Leonid Mirny Profile
Leonid Mirny

@leonidmirny

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Joined April 2014
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@leonidmirny
Leonid Mirny
2 months
I'm truly honored that the work on my group in Chromosome Biophysics has been so highly recognized. Particularly touched to receive this prize from Tel-Aviv University in Israel. Particularly now - in these difficult times. Honored to share this award with @cees_dekker , wish
@BioSoftTAU
BioSoft@TAU
2 months
and the 2024 @TelAvivUni Sackler Prize in Biophysics goes to... Cees Dekker, Leonid Mirny, and Petra Schwille - see you at the awards symposium and ceremony on November 21 @cees_dekker @leonidmirny @SchwilleLab
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@leonidmirny
Leonid Mirny
4 years
We just posted a very important paper on #cancer #immunotherapy with @carino_dg . Widely believed and #FDA -approved biomarker of response - the total number of mutations in cancer (mutational burden) is bogus. We reanalyzed all data - no statistic significance #DataScience
@biorxivpreprint
bioRxiv
4 years
Limited evidence of tumour mutational burden as a biomarker of response to immunotherapy #bioRxiv
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@leonidmirny
Leonid Mirny
8 months
Are chromosomes (epigenetic) memory machines? 1/4 Likely so - Interplay of chromosome folding and dynamics of histone marks can store a pattern of marks for ~100 cell divisions. Happy to see our work with @jeremyaowen @osmanovicdino1 out @ScienceMagazine
@jeremyaowen
Jeremy Owen
8 months
1/ My work on epigenetic memory with @leonidmirny , @osmanovicdino1 is out @ScienceMagazine ! How can *stable* memory be encoded in patterns of *dynamic* epigenetic marks? We find 3D folding of genome can stabilize memory, if 3 ingredients are present...
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@leonidmirny
Leonid Mirny
8 months
3/4 Epigenetic memory is stored differently through the cell cycle: Interphase - the memory is in folding of dense heterochromatin condensate – marks follow the folding. Metaphase - memory is in the mark pattern – chromosome folding will follows the marks
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@jeremyaowen
Jeremy Owen
8 months
3/ Our work points to a solution—3D genome folding can stabilize memory! In our model of a markable chromatin polymer, 3 ingredients are required to make this work: (1) self-attraction of marked regions, (2) enzymes that spread marks in 3D, and, critically, (3) limited enzyme.
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@leonidmirny
Leonid Mirny
6 years
Slides from my talk at #kschromatin
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@leonidmirny
Leonid Mirny
2 years
Are chromosomes memory machines? We just posted a @biorxivpreprint with @jeremyaowen and Dino Osmanovic showing how 3D genome organization can help stabilize epigenetic information.
@jeremyaowen
Jeremy Owen
2 years
1/ How do cells remember their cell type? Could one function of 3D genome folding be to help sustain this epigenetic memory? You heard my talk last week at #cshlepich22 , now our preprint is out!
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@leonidmirny
Leonid Mirny
3 months
@lpachter Excellent demo, Lior! Can't stop fighting this "p=0.01; r=0.1" issue among students in bioinformatics. Fundamentally, ppl don’t understand the difference btwn effect size and statistical significance (frequently against some straw-man null hypothesis).
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@leonidmirny
Leonid Mirny
6 years
We report very important "negative" result. Condensin inactivation **during interphase** doesn't affect chromosome organization or gene expression (in mice). Unlike cohesin! Division of labor between SMC: cohesin -- interphase, condensin -- metaphase. Great job @nv1ctus !
@nv1ctus
Nezar Abdennur
6 years
Here, we present an important "negative" result to guide us positively toward understanding the exact roles of SMC complexes throughout the cell cycle.
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@leonidmirny
Leonid Mirny
9 months
Attempts to remove Eisen from #eLife aims to align political views of editors with the crowd - this undermines basic principles of science. Since political opinions correlate with origin/religion this mobbing runs a risk of targeting editors based on race and religion. 2/2
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@leonidmirny
Leonid Mirny
4 years
We posted a surprising finding that SMC complexes can bypass each other in vivo. This generates crazy Hi-C patterns! (w/ @hugoresearch and Xindan Wang). Very much inline with amazing single-molecule experiments of @cees_dekker . Topological puzzle how it happens...
@hugoresearch
Hugo Brandao
4 years
Ever seen a chromosome fold into a star-shape? Ever seen a Hi-C map like this? Curious to know how we made it? Check out our preprint: DNA-loop extruding SMC complexes traverse one another in vivo. Many more cool chromosome structures inside!
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@leonidmirny
Leonid Mirny
3 years
Our paper indicating that SMCs can bypass each other in vivo is out @ NatureSMB. Great collaboration with @hugoresearch , Xindan Wang and her lab! Learning traffic laws of loop extrusion from engineered strains. Crazy Hi-C maps that you have never seen before.
@hugoresearch
Hugo Brandao
3 years
What happens when DNA-loop-extruding SMCs collide with one another in a living cell? Our article on SMC complexes bypassing one another in vivo is out @NatureSMB , in a wonderful collaboration with Xindan Wang, @leonidmirny , Warren Ren and @Xciencepig .
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@leonidmirny
Leonid Mirny
4 years
We are #dataparasites who found mistakes in statistics in original works @NEJM and other journals. @atulbutte @zakkohane . #Bioinformatics rules
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@leonidmirny
Leonid Mirny
9 months
Mike Eisen is leading advocate of #openaccess ; revolutionized publishing: #PLOS and new #eLIfe . Having him EiC of #eLife provides reassurance of fair and transparent review process. His political opinions/sense of humor are of little importance for me. 1/2
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@leonidmirny
Leonid Mirny
3 months
As a faculty @MIT I'm deeply disturbed by current events on campus. MIT has moved its Communal Seder from MIT Hillel to an undisclosed location further from a new "peaceful" pro-Palestinian encampment - thus admitting the risk it creates to jewish members of MIT community. This
@TaliaKhan_MIT
Talia Khan
3 months
The pro-terror encampment is adjacent to the @MIT Hillel building. Instead of getting rid of the encampment and/or ensuring our safety, they are moving the Jews to another location so that we can celebrate Passover safely tonight. This is crazy! (New location removed for
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@leonidmirny
Leonid Mirny
3 years
@mbeisen I'd rather have a woman scientist in this position. Someone like Shirley Tilghman. Rather than someone with a reputation of stealing from women...
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@leonidmirny
Leonid Mirny
4 years
New paper from our group: @Irate_Physicist shows that chromosome compaction by loop extrusion works even if only ~20% of SMCs are two-sided, provided they stay on DNA much longer than others. Asymmetric extrusion seen by @brugueslab in single-mol exprmnts also works. Crazy SMCs!
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@leonidmirny
Leonid Mirny
6 years
Chromatin meets evolution! New paper by @gfudenberg and Katherine Pollard Chromatin features constrain structural variation across evolutionary timescales
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@leonidmirny
Leonid Mirny
3 years
Heterochromatin, DNA methylation and loop extrusion -- are all intertwined -- new preprint from our team led by @nv1ctus and @GeorgeSpracklin . The first molecular perturbation that changes compartments!
@nv1ctus
Nezar Abdennur
3 years
Very excited to announce our preprint on heterochromatin and genome architecture! With @GeorgeSpracklin , Max Imakaev, Neil Chowdhury, @leonidmirny @job_dekker and Sriharsa Pradhan @NEBiolabs .
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@leonidmirny
Leonid Mirny
3 months
Happy to see out paper with Erica Hildebrand ( @dekker_lab ), Kirill Polovnikov @kipolovnikov and Job Dekker @job_dekker out in Mol Cell @4DNucleome . How do cells manage topology of their chromosomes? 0/3
@MolecularCell
Molecular Cell
3 months
Online Now: Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis
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@leonidmirny
Leonid Mirny
4 years
We @carino_gurjao just posted a major update of our study demonstrating the lack of association between cancer response to immunotherapy and tumor mutational burden. Now with pan-cancer data for >2500 ICB-treated patients from public sources
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@leonidmirny
Leonid Mirny
6 years
@job_dekker ask what we should refer as "loop" in his fantastic talk at Keystone meeting #keystoneconference #chromatin
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@leonidmirny
Leonid Mirny
6 years
Very proud to be a part of this fantastic team that produced Congratulations to @pkerpedjiev @nv1ctus @ngehlenborg and others! Excellent tool! It truly changed the way we study Hi-C data.
@pkerpedjiev
Peter Kerpedjiev
6 years
Our HiGlass paper is finally out in Genome Biology!! 🔎🎉 Explore, compare and share large genomic (and other) datasets online () or privately using Docker (). With @ngehlenborg , @flekschas & @nv1ctus . 1 / 11
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@leonidmirny
Leonid Mirny
8 months
Our paper with @kipolovnikov et al shows how loops change topological properties of polymers (spoiler: loops make polymer less entangled), and how loops in chromosomes can be detected in Hi-C data. @prx
@kipolovnikov
Kirill
8 months
Happy to share that our theory of loops extruded on chromosomes is finally out in Physical Review @X ! Loops make it less crumpled! Big thanks to @leonidmirny @hugoresearch Sergey Belan, Max Imakaev and my PhD student Bogdan Slavov!
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@leonidmirny
Leonid Mirny
6 years
Congratulations, Hugo Brandao and David Rudner! Direct evidence of active #loopextrusion by SMC in vivo.
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@leonidmirny
Leonid Mirny
2 months
Excited to share now updated bioRxiv with @golobor , @job_dekker and Bill Earnshaw labs. Driven by Kumiko Samejima and Johan Gibcus. * Interactions between motors determine shapes of mitotic chromosomes * Loop-extruding motors can do different things when they meet: - Condensin
@golobor
Anton Goloborodko @[email protected]
3 months
1/ We are excited to release our new preprint: "Rules of engagement for condensins and cohesins guide mitotic chromosome formation"
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@leonidmirny
Leonid Mirny
6 years
@michaelhoffman Slides are available here
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@leonidmirny
Leonid Mirny
8 months
4/4 Chromosomal storage of epigenetic memory is similar to associative memory in neural networks. Chromosome folding that places marked histones together - is like strengthening of connections between firing neuron: "fire together - wire together" becomes "marked together -
@jeremyaowen
Jeremy Owen
8 months
1/ My work on epigenetic memory with @leonidmirny , @osmanovicdino1 is out @ScienceMagazine ! How can *stable* memory be encoded in patterns of *dynamic* epigenetic marks? We find 3D folding of genome can stabilize memory, if 3 ingredients are present...
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@leonidmirny
Leonid Mirny
2 years
Loops in chromosomes leave a distinct signature in Hi-C data. A new polymer model - a chain folded into loops - can be solved analytically, revealing otherwise invisible loops. Great teamwork: @hugoresearch , Kirill Polovnikov Sergei Belan, Max Imakaev.
@hugoresearch
Hugo Brandao
2 years
Did you know chromosomal loops can repel one another? Did you know that Hi-C maps have a hidden signature that tells you the sizes of chromosomal loops? We came up with a theory that describes interphase chromosomes folded into loops! Check it out!
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@leonidmirny
Leonid Mirny
6 years
Real-time imaging of DNA loop extrusion by condensin Instant classic! Congratulations @cees_dekker @mahipalganji ! #smcisamotor
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@leonidmirny
Leonid Mirny
6 years
I'm shocked and devastated... Maxime was an amazing person: kind, warm and generous. We have been collaborating for many years, enjoyed science and arts together... I cannot believe we lost him...
@institut_curie
Institut Curie
6 years
. @Institut_Curie a l’immense tristesse d’annoncer le décès de Maxime Dahan, directeur de l’Unité de Physico-chimie, acteur majeur de la recherche aux interfaces entre physique & biologie. C’est une perte humaine et scientifique. Nos pensées vont à sa famille & ses collaborateurs
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@leonidmirny
Leonid Mirny
6 years
Welcome to #Norwegian Airlines :( . "The engineer " fail to fix it but I managed so far to attach it.
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@leonidmirny
Leonid Mirny
2 months
Very proud and happy for my former student @jeremyaowen who made a great career move to start an experimental research!
@jeremyaowen
Jeremy Owen
2 months
Thrilled and honored by @DamonRunyon ’s support! Very grateful to my mentors Tom and Ned, and to every single member of the @MuirLab for welcoming a theorist who wants to do experiments!
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@leonidmirny
Leonid Mirny
6 years
Excellent feature by Elie Dolgin about phase separation in the nucleus.
@ElieDolgin
Elie Dolgin
6 years
Like oil in water, the contents of cells can segregate into droplets. It’s called phase separation, and biologists are seeing it everywhere.
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@leonidmirny
Leonid Mirny
8 months
2/4 Spreading of histone marks on a chromosome is identical to spreading of infection (SIS model). Chromosome folding establishes a "social network" of histone proximity, and marks spread on this network like infection - staying in densely connected areas
@jeremyaowen
Jeremy Owen
8 months
3/ Our work points to a solution—3D genome folding can stabilize memory! In our model of a markable chromatin polymer, 3 ingredients are required to make this work: (1) self-attraction of marked regions, (2) enzymes that spread marks in 3D, and, critically, (3) limited enzyme.
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@leonidmirny
Leonid Mirny
2 months
@JumanaAHA @MIT Thank you, Jumana -- This is super-helpful. There were discussion on twitter about exact translation. I'm a great supporter of pro-ceasefire demonstrations, e.g. in Israel right now, but my worry that these kids in the US simply don't know what they are saying and doing.
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@leonidmirny
Leonid Mirny
3 months
In 2002 Hamas bombed the Seder in Netanya - the deadliest attack of the 2nd intifada. Today Hamas, via its deliberate or deceived supporters, made thousands of US students celebrate intifada, while making jews across US campuses celebrate Passover in hiding, or feeling
@lpachter
Lior Pachter
3 months
Tonight's seder is 22 years after the Park Hotel seder bombing by Hamas that killed 30 (incl. holocaust survivors) + injured 140. It was planned by Abbas Al-Sayed who got 35 life sentences for it. Seems he's on the list of prisoners Hamas wants freed in exchange for hostages. 1/
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@leonidmirny
Leonid Mirny
2 years
@mbeisen By breaking connection with russian scientists we only weaken russian opposition. To #StopPutin we need strong opposition with links to the west. But institutional connections should be broken.
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@leonidmirny
Leonid Mirny
6 years
#peerreview disagree w/citation “Once you eliminate the impossible, whatever remains...the truth” I doubt A.C.Doyle is a reference when it comes to debating scientific matters. I find this very disrespectful of sober; strictly rational spirit should animate scientific discussion
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@leonidmirny
Leonid Mirny
8 months
MIT News about our paper in @ScienceMagazine
@jeremyaowen
Jeremy Owen
8 months
Thanks to MIT News for featuring our work (out today @ScienceMagazine )! This article by Anne Trafton provides a very nice overview / summary. Also discusses some of the future directions we are excited about.
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@leonidmirny
Leonid Mirny
6 years
Congratulation @ngehlenborg ! Very well deserved! is amazing and truly changed the way we examine Hi-C!
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@leonidmirny
Leonid Mirny
6 years
@cees_dekker @gfudenberg Fantastic visit to Cees Dekkers's Lab at TU Delft! Thank you, Cees! #smcisamotor :)
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@leonidmirny
Leonid Mirny
6 years
Science and Art do go together!
@GAlmouzni
Geneviève Almouzni
6 years
Science and Art go together - students displaying their creativity at the 14th #Epigenetics Course @institut_curie : Happening right now! With #PaulHarrison
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@leonidmirny
Leonid Mirny
5 years
@Chromozz @nv1ctus @SueHadjur First results from the model 05/2014 show TADs with corner-peaks (aka "dots") and "flames" They were observed in experiments in 12/2014 (Rao et al). And no -- we haven't seen these data :)
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@leonidmirny
Leonid Mirny
5 years
@Caroline_Bartma "Wow-really?!" in a single feeling :) Not sure there is a word for this...
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@leonidmirny
Leonid Mirny
3 months
Excellent example that reporting "significant correlation" makes no sense (I guess it's r=0.1 and p=0.01 in Lior's example).
@lpachter
Lior Pachter
3 months
I've noticed it's becoming increasingly common in genomics to report results of regressions with ridiculously low correlation as "significant" based on a tiny p-value (for the hypothesis that the slope = 0). Can you guess R^2, the p-value, and where the data below was published?
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@leonidmirny
Leonid Mirny
2 months
We need more of this.
@realajedelman
AJ Edelman, Israel Bobsled's Bear Jew
2 months
This is something I truly believe in. Visited the MIT campus to invite a civil dialogue with those walking by the anti Israel encampment. Even @normfinkelstein asked to debate but we wanted to keep it to MIT students to keep it engaging. Hundreds stopped by and a lot of great
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@leonidmirny
Leonid Mirny
4 years
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@leonidmirny
Leonid Mirny
4 years
@johan_elf_ @SebastianDeindl Congratulations! Looking forward to reading it. Very curious what's new in the field of protein-DNA sliding.
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@leonidmirny
Leonid Mirny
6 years
#Norwegian flights rerouted from #Gatwick are stranded on in Orsay airport. Passengers in the plane. No a/c or food. Started giving some water.
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@leonidmirny
Leonid Mirny
3 years
Hot off the press by @carino_gurjao et al. - specific mutational signature in colorectal carcinoma is associated with high intakes of red meat (processed and unprocessed) (of interest to @mbeisen @cd_mcfarland )
@CD_AACR
Cancer Discovery
3 years
Hot off the press: Read, Discovery and features of an alkylating signature in colorectal cancer.
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@leonidmirny
Leonid Mirny
5 years
@Chromozz @nv1ctus No we didn't! We started to work on extrusion+boundaries=>TAD in '13; reported first in May'14 (slide there, search "extrusion"). I heard 1st success in getting rid of cohesin by F.Spitz Mar'15 @ CurieEpigen. I spoke about the model May'15 @ ENS and EMBO
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@leonidmirny
Leonid Mirny
5 years
@successprocess @Caroline_Bartma it's a complicated feeling... gotta be a French word for it...
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@leonidmirny
Leonid Mirny
6 months
@ClausWilke @NimwegenLab @lpachter @BillAckman It's a spectrum. from an innocent to the villain. but students need to be taught what scientific misconduct is and that it comes in many shades.
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@leonidmirny
Leonid Mirny
6 years
@michaelhoffman Thank you, Michael. I'm surprised every speaker didn't start their talk asking people to tweet... It was a great meeting!
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@leonidmirny
Leonid Mirny
7 months
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@leonidmirny
Leonid Mirny
6 years
Flight to London has been diverted to Paris #Norwegian
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@leonidmirny
Leonid Mirny
5 years
@Chromozz @nv1ctus Glad you asked Julien! CTCF directionality is not important part of the model, but CTCF barriers are! Early'14 model didn't have directionality; worked fine. We learned a/CTCF directionality from Rao 12/'14 and @SueHadjur AmosTanay 3/'15. We added it then.
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@leonidmirny
Leonid Mirny
3 months
@SashaGusevPosts “Venting” targeted to a group quickly becomes harassment. I don’t see how a mob pushing Jewish students off campus is not the one
@jessicaschwalb7
Jessica Schwalb
3 months
This is what happens when you walk onto @Columbia Gaza Solidarity encampment…happened just now
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@leonidmirny
Leonid Mirny
4 years
Congratulations, @AsifaAkhtar1 !
@jallepap
Prasad Jallepalli, MD, PhD
4 years
Asifa Akhtar is a sign of new things to come at the Max Planck Society
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@leonidmirny
Leonid Mirny
3 months
3/3 Two stage exit solves the problem: Stage 1: chromosomal loops expand, topo II active – loop and chromosomes become unentangled. Stage 2: loops released, topo II isn’t active – chromosome open up yet don’t mix, establishing normal G1 folding.
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@leonidmirny
Leonid Mirny
2 months
Sad news: Anton Zilman, a fellow theoretical biophysicist from UofToronto, a friend, and a charming and warm person has passed away.
@cees_dekker
cees dekker
2 months
Sad news indeed: Anton Zilman suddenly passed away. Long-time colleague with major contributions to understanding the biophysics of transport through the nuclear pore complex. And a great guy! We'll miss him.
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@leonidmirny
Leonid Mirny
4 years
@PetrovADmitri Really sorry to hear this... And what an amazing surprise party you threw for him!
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@leonidmirny
Leonid Mirny
6 years
@mahipalganji Congratulations! This paper is an instant classic @cees_dekker
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@leonidmirny
Leonid Mirny
6 months
@ClausWilke @lpachter @BillAckman Plagiarism in natural sciences is not uncommon (and I'm a victim of it) but it's different defines it as "Plagiarism is the appropriation of another person's ideas, processes, results, or words without giving appropriate credit." Not easy to detect...
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@leonidmirny
Leonid Mirny
6 years
@Irate_Physicist @YoYo_Ma @MIT ...and some serious lecturing on JC Bach' sonatas with mesmerizing live demonstrations!
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@leonidmirny
Leonid Mirny
6 years
@benoitbruneau @ngehlenborg @job_dekker @4DNucleome @Harvard @MIT @UMass I agree. It should have been done at a larger scale. I believe the organizers wanted to start with a smaller scale trial run.
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@leonidmirny
Leonid Mirny
5 years
In memory of an amazing p
@golobor
Anton Goloborodko @[email protected]
5 years
our colleagues @institut_curie are setting up a prize in memory of Maxime Dahan:
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@leonidmirny
Leonid Mirny
6 years
Great collaboration with the labs of Irina Solovei and @job_dekker
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Leonid Mirny
6 months
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@leonidmirny
Leonid Mirny
2 years
@safecast Looks like they are all down again...
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@leonidmirny
Leonid Mirny
2 months
@persianjewess @Columbia @jewsinschool Their name is Khymani James -- they spoke to reporters under that name.
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