Miguel López Rivera
@riveralopz.bsky.social
PhD student @ Harvard, Kranzusch Lab
Pinned
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
Reposted by Miguel López Rivera
Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics.
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doi.org
October 5, 2026 at 5:37 PM
Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics.
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🧵
Reposted by Miguel López Rivera
Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org
New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo
www.science.org/doi/10.1126/...
New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo
www.science.org/doi/10.1126/...
October 1, 2026 at 7:07 PM
Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org
New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo
www.science.org/doi/10.1126/...
New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo
www.science.org/doi/10.1126/...
Reposted by Miguel López Rivera
Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com!
Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems.
www.nature.com/articles/s41...
Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems.
www.nature.com/articles/s41...
September 25, 2026 at 10:08 AM
Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com!
Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems.
www.nature.com/articles/s41...
Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems.
www.nature.com/articles/s41...
Reposted by Miguel López Rivera
Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...
September 16, 2026 at 10:14 AM
Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...
Reposted by Miguel López Rivera
We’re reposting some trending articles from our recent past, for those that may have missed them.
Below is an excellent resource from @aharms485.bsky.social lab expanding the BASEL phage collection
🧪#ViroSky #Microsky
Below is an excellent resource from @aharms485.bsky.social lab expanding the BASEL phage collection
🧪#ViroSky #Microsky
#TrendingNow | Using a modified host, this study adds 36 new phages to the BASEL collection of phages that infect E. coli, revealing key roles of the O-antigen barrier in host recognition and restriction-modification systems in bacterial immunity. #ICYMI #MicroSky 🧪 buff.ly/grvuhX2
Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage–host interactions
The BASEL collection of phages that infect E. coli has been a valuable resource, but is limited by the peculiarities of the host strain used. This study uses a modified host to expand the collection…
buff.ly
September 12, 2026 at 10:26 AM
We’re reposting some trending articles from our recent past, for those that may have missed them.
Below is an excellent resource from @aharms485.bsky.social lab expanding the BASEL phage collection
🧪#ViroSky #Microsky
Below is an excellent resource from @aharms485.bsky.social lab expanding the BASEL phage collection
🧪#ViroSky #Microsky
Reposted by Miguel López Rivera
Discovery of chimeric RNAs and thousands of new proteins in mammalian cells – including a new regulator of inflammasome signaling!
www.nature.com/articles/s41...
www.jacksonimmunology.com
www.nature.com/articles/s41...
www.jacksonimmunology.com
September 2, 2026 at 5:13 PM
Discovery of chimeric RNAs and thousands of new proteins in mammalian cells – including a new regulator of inflammasome signaling!
www.nature.com/articles/s41...
www.jacksonimmunology.com
www.nature.com/articles/s41...
www.jacksonimmunology.com
Reposted by Miguel López Rivera
Can we design molecules that rewrite how organisms interact with the environment? I'm delighted to share our lab's latest work, where we use structural biology and chemistry to modulate insect behavior in a clade of destructive agricultural pests. Congrats Steve and team!
Huge thanks to the team! Sasha Mcdowell, Pramod KC, Marija Simjanoska, Sanjana Mandala, Xiao Zhang, Hanjie Jiang, Phil Cole, Jeff Riffell, Qinheng Zheng, @delmarmollab.bsky.social
Read the full updated preprint here: www.biorxiv.org/content/10.1...
Read the full updated preprint here: www.biorxiv.org/content/10.1...
Molecular logic of pheromone recognition enables rational design of insect behavior modulators
Reproductive success across animal taxa relies on the unequivocal identification of volatile chemical cues used for sexual communication. These chemical signals, called pheromones, are often structura...
www.biorxiv.org
August 25, 2026 at 9:39 PM
Can we design molecules that rewrite how organisms interact with the environment? I'm delighted to share our lab's latest work, where we use structural biology and chemistry to modulate insect behavior in a clade of destructive agricultural pests. Congrats Steve and team!
Reposted by Miguel López Rivera
Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Bacterial diadenylate cyclase domains synthesize diverse nucleotide signals in anti-phage defense
Bacterial diadenylate cyclase (DAC) enzymes synthesize the nucleotide signal 3′3′ cyclic di-AMP (3′3′-c-di-AMP) to control osmoregulation, cell-wall homeostasis, and DNA-damage responses. Here we disc...
www.biorxiv.org
August 12, 2026 at 5:49 PM
Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Miguel López Rivera
We are excited to share two preprints reporting a mosquito-specific receptor for chikungunya virus and other alphaviruses! 🤩 www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
@harvardmicro.bsky.social @harvardvirology.bsky.social @hhmi-science.bsky.social
www.biorxiv.org/content/10.6...
@harvardmicro.bsky.social @harvardvirology.bsky.social @hhmi-science.bsky.social
July 30, 2026 at 4:06 PM
We are excited to share two preprints reporting a mosquito-specific receptor for chikungunya virus and other alphaviruses! 🤩 www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
@harvardmicro.bsky.social @harvardvirology.bsky.social @hhmi-science.bsky.social
www.biorxiv.org/content/10.6...
@harvardmicro.bsky.social @harvardvirology.bsky.social @hhmi-science.bsky.social
Reposted by Miguel López Rivera
1/10
🚨Preprint! One RING to rule them all (phages)👑💍⚔️
Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇
biorxiv.org/content/10.6...
🚨Preprint! One RING to rule them all (phages)👑💍⚔️
Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇
biorxiv.org/content/10.6...
July 16, 2026 at 6:59 PM
1/10
🚨Preprint! One RING to rule them all (phages)👑💍⚔️
Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇
biorxiv.org/content/10.6...
🚨Preprint! One RING to rule them all (phages)👑💍⚔️
Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇
biorxiv.org/content/10.6...
Reposted by Miguel López Rivera
One of the coolest structures presented at the recent SISB2026 meeting, great to see this story from @rafomics.bsky.social and @guillermo-montoya.bsky.social on a giant retron ring-shaped assembly now out:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
July 15, 2026 at 4:55 PM
One of the coolest structures presented at the recent SISB2026 meeting, great to see this story from @rafomics.bsky.social and @guillermo-montoya.bsky.social on a giant retron ring-shaped assembly now out:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Miguel López Rivera
Another chapter of my thesis is out! We asked whether we could pair proteome-wide AlphaFold screening with Tn-seq to identify biologically relevant protein-protein interactions. We identify ClcR (formerly YerH) as a component of the Rod complex in Gram-positive bacteria. www.pnas.org/doi/10.1073/...
A broadly conserved gram-positive lipoprotein regulates cell elongation | PNAS
The cell wall peptidoglycan (PG) protects virtually all bacteria from osmotic lysis
and specifies cell shape. Synthesis of this exoskeleton is carr...
www.pnas.org
June 23, 2026 at 8:00 PM
Another chapter of my thesis is out! We asked whether we could pair proteome-wide AlphaFold screening with Tn-seq to identify biologically relevant protein-protein interactions. We identify ClcR (formerly YerH) as a component of the Rod complex in Gram-positive bacteria. www.pnas.org/doi/10.1073/...
Reposted by Miguel López Rivera
Spanish government launches a plan to study women’s health, which has been so neglected 👏🏼👏🏼
El gobierno lanza un plan para apoyar la investigación sobre la salud de la mujer, tan abandonada hasta ahora
elpais.com/salud-y-bien...
El gobierno lanza un plan para apoyar la investigación sobre la salud de la mujer, tan abandonada hasta ahora
elpais.com/salud-y-bien...
El Gobierno lanza un plan para que la ciencia también se interese por investigar en salud de la mujer
El Ejecutivo propone triplicar la inversión en I+D para atajar la brecha de género y reservar fondos para proyectos centrados en dolencias infraestudiadas en ellas
elpais.com
June 20, 2026 at 1:25 PM
Spanish government launches a plan to study women’s health, which has been so neglected 👏🏼👏🏼
El gobierno lanza un plan para apoyar la investigación sobre la salud de la mujer, tan abandonada hasta ahora
elpais.com/salud-y-bien...
El gobierno lanza un plan para apoyar la investigación sobre la salud de la mujer, tan abandonada hasta ahora
elpais.com/salud-y-bien...
Reposted by Miguel López Rivera
Researchers in 2023 uncovered the lineage and legacy—including more than 40,000 living relatives—of free and enslaved African Americans who labored at the Catoctin Furnace in Maryland, between 1774 and 1850.
Learn more on #Juneteenth: https://scim.ag/4aBMT27
Learn more on #Juneteenth: https://scim.ag/4aBMT27
June 19, 2026 at 7:32 PM
Researchers in 2023 uncovered the lineage and legacy—including more than 40,000 living relatives—of free and enslaved African Americans who labored at the Catoctin Furnace in Maryland, between 1774 and 1850.
Learn more on #Juneteenth: https://scim.ag/4aBMT27
Learn more on #Juneteenth: https://scim.ag/4aBMT27
Reposted by Miguel López Rivera
Preprint: Plant pathogens cleave 2’cADPR to suppress TIR immune signaling
Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵
www.biorxiv.org/content/10.6...
Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵
www.biorxiv.org/content/10.6...
Plant pathogens cleave 2'cADPR to suppress TIR immune signaling
Small molecules produced by TIR (Toll-interleukin-1 receptor) domains are essential for plant immune signaling. A central TIR-derived signal is 2'cADPR, a cyclic ADP-ribose (ADPR) molecule that is gen...
www.biorxiv.org
June 17, 2026 at 8:53 AM
Preprint: Plant pathogens cleave 2’cADPR to suppress TIR immune signaling
Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵
www.biorxiv.org/content/10.6...
Inspired by knowledge on how phages inhibit bacterial immunity, we now show that disease-causing bacteria inhibit plant immunity in a similar way. A 🧵
www.biorxiv.org/content/10.6...
Reposted by Miguel López Rivera
How do human cells defend against viruses?
@sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics
www.biorxiv.org/content/10.6...
@sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics
www.biorxiv.org/content/10.6...
June 12, 2026 at 8:24 PM
How do human cells defend against viruses?
@sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics
www.biorxiv.org/content/10.6...
@sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics
www.biorxiv.org/content/10.6...
Reposted by Miguel López Rivera
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature.
Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis.
doi.org/10.1038/s415...
Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis.
doi.org/10.1038/s415...
June 10, 2026 at 3:00 PM
Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature.
Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis.
doi.org/10.1038/s415...
Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis.
doi.org/10.1038/s415...
Reposted by Miguel López Rivera
Cheap and easy method for nanopore sequencing phage DNA directly from plaques.
Proud of lab members Brenna and Patrick for doing this work *with absolutely no help from me* !!
www.nature.com/articles/s41...
Proud of lab members Brenna and Patrick for doing this work *with absolutely no help from me* !!
www.nature.com/articles/s41...
Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction - Scientific Reports
Scientific Reports - Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction
www.nature.com
June 5, 2026 at 12:52 AM
Cheap and easy method for nanopore sequencing phage DNA directly from plaques.
Proud of lab members Brenna and Patrick for doing this work *with absolutely no help from me* !!
www.nature.com/articles/s41...
Proud of lab members Brenna and Patrick for doing this work *with absolutely no help from me* !!
www.nature.com/articles/s41...
Reposted by Miguel López Rivera
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe.
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
June 6, 2026 at 10:34 AM
Folddisco is now published @natbiotech.nature.com. It’s a fast motif search for similar 3D DISCOntinuous residues like catalytic sites or zinc fingers across the entire protein universe.
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
📄 www.nature.com/articles/s41...
💾 folddisco.foldseek.com
🌐 https://search.foldseek.com/folddisco
Reposted by Miguel López Rivera
Excited to see our work out in @natmicrobiol.nature.com! We uncovered broad functional diversity within phage sponge families🧽.
Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social !
www.nature.com/articles/s41...
Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social !
www.nature.com/articles/s41...
June 3, 2026 at 6:39 AM
Excited to see our work out in @natmicrobiol.nature.com! We uncovered broad functional diversity within phage sponge families🧽.
Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social !
www.nature.com/articles/s41...
Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social !
www.nature.com/articles/s41...
Reposted by Miguel López Rivera
@romihadary.bsky.social and @soreklab.bsky.social 's discovery that sponge proteins constitute enormous families of viral immune evasion factors is now out in @natmicrobiol.nature.com
@reneechang.bsky.social and our lab were happy to help with this story!
www.nature.com/articles/s41...
@reneechang.bsky.social and our lab were happy to help with this story!
www.nature.com/articles/s41...
June 2, 2026 at 6:09 PM
@romihadary.bsky.social and @soreklab.bsky.social 's discovery that sponge proteins constitute enormous families of viral immune evasion factors is now out in @natmicrobiol.nature.com
@reneechang.bsky.social and our lab were happy to help with this story!
www.nature.com/articles/s41...
@reneechang.bsky.social and our lab were happy to help with this story!
www.nature.com/articles/s41...
Reposted by Miguel López Rivera
A new function for RyR domains in nucleotide signaling!
Excited to share @riveralopz.bsky.social's story at SISB2026 and the pre-print now. Thanks to @reneechang.bsky.social collaborators in Graham Hatfull's and @soreklab.bsky.social groups @kfreeman.bsky.social @romihadary.bsky.social and Jim Sun
Excited to share @riveralopz.bsky.social's story at SISB2026 and the pre-print now. Thanks to @reneechang.bsky.social collaborators in Graham Hatfull's and @soreklab.bsky.social groups @kfreeman.bsky.social @romihadary.bsky.social and Jim Sun
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
May 29, 2026 at 4:06 PM
A new function for RyR domains in nucleotide signaling!
Excited to share @riveralopz.bsky.social's story at SISB2026 and the pre-print now. Thanks to @reneechang.bsky.social collaborators in Graham Hatfull's and @soreklab.bsky.social groups @kfreeman.bsky.social @romihadary.bsky.social and Jim Sun
Excited to share @riveralopz.bsky.social's story at SISB2026 and the pre-print now. Thanks to @reneechang.bsky.social collaborators in Graham Hatfull's and @soreklab.bsky.social groups @kfreeman.bsky.social @romihadary.bsky.social and Jim Sun
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
May 29, 2026 at 11:02 AM
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...