Ed Buckler
@EdBuckler
Followers
1K
Following
80
Media
2
Statuses
47
Joined May 2014
Over two decades ago, we mapped the variant making sweet corn sweet—after tremendous effort. PlantCaduceus easily identifies this single base pair causal variant. 🌽. Give it a try—this model paves the way for treating all plants as a single molecular system!
0
1
11
What’s remarkable about PlantCaduceus is its ability to be fine-tuned in Arabidopsis and still retain accuracy in distant species like major grass crops, such as corn. 🌱→ 🌽🌾. This class of models are a game changer for plant genomics!
biorxiv.org
Interpreting function and fitness effects in diverse plant genomes requires transferable models. Language models (LMs) pre-trained on large-scale biological sequences can learn evolutionary conserv...
1
5
17
PlantCaduceus - Cross-species modeling of plant genomes .Led by Jingjing Zhai and Aaron Gokaslan, with the Kuleshov lab, we’re having our “ChatGPT moment” with DNA Large Models. PlantCaduceus predicts functional DNA sequences with single base resolution across flowering plants.
1
21
39
RT @theNASciences: Congratulations Johannes Lehmann of @CornellCALS, newly inducted #NASmember! #NAS161 #soilscience
0
24
0
New whole-genome alignment tools are needed for tapping into plant div.
2
32
89
RT @CoopMaize: Comments were made last night at #MGM2023 that were hurtful to members of our community. Discrimination and harassment, even….
0
16
0
RT @MerKhaiBurch: Dr.MariaElena Zavala's talk at #MGM2023 was amazing. Dr. Zavala talked about research, mentors & work to increase the num….
0
98
0
RT @pcronald: .#JaneSilverthorne dedicated her career to helping #scientists succeed and to raising public awareness of the importance of #….
0
2
0
My great colleague @LongLab published a neat paper on how plants deal with light, but @MerKhaiBurch is right; yield increases that don’t replicate should not be claimed in abstracts or press releases.
ANOTHER paper in @ScienceMagazine came out claiming a 33% increase in soy yield. Since my last “yield” tweet took off - lets do it again!. From a (wanna be) plant breeder 5 years into my PhD, let me explain how this 33% increase in yield is misleading 🧵
2
9
43
Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks Congrats Travis Wrightsman and team on the really nice paper!.
acsess.onlinelibrary.wiley.com
Cross-species models of chromatin state from sequence are comparable or superior to within-species models. Model performance is highest on accessible regions open in many tissues. Transcription fa...
0
18
47
Wonderful to see @edanquah240 again! Agree so much we can do together and for the next generation to design better food systems.
Erasing inequities in capacity to innovate in the Ag. Development space will save our world. Inescapable conclusion in meetings with Ed Buckler and Vern Gracen today at Cornell University. @gatesfoundation @RockefellerFdn @Agnes_Kalibata @AGRAAlliance @UnivofGh @CornellGlobal
0
3
11
RT @MerKhaiBurch: A misleading paper in @ScienceMagazine just came out talking about how a single gene can increase rice yield by 41-68%. A….
science.org
Overexpression of a single transcription factor improves the agricultural productivity of rice.
0
350
0
New preprint from Travis Wrightsman introducing an ML model to predict chromatin state across plant species just from DNA sequence!
biorxiv.org
Accessible chromatin regions are critical components of gene regulation but modeling them directly from sequence remains challenging, especially within plants, whose mechanisms of chromatin remodel...
0
17
56
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation - congrats on the team for making haplotype graphs useful for genomic AND breeding. The R and BrAPI web services will be game changers.
biorxiv.org
Motivation Pangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better...
1
55
128
AnchorWave is a really cool whole-genome alignment pipeline developed by @baoxing_song @mcstitzer to deal with those ubiquitous hard-to-align genomes with lots of transposons.
biorxiv.org
Millions of species are currently being sequenced and their genomes are being compared. Many of them have more complex genomes than model systems and raised novel challenges for genome alignment....
0
21
70
Haplotype Associated RNA Expression (HARE) Improves Prediction of Complex Traits in Maize .Because the cis-component of expression is more consistent across tissues, @AnjuAnjugiri1 is able to improve genome-wide prediction in a wide range of contexts.
biorxiv.org
Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for prediction within...
0
10
29
RT @CoopMaize: Congratulations to Dr. Bill Sheridan, recipient of the 2021 MGC R. Emerson Lifetime Achievement Award. #MGM2021
https://t.….
0
6
0
RT @CoopMaize: Congratulations Dr. Nathan Springer @SpringerNathan, 2021 recipient of the MGC L. Stadler Mid-Career Award in recognition of….
0
20
0
RT @CoopMaize: Congratulations to Dr. Andrea Eveland, 2021 recipient of the MGC M. Rhoades Early Career Award in recognition of her signifi….
0
12
0
RT @CoopMaize: Today the MGC honors the memory of Dr. Don Auger with a 2021 R. Emerson Lifetime Achievement Award. #MGM2021 .
0
11
0