October 2024
Simone will present at the Advances in Proteomics & Metabolomics 2024 symposium (organized by Technology Networks). Register for free if you want to attend (link).
A little symbolic accomplishment for the Sidoli Lab. Our PubMed index reached 200 items (link). They are not 200 publications yet; there are a few preprints. But we are getting there as fast as we can!
Simone presents the lab work at Fordham University! Thank you Dr. Kaoutsar Nasrallah for the invitation!
New collaboration with the lab of Dr. Li Gan (Weill Cornell) published in Neuron: “Alzheimer's disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model” (link).
Congratulations to Sarah for having her collaborative work published in Nature Communications! Thank you for working with us, Dr. Danwei Huangfu lab (MSKCC) (link).
Congrats to Jenny as well for this collaboration with Dr. Nikolaos Frangogiannis lab (Einstein) published in Cardiovascular Research (link).
Simone meets with our incredibly generous Einstein donor, Dr. Ruth Gottesman, to illustrate the latest advances of the proteomics team at Einstein. Just a quick reminder of the donation (one of many) that the Gottesman family did to Einstein; the last one of 1 billion dollars! (link)
September 2024
Welcome to the lab to Rosita Nicolella Gentile from the University of Parma (Italy)! Her visit is sponsored by the ENRICH grant, provided by the European Union, and led by Rosita’s PI Dr. Roberta Pinalli.
The PROVIDENT grant, awarded to Dr. Kartik Chandran (Einstein) has been funded!! This is a huge consortium (13 institutions, $14 million in funding) to establish a platform for promptly studying and tackling new pandemic viruses. Our lab will participate as the proteomics team to analyze virus particles and host responses.
Simone comes back from the congress of the Brazilian Proteomics Society in Sao Paulo, Brazil (link). Thank you Giuseppe for the invitation; it has been an amazing experience!
Congratulations to Max, who has been awarded a T32 training grant from the Training Program in Cellular and Molecular Biology and Genetics (CMBG). Thank you to the leader Charles Query and to the selection committee!
Simone and Max participate to the CMBG retreat in Edith Macy.
Important collaborative papers published in Science, Nature and Nature communication this month! Here they are:
Micronuclear collapse from oxidative damage, Science (Bakhoum lab, MSKCC) (link)
Deciphering the impact of genomic variation on function, Nature (IGVF Consortium) (link)
The scaffolding function of LSD1 controls DNA methylation in mouse ESCs (Aguilo lab, Umeå University, Sweden) (link). Thank you Stephanie for working hard on this paper!
The Einstein Institute for Immunotherapy for Cancer and Inflammatory Disorders has launched, and our lab is part of it (link)
August 2024
The lab welcomes Giulia Barotti from the University of Parma (Italy)! She is coming from the laboratory of Dr. Barbara Montanini, and she will work with us for the next nine months.
Welcome as well to Javier Janet, new rotation student in the lab!
Congratulations to Max! He has been accepted to be part of the CMBG training grant! For the next two years, he will be joining the family of the Cellular and Molecular Biology and Genetics sponsored students.
The summer experience of Andrew and Andreina comes to an end. Thank you for the smiles and hard work you put this summer! You will be missed!
Two new articles from the lab have been submitted to scientific journals and anxiously awaiting reviewers’ comments! In the meantime, here is their pre-prints. The first is the role of EXOSC4 in regulating spurious transcription led by Stephanie (link), and the second one is a new method to study histone modifications at the single cell level led by Ronnie (link).
We got a notice of award for a collaborative grant with the U.S. Army Medical Research Institute of Infectious Diseases. Drs. Stephanie Monticelli and Kartik Chandran will work with us to perform some proteomics experiments on the Crimean–Congo hemorrhagic fever virus.
A big thank you also to Drs. Rohit Jangra and Jeremy Kamil (LSU) for including us in a collaborative grant studying “Host Virus Interactions in Hantavirus Glycoprotein Assembly”.
A few new collaborative papers out of the gates! “Enrichment of histone tail methylated lysine residues via cavitand-decorated magnetic nanoparticles for ultra-sensitive proteomics” with the lab of Dr. Roberta Pinalli (University of Parma, Italy), published in Chemical Science (link).
“KAT2A and KAT2B prevent double-stranded RNA accumulation and interferon signaling to maintain intestinal stem cell renewal” with the lab of Dr. Michael Verzi (Rutgers) published in Science Advances (link).
“Patient-specific mutation of Dync1h1 in mice causes brain and behavioral deficits” with the lab of Dr. Bridget Shafit-Zagardo (Einstein) published in Neurobiology of Disease (link).
July 2024
Agnese is leaving the lab after her five months in the team. Thank you so much for the amazing contribution you provided! Best of luck with the completion of your PhD.
Welcome to Andrew Ames and Andreina Wu, our two high school students joining us for the summer program BEYOND ALBERT. Max is going to be their primary mentor for the summer.
The lab participates to the New York City Chromatin Club! Stephanie gave an oral presentation, and Ronnie presented a poster. What an experience! Thank you to Dr. Emily Bernstein (Mount Sinai) for leading the organization of it. Hopefully, next year we do it at Einstein!
Congrats to Sarah, who got accepted to participate to the Gordon Conference on Chromatin's Impact on Genome Function Across Size and Time-Scales!
New publication from the lab: “Effect of dynamic exclusion and the use of FAIMS, DIA and MALDI-mass spectrometry imaging with ion mobility on amyloid protein identification”, Clinical Proteomics (link). Thank you Jenny for leading this massive work!
New collaboration with the lab of Dr. Eric Nestler (Mount Sinai) published in Neuron: “Mono-methylation of lysine 27 at histone 3 confers lifelong susceptibility to stress” (link).
Another collaborative paper with the lab of Dr. Gaetano Santulli (Einstein): “Ketogenic diet improves chromatin remodeling and rescues mitochondrial dysfunction in ischemic heart disease by regulating PGC-1alpha transcription”, published in Vascular Pharmacology (link).
Ok ok, one more! Great collaboration with the lab of Dr. Payel Sen (NIA): “Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging”, published in Nature Communications (link).
Big news regarding funding! The lab is part of a Hevolution grant consortium led by Dr. Ana Maria Cuervo (Einstein) aiming to investigate senescence in aging.
June 2024
A big congratulations to Ronnie who won the Walter R. Nicolai student award at the AGE meeting this week!
Congratulations to Stephanie who got accepted for a talk at the NYC Chromatin Club, and to Sarah and Ronnie who got accepted for a poster!
Check out the Nightline special on ABC News. There are some shots here and there with familiar faces (link).
Our lab hosts Dr. Chrisna Gouws, Professor at the North-West University in Potchefstroom (South Africa). Thank you for coming and sharing your science with us!
We have the names of our high school students for the summer: Andrew Ames and Andreina Wu Hou. Looking forward to welcoming them to the team!
Congrats to Jenny for her collaborative paper with the Frangogiannis lab: Fibroblast Smad7 Induction Protects the Remodeling Pressure-Overloaded Heart (link).
May 2024
Laura writes a very nice short review about the links between aging, cancer and chromatin (link). Thank you to keep working with us even though you are back home!
Simone enters for the first time the list of the “Best scientists” edited by Research.com, positioning himself as #1051 in Molecular Biology in the United States (link). Obviously, still a looong way to go to impact science like the world leaders. But a little satisfaction that keeps us in the map!
The lab welcomes officially Max in the team! He signed off to have his PhD to be co-mentored by our team and the team of Dr. Jeffrey Pessin (Diabetes Center). We will work on single cell spatial proteomics; challenging and exciting times ahead!
The lab says goodbye to Ankita! Thank you for everything you did in the lab, and thank you very much to Dr. Atefeh Rabiee for sharing with us her talent and time.
Congratulations to Ronnie for having a poster presentation at the Single Cell Proteomics Symposium in Boston and winning a travel award! Great work! He will attend the symposium together with Max.
Congrats to Sarah as well, who got accepted to participate to the Gordon Conference on Chromatin in July (link). It is a very prestigious one; they take only a limited number of attendees. Well done!
New collaboration with the lab of Dr. Eric Nestler: Decoding cocaine-induced proteomic adaptations in the mouse nucleus accumbens, published in Science Signaling (link). Thank you for always working with us, Dr. Philipp Mews!
The postdocs of Einstein voted and they approved with majority to be represented by the Union UAW. UAW will represent our postdocs at Einstein from now on.
Carlos is absent from work for a few days because he participates to the filming of the new Spike Lee/Denzel Washington movie "High and Low". Oh my! The things that don't happen in this lab…
Thank you to Dr. Kojo Elenitoba-Johnson (Chair of Pathology and Laboratory Medicine at MSKCC) for visiting Einstein! It has been a great pleasure to host you and hear about your science.
April 2024
The lab says goodbye to Yan! Thank you for the amazing work you did these three years in the lab, part as lab member and part when mentored by Mike Brenowitz. 11 papers published together, and a really cool one to come on oxidation footprinting! It was really great to have you in the team, and all the best at Relay Therapeutics!
Well done to Ronnie for having his first-author work with the lab of Jan Vijg online in BioRxiv (link)!
Congratulations to Edwin for his newest publication in Nano Research (link)!
A new collaboration with the lab of Dr. Julie Secombe is published in Nucleic Acid Research (link). Thank you for working with us once again!
A collaboration with Drs. Jeffrey Pessin and Daorong Feng is published in Nature Communications (link). I am sure this is the first of a long series :-)
The lab becomes a movie set for an entire day. The crew from the Einstein Development Filming and the Night Line crew from ABC took some shots of our lab in action!
Einstein has a new Institute for Immunotherapy of Cancer, and we have been asked to be part of it as members! All the best to the Director, Dr. Xingxing Zang for the work ahead!
March 2024
The lab welcomes Maxwell Horton for his rotation in our team. He will work on spatial single cell proteomics in aging liver (link to team)!
The lab hosted Dr. Megan Lim (MSKCC) at Einstein for a seminar. Thank you so much for including us in your busy schedule!
A large portion of the team goes to the Epigenetics Symposium in Philadelphia, organized by the FoxChase Cancer Center. What a day!
Jazmine and Stephanie present at the Einstein Chromatin Club their research on identifying the histone code and characterizing the biological role of specific hybrid histone modifications
Congrats to Stephanie for her recent collaboration with the lab of Dr. Britta Will: An iron rheostat controls hematopoietic stem cell fate (Cell Stem Cell, link)
Congrats to Sarah as well for her collaborative work with the lab of Dr. Constance Alabert: RNA polymerase II promotes the organization of chromatin following DNA replication (EMBO Reports, link)
February 2024
The Sidoli Lab is anxiously waiting to welcome Agnese to the lab (link to team)! Just one more week, and then we will have the first Italian (beside Simone) in the group ;-)
Congratulations to Stephanie for her new collaboration with the Morey lab (U Miami) titled: Methylation of histone H3 lysine 36 is a barrier for therapeutic interventions of head and neck squamous cell carcinoma (Genes and Development, link).
The lab welcomes the high school students from the program BEYOND Einstein for a three-days training on the analysis of histone modifications. Thank you to Sarah, Ronnie, Jazmine and Ankita for taking good care of them!
The lab invited Dr. Andrey Tvardovskiy to give a seminar at Einstein on February 20th! He will tell us about his research program on “Decoding Chromatin States by Proteomic Profiling of Nucleosome Modification Readers”. Zoom link available upon request.
Congratulations to Edwin for his new baby!! So great to see his family growing!
Simone has achieved a small exciting milestone. According to Google Scholar, he has now an H-index of 50, meaning that he has now published at least 50 papers that have each been cited at least 50 times.
January 2024
Many updates in January 2024. We have been silent for a while, wrapping up the work of 2023. New record year for us, as usual. 27 published manuscripts, 28 manuscripts in the peer-review process, 8 manuscripts in advanced stage of preparation. The Core cracked great numbers too: 5,600 samples belonging to 180 different collaborators. Now you know why we have been busy at the end of 2023 :-)
The lab says goodbye to Eddie. He worked at Einstein for 34 years!! He has been an amazing mentor, a great colleague and a very important asset for our instrumentation, small molecule analysis and overall knowledge in analytical chemistry. We will not be able to replace him, but we will surely find a way to continue his legacy.
The lab starts 2024 with a roar! CelVivo installed three new ClinoStar 2.0 incubators, the first three in the world! These new incubators will allow to grow cells in 3D with possibility of creating hypoxia environment. More than that, they are completely re-engineered with new engines and remote control. It will be fun.
The lab receives the Hevolution Grant! Thank you so much to AFAR for helping us in the process. We are looking forward to discover new secrets of histone modifications in aging.
We already have a new (temporary) lab member. Ankita Poojari will work in our lab for three months (link to team), visiting from the lab of Dr. Atefeh Rabiee at the University of the Pacific (CA, USA)
Lots of new papers since the last update. Two from our lab, an editorial on AI and proteomics (link) and a review on breath proteomics (link). One collaboration with our old friends Drs. Martin Carroll and Pamela Sung (link). One paper with our new friend Dr. Peri Kurshan (link).
Check out our little post on the FEBS Newsletter about our article on artificial intelligence and proteomics (link)
Our BEYOND Einstein program has organized an extra training for the high school student class that worked with us in the summer of 2023. We will host six high school students next month to teach them how to analyze histone modifications with mass spectrometry!
Congratulations to our old friend Laura, who won the best poster award at the EuBIC-MS Winter School. She presented the single cell histone work that she is developing with Ronnie.