic.bsky.social at the main @csic.es site. Three days of #compbio and #bioinfo discussions ahead!
Picture of the presentation session of the 2nd General Assembly of the compbio hub of CSIC
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I2SysBio @i2sysbio.es · 11/03/2025
🚨Job offer at our research institute I2SysBio 🇪🇸: Contract for International Program Management, specialized in ERC @erc.europa.eu programs 🧪 #science #researchgrants #JOBOFFER #i2sysbio @ucciuv.bsky.social @csic.es @uv.es i2sysbio.es/position/4/
i2sysbio.es
i2sysbio - Position
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Derek Thompson @dkthomp.bsky.social · 27/02/2025
Unbelievable news. Pancreatic is one of the deadliest cancers. New paper shows personalized mRNA vaccines can induce durable T cells that attack pancreatic cancer, with 75% of patients cancer free at three years—far, far better than standard of care. www.nature.com/articles/s41...
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BCBHubCSIC @bcbhubcsic.bsky.social · 06/02/2025
📢 The recorded session is available at this YouTube link youtu.be/TzZpObN1fhs
youtu.be
Arnau Montagud presents the tool PROFILE
YouTube video by Conexión CSIC BCB
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Ⓙⓐⓥⓘⓔⓡ🇵🇸🍉 Ⓑⓤⓒⓔⓣⓐ🇺🇦🇪🇺 @javierbuceta.bsky.social · 04/02/2025
If you are into modeling of multicellular systems you don't want to miss this! www.embl.org/about/info/c... @i2sysbio.bsky.social @crg.eu @barcelonacollaboratorium.com @embl.org
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Maria Dzunkova @dzunkovam.bsky.social · 28/01/2025
🚨5th of February - online bioinformatic seminar organized by @bcbhubcsic.bsky.social @csic.es on integrating multi-omics data to create comprehensive Boolean models of biological systems, presented by Arnau Montagud @arnaumontagud.bsky.social , researcher at I2SysBio @i2sysbio.bsky.social 🖥🧬
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BCBHubCSIC @bcbhubcsic.bsky.social · 27/01/2025
@arnaumontagud.bsky.social @i2sysbio.bsky.social presents the bioinformatic tool PROFILE, designed to analyse and model biological data, focusing on integrating multi-omics data to create comprehensive Boolean models of biological systems. 👉Feb 5, at 11:50 CET via us06web.zoom.us/j/88169246545
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Ana Maria Barral @bioprof.bsky.social · 13/01/2025
🧪 let's see the impact of 🔵 sky for finding expertise! My dept is in ASAP need of somebody with bioinformatics expertise to provide content for several course developments. Work is remote and contract, courses will be online asynch. Courses are for bio and data science majors. Pls spread the word! 🙏
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PhysiCell Project. @physicell.bsky.social · 15/01/2025
A fun FYI: PhysiCell was first publicly presented in 2015, with first open source release in 2016. So let's call 2025 our 10th anniversary! 🧪
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Ana Conesa @anaconesa.bsky.social · 08/01/2025
Proud of @conesalab.bsky.social and @MSCActions @LongtrecEU amazing doctoral candidate @Tian_Yuan_Liu for this timely and comprehensive review on #LongReadSequencing to profile the epigenome and reveal complex chromatin states. Published in @naturegenet.bsky.social www.nature.com/articles/s41...
nature.com
Profiling the epigenome using long-read sequencing - Nature Genetics
Long-read sequencing technologies have revolutionized genomics and transcriptomics, and more recently enabled comprehensive epigenomic profiling. These advances now also allow investigation of the rel...
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Paco a la Naranja 🍊 @pacoalanaranja.es · 21/12/2024
Agraïr a Bromera el gran treball que ha fet amb el llibre #LaCulturadelEsmorzar. En especial a Marc Senabre que a banda de bon editor, és un immillorable domador de bèsties. També als amics que ens han acompanyat en el camí @julipereto.bsky.social, i a la taula Ricard Camarena (No és Lobezno)
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Guillem Salazar @guillemsalazar.bsky.social · 10/12/2024
Estrenant-me, molt il•lusionat, al @i2sysbio.bsky.social
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Harmit Singh Malik @harmitmalik.bsky.social · 09/12/2024
I participated in a faculty panel a few weeks ago in which senior (ahem) faculty gave advice on careers in academia by pretending luck had very little to do with our success. One piece of advice riled me up, in which it was argued that a reason for their success was their ability to say no. 1/
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Meghie Rodrigues @meghier.bsky.social · 26/11/2024
Thank you so much to whoever put this very comprehensive list of #science Bsky starter packs together. This is just amazing: docs.google.com/document/d/1...
docs.google.com
Starter packs
BIOLOGY General Science community https://go.bsky.app/HVYAMEA Research Institutions in Life Sciences https://go.bsky.app/LxXpcvJ LGBTQIA+ in STEM https://go.bsky.app/BFc4wgf LGBTQIA+ in STEM 2 h...
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I2SysBio @i2sysbio.es · 04/12/2024
17 #PhD positions available within the #MSCA doctoral network project INCITE (Insect Clock Initial Training Experience) in UK, Germany, France, Poland, Netherlands, Italy, Czechia, Israel and at our institute in Valencia in Spain! Deadline 25/01/2025 More info: incite.entu.cas.cz
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Maria Dzunkova @dzunkovam.bsky.social · 04/12/2024
17 PhD opportunities in 🦠🧫🧪🔬🧬🖥🦟🪳across 9 European countries in a #MSCA doctoral network including our @i2sysbio.bsky.social institute
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Olivier Simard-Casanova @o.simardcasanova.net · 28/11/2024
Today’s workshop is about #OpenScience at @univlorraine.bsky.social More specifically, it’s about opening code written for scientific research, an emerging area of open science The room is full, it’s nice to see the scientific community embracing open science jsolorraine2024.sciencesconf.org
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Erin Biba @erinbiba.bsky.social · 27/11/2024
Ok here’s a thread of feeds that aren’t topic themed but utilitarian and do things like show you different versions of your timeline or provide services that should be official Bluesky features. 🧵
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Laura Cantini @cantinilab.bsky.social · 27/11/2024
We' re #hiring a #postdoc in my team at @pasteur.fr and @cnrs.bsky.social funded by Institut PRAIRIE to work on the inference of molecular mechanisms from the integration of spatial transcriptomics and #singlecell multi-omics data. Learn more at emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Post-doctorat (H/F) en développement de méthodes d'apprentissage automatique pour les données omiques unicellulaires
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Blai Vidiella @blaividiella.bsky.social · 12/11/2024
Why doesn’t evolution follow a path of constant #adaptation? Over the past 50 years, punctuated equilibrium has expanded leading to a unified framework for punctuated #evolution across scales—from genes to #ecosystems & our planet. Our new collaboration at doi.org/10.1111/pala...
An illustration of Punctuated Evolution across scales and systems. This is a redrawing from the article "The many ways toward punctuated evolution" at the Journal of Palaeontology. It shows PE in real data from genes (in viruses, bacteria and oncology) to ecosystems (paleoecology). The authors are Salva Duran-Nebreda, Blai Vidiella, Andrej Spiridonov, Niles Eldredge, Michael J. O'Brien, R. Alexander Bentley, & Sergi Valverde.
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Mitch Guttman @mitchguttman.bsky.social · 27/11/2024
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...
nature.com
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
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Altmetric @altmetric.com · 18/11/2024
We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics
docs.bsky.app
Action Intent Links | Bluesky
Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...
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Maria Dzunkova @dzunkovam.bsky.social · 21/11/2024
At @i2sysbio.bsky.social, together with my collaborators from Tunisia, we have a new paper about genomes of isolates from tannery effluents. These strains can be used for bio-remediation of areas affected by heavy metals used in leather tanning www.sciencedirect.com/science/arti... 🦠🧫🖥️🧬 #MicroSky
sciencedirect.com
Genomic features of metal-resistant bacteria suitable for tannery effluent bioremediation
Biological treatments are widely used to manage tannery wastewater, but their effectiveness depends on the specific conditions of each tannery, drivin…
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