Lotus Lofgren @LotusLofgren Twitter profile | Pikagi

Pikagi

Lotus Lofgren

@LotusLofgren

2,103

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Fungal evolutionary ecology, genomics, bioinformatics, sci-art, code, data viz. She/her/Dr.

Postdoc @DukeBiology

https://t.co/xjlc58ZZUw

Joined September 2014

Don't wanna be here? Send us removal request.

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@LotusLofgren

Lotus Lofgren

6 months

Elated to share that this January, I’ll be opening the doors to the Lofgren Mycology Laboratory at Berkeley in the @PMB_Berkeley dep. Our group will work on the ecology and evolution of fungi and their hosts, with a focus on ectomycorrhizal symbiosis, metabolism, and genomics.

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@LotusLofgren

Lotus Lofgren

5 months

🚨I will be hiring two postdoctoral scholars to start early 2025 at our new lab at UC Berkeley🚨 If you are attending MSA in Toronto next week and want to chat about either of these positions, please contact me! 🌱🍄 📄Details & application instructions:

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@LotusLofgren

Lotus Lofgren

5 years

Excited to share that in I’ll be joining @stajichlab @UCRiverside in Sep working on fungal pop/evo genetics & comparative genomics! Couldn’t ask for a better group to postdoc with and can’t wait to dive into a new system & new tools. Packing for hot weather & ALLTHEGENOMES🧬🍄🏝

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@LotusLofgren

Lotus Lofgren

5 years

I somehow got Dr’d yesterday. So so grateful for the support and mentorship from so many, but especially @UMNFuN over the last five years 🍄🧬🎓

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@LotusLofgren

Lotus Lofgren

3 years

Excited to be a part of this great collection of reviews for the @CurrentBiology special issue on biodiversity along with mentor @hyphaltip : “Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes”

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Fungal biodiversity and conservation mycology in light of new technology, big data, and changing...

Fungi are everywhere, yet we have only named and described a minute fraction of the fungal world. In this Review, Lofgren and Stajich review the state of fungal diversity research, highlighting...

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@LotusLofgren

Lotus Lofgren

2 years

Our JGI CSP building ectomycorrhizal synthetic communities to tease apart complex secondary metabolomes was awarded🎉. Could NOT be more excited for this project and everything we’re going to learn! Thank you @jgi ! with @TheKellerLab @sarambranco

@jgi

Joint Genome Institute

2 years

Ectomycorrhizal fungi are essential to forest health, providing their hosts w/soil nutrients and water in exchange for plant carbon. @LotusLofgren of @DukeBiology will study how EMF interact with complex consortia to establish and maintain symbiosis. #2023CSP CC: @MycoCosm (9/22)

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@LotusLofgren

Lotus Lofgren

3 years

Ecstatic to be selected as a Tri-I MMPTP postdoctoral fellow. I’m grateful to join this amazing program and community of researchers and excited to embark on new training, projects, and collaborations across fungal genomics and fungal ecology✨🍄💻✨

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@LotusLofgren

Lotus Lofgren

5 years

Seeing this is making it feel really really real in here ya’ll. T - 6 days.

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@LotusLofgren

Lotus Lofgren

7 months

Out this morning! Where we argue the need for genus-level model systems in fungi and why Suillus should be one of them, provide a primer on the genus, and how the International Suillus Consortium is addressing grand challenges to system development.

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Suillus: an emerging model for the study of ectomycorrhizal ecology and evolution

Research on mycorrhizal symbiosis has been slowed by a lack of established study systems. To address this challenge, we have been developing Suillus, a widespread ecologically and economically...

nph.onlinelibrary.wiley.com

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@LotusLofgren

Lotus Lofgren

2 years

Announcing SPORES, a new program that sends underrepresented undergraduates to the 2023 MSA annual meeting in Flagstaff Jul 29-Aug 3 Awardees get free meeting registration, mentoring by an established mycologist, banquet ticket, and a 1-year MSA membership

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@LotusLofgren

Lotus Lofgren

4 years

Our comparative genomics paper on the host specialist genus Suillus is now out in early view in New Phyt! Here’s what we found:

Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi

While there has been significant progress characterizing the ‘symbiotic toolkit’ of ectomycorrhizal (ECM) fungi, how host specificity may be encoded into ECM fungal genomes remains poorly understo...

nph.onlinelibrary.wiley.com

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@LotusLofgren

Lotus Lofgren

3 years

Following my heart back to the forest and heading to NC this month to continue postdoc-ing at @DukeBiology (Vilgalys lab). Forever grateful to my first postdoc mentor @hyphaltip and my @Stajichlab mycofam for their support, guidance, and community over the last two years in SoCal

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@LotusLofgren

Lotus Lofgren

6 years

Our paper on fungal rDNA copy number with @UMNFuN @JessieUehling @fmartin1954 @sarambranco is out in early view in Molecular Ecology! DM for preprint.

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@LotusLofgren

Lotus Lofgren

5 years

First week @UCRiverside spent at the ZyGoLife workshop lead by new postdoc mentor @hyphaltip . Couldn’t have asked for a better crash course to start off life at @stajichlab

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@LotusLofgren

Lotus Lofgren

5 years

My advisor Peter Kennedy is having his promotion to full prof. public talk tomorrow at 3:30!

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@LotusLofgren

Lotus Lofgren

3 years

SO excited to finally post this preprint from my 2 year postdoc w/ @hyphaltip + @cramer_lab colab using pan-, pop-, and phylogenomics, to assess pop.structure, recombination, lineage specific diversity, and evidence for metabolic specificity in A.fumigatus

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Combined Pan-, Population-, and Phylo-Genomic Analysis of Aspergillus fumigatus Reveals Population...

Aspergillus fumigatus is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population...

www.biorxiv.org

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@LotusLofgren

Lotus Lofgren

2 years

@Dylan_J_Enright @kasson_wvu @TaniaKurbs @MonikaSFischer I use an LED light box I made for about $50 with stuff from the hardware store. I used the linked paper as a template (works great, would recommend):

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@LotusLofgren

Lotus Lofgren

6 years

NYE 16/17, I proposed to my BF by hiding an artist conk in a display at @AMNH Walked down the aisle at @BellMuseum (to the theme from Sagan’s Cosmos) Now 国立科学博物館 Museum on honeymoon. Still can’t believe I found someone else this excited about dead bugs & bird skeletons🔬❤️

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@LotusLofgren

Lotus Lofgren

3 years

My girl @TaniaKurbs killing it at #Fungal22 on the in-host evolution of black yeast

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@LotusLofgren

Lotus Lofgren

6 years

It took me five years of PhD work to learn that when stuck with new package/program/pipeline to *email the authors* rather than bang my head against the keyboard for days. Most are amazingly helpful, and if there’s actually a bug or an annotation gap, they want to know! #phdchat

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@LotusLofgren

Lotus Lofgren

2 years

Tom was one of the first people to welcome me into the mycofam at my very first MSA when I went alone as an undergrad. A fighter, a myco ambassador, an amazing mentor, and the best kind of human. We’ve lost one of our best.

@FungalDreamTeam

Allison Walker

@FungalDreamTeam

2 years

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@LotusLofgren

Lotus Lofgren

3 years

The always insightful @jlsteenwyk on using gene covariation networks to inform functional coevolution at #fungal22

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@LotusLofgren

Lotus Lofgren

4 years

Please share with undergrads who are interested in applying to graduate school in STEM fields this round. All are welcome, but those who identify as BIPOC, first gen, LGBTQI, or female are especially encouraged to sign up:

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@LotusLofgren

Lotus Lofgren

9 years

What my fungus sees back through the magnifier. Keep it together boys. #distractinglysexy http://t.co/DbaoAYlavw

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@LotusLofgren

Lotus Lofgren

5 years

Congrats to @hyphaltip and @christina_cuomo @fisher_mat and Robb Cramer! 🍄 takeover!

@ACasadevall1

Arturo Casadevall

5 years

Congratulations to the 68 scientists elected to the American Academy of Microbiology. The class of 2020 includes scientists from 11 countries.

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@LotusLofgren

Lotus Lofgren

6 years

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@LotusLofgren

Lotus Lofgren

7 years

Our paper on native grass hosts and F. graminearum mycotoxins is now out Open Access in New Phytologist!

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Fusarium graminearum: pathogen or endophyte of North American grasses?

See also the Commentary on this article by Selosse et al., 217: 968–972.

nph.onlinelibrary.wiley.com

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@LotusLofgren

Lotus Lofgren

5 years

Many thanks to the Cramer Lab at Dartmouth for hosting me for these last two weeks and selling me on A.fumigatus life.

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@LotusLofgren

Lotus Lofgren

5 years

Grateful to get my forest fix and an amazing introduction to California Mushrooms in NorCal at the infamous Mendocino foray this weekend, repping UCR and @stajichlab with @BYUnleashed

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@LotusLofgren

Lotus Lofgren

3 months

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Suillus hypogaeus: First record of a truffle Suillus

Suillus (order Boletales) is a diverse genus of epigeous, mushroom-forming fungi native to temperate forests across the Northern Hemisphere; however, some species are also present in areas where Pi...

www.tandfonline.com

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@LotusLofgren

Lotus Lofgren

6 years

Back in the states after a week at the Wellcome Genome Campus in Cambridge UK for the Fungal Pathogen Genomics Workshop. Truly brilliant instructors, keynotes and location. Grateful to the U MN’s PMB department for supporting the trip. Can’t wait to start applying new skills.

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@LotusLofgren

Lotus Lofgren

6 years

Had an amazing #IMC11 ! Already looking forward to the next one in Amsterdam! Grateful to @MSAFungi for the travel award and to @IMA_Mycology for the poster award! Thank you myco fam!

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@LotusLofgren

Lotus Lofgren

5 years

“metadata is a love note to your future self” @kekoziar at the @RLadiesRiversd meeting tonight

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@LotusLofgren

Lotus Lofgren

1 year

Many thanks to the CIFAR organizers and leadership team for such a fantastic meeting- particularly impressed with the work that went into constructing two diverse, successful, and educational trainee days.

@AsiyaGusa

Asiya Gusa

1 year

CIFAR Fungal Kingdom meeting in Toronto—more pics ❤️ Check out D. Bacinello’s shirt—a gift from Joe 🍄 @DukeHeitman

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@LotusLofgren

Lotus Lofgren

5 years

Whoa. The most insanely satisfying follower and following # in the history of ever.

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@LotusLofgren

Lotus Lofgren

6 months

@UMNFuN @hyphaltip @vilgalys @mykophile @CorbyKistler @cramer_lab @TheKellerLab @magwenelab @DukeHeitman @sarambranco @umncbs @UCRiverside @DukeBiology I’ll be hiring a lab manager (for what I hope will be a long term position), and TWO postdocs (!), to start Jan 2025. Formal postings soon. I will also be at the MSA meeting in Toronto next month if you want to chat about one of these positions in person!

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@LotusLofgren

Lotus Lofgren

5 years

treeio : an R package for phylogenetic tree input and output with richly annotated and associated data

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@LotusLofgren

Lotus Lofgren

4 years

Some of you may know that I’m the current postdoc campus chair for UAW8510. I’m proud today that our union has taken a position calling for police union disaffiliation from the AFLCIO. #blacklivesmatter

IUPA Statement – UAW Local 5810

We, UAW5810, the Union of Postdocs and Academic Researchers at the University of California, call on the AFL-CIO to disaffiliate from the International Union of Police Associations (IUPA).

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@LotusLofgren

Lotus Lofgren

5 years

Decelerated carbon cycling by ectomycorrhizal fungi is controlled by substrate quality and community composition - Fernandez - - New Phytologist - Wiley Online Library

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Decelerated carbon cycling by ectomycorrhizal fungi is controlled by substrate quality and commun...

See also the Commentary on this article by Smith & Peay, 226: 292–294.

nph.onlinelibrary.wiley.com

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@LotusLofgren

Lotus Lofgren

3 years

@DrJohannaRhodes bringing the data on the evolution of anti-fungal resistance in A.fumigatus at #fungal22

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@LotusLofgren

Lotus Lofgren

6 months

I’m so excited to be joining the Berkeley community, and honored to have landed in a program that has had such an indelible impact on the field. I can’t wait to get involved with the Bay Area mycology scene, and take up the torch of teaching fungal biology at UCB.

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@LotusLofgren

Lotus Lofgren

6 years

The number of web-server based bioinformatics tools that can’t be reached just a few years after publication is endlessly staggering to me. 4 tools just today lost in the ether. Why are stable repositories not *always* a requirement for publication??

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@LotusLofgren

Lotus Lofgren

5 years

Dr. Pawlowska ends a fantastic fungal-bacterial evo. talk by announcing a soon to be posted position at Cornell!

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@LotusLofgren

Lotus Lofgren

7 years

Our new pub: 'Ectomycorrhizal host specificity in a changing world: can legacy effects explain anomalous current associations?' now out in New Phytologist's Early View. With @UMNFuN

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@LotusLofgren

Lotus Lofgren

6 years

#IMC11 made even more amazing w/ house full of categorically badass female scientists. Thank you @sarambranco @JessieUehling @AbbeAtSea @anatinmyshoe some of the most illuminating, productive, scientifically challenging and inspiring talks I attended were in our own flat 🍄

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@LotusLofgren

Lotus Lofgren

7 years

Congrats to the new Itasca Bio. Research Station director @shroominn ! Can't wait to see you bring the rot up in the north woods.

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@LotusLofgren

Lotus Lofgren

5 years

Thrilled to find out last week that the UofMN’s Department of Plant and Microbial Biology has eliminated the GRE

@MarchForScience

March For Science

@MarchForScience

5 years

It's expensive, a waste of time, it doesn't predict completion very well, and it hinders diversity. Eliminate GRE requirements. #highered #phdchat

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Lotus Lofgren

5 years

🤯 SOMEONE plz go sequence mycorrhizal Podoserpula??

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@LotusLofgren

Lotus Lofgren

6 months

Deeply thankful to all the folks who invited me into their labs and gave me a chance in the first place- my PhD advisor Peter Kennedy @UMNFuN , as well as Jason @hyphaltip , Rytas @vilgalys , Kabir, @mykophile , Corby @CorbyKistler , Dave McLaughlin, and all the folks in their groups.

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@LotusLofgren

Lotus Lofgren

3 years

A periodic reminder to the academic community at large that a puppy dies every time you assume gender in your Response to Reviewers.

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@LotusLofgren

Lotus Lofgren

6 years

From pathogen to endophyte: an endophytic population of Verticillium dahliae evolved from a sympatric pathogenic population - Wheeler - 2019 - New Phytologist

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@LotusLofgren

Lotus Lofgren

3 years

We are looking for an undergraduate research technician to help out on two exciting projects working with graduate student Jake Nash and myself, doing fungal culture and molecular work. 10-15 hours a week, paid, work-study optional, training provided. @DukeBiology @DukeStudents

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@LotusLofgren

Lotus Lofgren

4 years

Nice talk by Dan Lindner supporting ⬆️competition ⬆️mass loss in decay fungi #MSAfungi20

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@LotusLofgren

Lotus Lofgren

9 years

Gill-print kid-made art for fungus day at the Midtown Farmer's Market! With @UMNMycology and @_MarketSci http://t.co/GPI9FCFxhB

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@LotusLofgren

Lotus Lofgren

6 months

@UMNFuN @hyphaltip @vilgalys @mykophile @CorbyKistler Thanks to my mentorship network @cramer_lab , @TheKellerLab , @magwenelab , @DukeHeitman , @sarambranco , and the rest of my Mycofam. I wouldn’t be here without the community, training, and opportunities I’ve received across @umncbs , @UCRiverside , @DukeBiology and the Tri-i MMPTP.

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@LotusLofgren

Lotus Lofgren

6 years

Sarah Gurr: it’s fungal host specialists, not generalists moving more quickly towards global disease saturation. #Fungal19

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Lotus Lofgren

6 years

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@LotusLofgren

Lotus Lofgren

8 months

Hoping to see the new proposal to remove the herbarium from the Biology dep. and elevate it to a college-level facility gain traction at Duke.

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‘To kill a program’: Duke to close herbarium after over 100 years of operation

The Duke Herbarium is the second-largest private university herbarium in the U.S. and is home to more than 825,000 plant specimens, including some specimens almost 200 years old. Universities across...

www.dukechronicle.com

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@LotusLofgren

Lotus Lofgren

3 years

Many thanks to Francis Trail and @ElaineBignell for moderating such an amazing and diverse plenary on cross species interactions at #fungal22 this morning.

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@LotusLofgren

Lotus Lofgren

4 years

Alexophoulos winner @sarambranco !! Well deserved #MSAfungi20

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@LotusLofgren

Lotus Lofgren

4 years

I’ve greatly enjoyed my term year as PostDoc rep for the MSA student board. We are looking for PDs to apply for this coming term- time commitment is low compared to impact and enjoyment! Description: Apply here:

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@LotusLofgren

Lotus Lofgren

5 years

TT position FIU including mycology and plant microbe interactions

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@LotusLofgren

Lotus Lofgren

6 years

@TobySpribille @kasson_wvu Same. Unschooled and didn’t get my GED until I had a reason to. About to defend at 35 and already disappointed to discover multiple postdoc positions and fellowships only open to under 35 year old “early career” researchers.

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@LotusLofgren

Lotus Lofgren

4 years

Today is #ShutDownSTEM #ShutDownAcademia I will be taking the day off from science to learn, reflect, and make an action plan for how I engage with anti-racist action in the academy and hope you will do the same.

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@LotusLofgren

Lotus Lofgren

6 years

@EcologistJosh Indeed there’s a second paper on the functional implications to relative abundance estimates forthcoming.

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@LotusLofgren

Lotus Lofgren

6 years

Registered for my first Fungal Genetics #Fungal19 ! See you in Pacific Grove @GeneticsGSA

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@LotusLofgren

Lotus Lofgren

6 years

Super cool work on 5mC methylation across fungi!

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@LotusLofgren

Lotus Lofgren

4 years

on our shared responsibility to understand the harms caused by the eugenic history of population genetics.

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@LotusLofgren

Lotus Lofgren

5 years

Good luck @funganomics !! Can’t wait to watch what great work comes from the new Wang lab!

@stajichlab

Stajich Laboratory

5 years

We are happy for Yan Wang @funganomics as he starts his next stage of his career as faculty at @UTSC . We had a dim sum send off meal and look forward to hearing how his new adventures go. It was great joy having you part of the lab Yan!

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@LotusLofgren

Lotus Lofgren

8 months

Urge Duke University to Reconsider Closing Their Herbarium

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@LotusLofgren

Lotus Lofgren

5 years

Interesting discussion here about SM-BGC prediction relevant to antiSMASH backing away from the use of ClusterFinder in ver 5.

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@LotusLofgren

Lotus Lofgren

6 years

@FungiDownUnder @UMNFuN Such an amazing trip and host lab! Many thanks to @fungidownunder and crew for being patient while I geeked out on Waratahs, and cubic wombat poo, and for trusting me with your plasmids!

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@LotusLofgren

Lotus Lofgren

5 years

Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat.

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@LotusLofgren

Lotus Lofgren

7 years

@I_A_Dickie @NewPhyt Thank you Ian! I'm thrilled!

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@LotusLofgren

Lotus Lofgren

6 years

Fantastic talk on using codon bias to make functional predictions by @AbbeAtSea at #IMC11 !

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@LotusLofgren

Lotus Lofgren

4 years

Phylogenomic ancestral state reconstruction identified Larix as the ancestral host of Suillus, with multiple independent switches, one host reversion, and one host expansion into generalism.

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@LotusLofgren

Lotus Lofgren

10 years

Spinellus fusiger on Mycena #Mycoparasites http://t.co/ECPHzTOppn

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Lotus Lofgren

6 years

Tad Fukami: manipulation of microclimate by early colonizers as a mechanism for priority effects. So. Cool. #Fungal19

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@LotusLofgren

Lotus Lofgren

5 years

@mcmomany starts off a great talk with work on bet hedging in A.fumigatus clonal populations germinating under stress

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@LotusLofgren

Lotus Lofgren

4 years

Using 46 Ectomycorrhizal genomes, we preformed both a genome-wide analyses, and a targeted analyses of three classes of molecules previously identified as important determinants of host specificity: small secreted proteins, secondary metabolites, and G‐protein coupled receptors.

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@LotusLofgren

Lotus Lofgren

6 years

THIS

@mjskay

Matthew Kay

6 years

There is a multiverse of possible ways data in a paper could have been transformed, analysed, or reported. Instead of a stale old PDF, what if you could change these options to inspect that multiverse? 2/7

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@LotusLofgren

Lotus Lofgren

6 years

@cwfernandez @JAaronHogan @Colleen_Iversen @susanjcheng @SSSA_soils @LarryMattYork @ChrisInKnox @NewPhyt @TruffleSmithLAB Oooo! Maybe dead! Look at @TruffleSmithLAB 2009 paper

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@LotusLofgren

Lotus Lofgren

7 months

With @sarambranco @PerezPazosE @UMNFuN @jruytinx @xerantheum @Sunnyhl158 @KeYHfungi @zhang_kaile @vilgalys

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@LotusLofgren

Lotus Lofgren

1 year

@AsiyaGusa @poppy_clark @blake_billmyre Thanks to @ShapiroRebecca @jose_fmg @AmritaBharat and Iuliana Ene ! And of course @DukeHeitman and @CowenLab

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@LotusLofgren

Lotus Lofgren

5 years

@mykophile @FranFungi @mykophile def your fault Kabir. I’m forever thankful that you were in MN when you were. Fungus and I may have never met!

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@LotusLofgren

Lotus Lofgren

5 months

#MSAfungi24

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@LotusLofgren

Lotus Lofgren

4 years

Targeted analyses showed that genes encoding secondary metabolites (Terpenes and NRPS), but not small secreted proteins or G‐protein pathways, are more abundant and diverse in Suillus.

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@LotusLofgren

Lotus Lofgren

4 years

Suillus are beautiful, slimy, Ectomycorrhizal fungi, famous for being very host specific (almost exclusively) with plants in the family Pineaceae

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@LotusLofgren

Lotus Lofgren

5 years

@hyphaltip @DrLabRatOry Agreed. Long multi-copy regions like rDNA cassettes rarely make it into assemblies- just an artifact of needing to assign a single location to a sequence that exists in multi-copy space. As Jason suggests, you can find it using independent alignment to an ITS reference.

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@LotusLofgren

Lotus Lofgren

6 years

UC cuts Elsevier

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@LotusLofgren

Lotus Lofgren

5 years

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@LotusLofgren

Lotus Lofgren

6 years

@xerantheum @pjboynton @kristenobacter No correlation with gene content either! Would be cool to look at differences in the promoters - haven’t done that. Likely that most isolates far surpass the min copy number needed to meet protein demand, so is there a benefit of those $ extra copies?

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@LotusLofgren

Lotus Lofgren

6 years

This paper on Epichloe SSPs is amazing- and check out the author’s beautiful code supplementals. 🖤

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Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne

Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby...

journals.plos.org

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@LotusLofgren

Lotus Lofgren

5 years

@mykophile @KKTreseder thanks both! Excited to talk about this project at ESA on Thursday.

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@LotusLofgren

Lotus Lofgren

4 years

@Foaming_Agent I am plant

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@LotusLofgren

Lotus Lofgren

7 years

@fmartin1954 kicking off the last day of #ICOM9

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@LotusLofgren

Lotus Lofgren

5 years

@DukeHeitman talking RNAi pathways and fungal epimutations at UCR today. So. Cool. 🤯

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@LotusLofgren

Lotus Lofgren

3 years

Excited for new collaborations, eastern forests, vinegar barbeque, and all the 🍄🍄🍄

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@LotusLofgren

Lotus Lofgren

7 years

Laszlo Nagy, 4 gene expansion events associated with ECM specific lifestyle #ICOM9

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@LotusLofgren

Lotus Lofgren

4 years

We found that relative to other ectomycorrhizal fungi, Suillus have highly dynamic genomes including numerous rapidly evolving gene families and many domain expansions and contractions.

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