Chris McFarland

The Cancer Evolution Lab at Case is up at mcfarlandlab.org! We're looking to hire two postdocs: jobrxiv.org/job/case-weste…

Our recent @PRX_Life paper was selected as the very first journal cover and it looks great :) Past thread explaining why we're are just so excited about this result below:

Excited to share new paper led by postdoc @JeffMaltas (on the job market!) out today in @PRX_Life (1/4 🧵) Frequency-Dependent Ecological Interactions Increase the Prevalence, and Shape the Distribution, of Preexisting Drug Resistance #cancer #ecology journals.aps.org/prxlife/abstra…

Excited to showcase our poster at #AACR on Tuba-seq and the latest innovation in lung cancer discovery! Visit Section 26 to learn more. #AACR24 #AACR #cancerresearch #lungcancer @AACR @CancerEvoLab @cwru @CWRUSOM @CWRUPostdocs

Add in some good statistical approaches to fit non-monotone growth rates and you have a nice complete method. Comments welcome!!

Proud of @cwrumstp student Eshan King for publishing 1st thesis paper this week @PLOSCompBiol! In it, we explore how #FitnessSeascapes encode multple #evolutionary trade-offs during changing drug dosing (either in space or time). Short thread journals.plos.org/ploscompbiol/a…

So happy to share a Case spotlight of Dr. Athar Khalil - the CanEvo group wouldn't exist without Athar thedaily.case.edu/postdoc-spotli…

Come check my poster @aacr NCI-EROTIC international conference on Molecular Targets and Cancer Therapeutics A177 #Boston @CancerEvoLab

Our group is now hiring a Junior Technician. Please checkout details at linkedin.com/jobs/view/3664…, and reach out to me for any questions!

@_ellie_cat @UCRiverside WOOOO!!!!

first time presenting this exciting new work from @colincess! he will have to do a #tweetorial when the paper comes out! #mathonco

Had a blast at #MathOnc23 - thank you @NikosDim3 for the gorgeous photo 🤩

Really happy to participate in #MathOnco23 ! What an exciting community!!

We have our first graduate: Xiangzhen Wei successfully defended his Master Thesis! Xiangzhen has been working collaboratively to extend TuBa-seq to model heterozygous losses for pharmacogenomic modeling. Congrats!!!

@Dagim26 @JeffMaltas @durmaz_aa @hinczewskilab @CancerConnector This paper reminded me of Haldane's Sieve, but for ecological interactions. Crazier still: every drug resistant variant Dagim measured exhibits a positive ecological interaction with ancestor!!

Happy to share our pre-print describing how frequency dependent interactions b/n resistance & sensitive cells affect the prevalence & distribution of pre-existing drug resistant cells. biorxiv.org/content/10.110…. @JeffMaltas @durmaz_aa @CancerEvoLab @hinczewskilab @CancerConnector

@skryazhi This raises another question: given that sequencing is the biggest cost, shouldn't barcode lengths be a commonly-ordered read length (e.g. either 50, 100, or 150 bp)?

@CancerEvoLab It's a potentially good idea. I haven't thought too much about it. My initial thoughts: (1) the biggest cost is in sequencing, so length matters little until your barcode primers get too big and your reads get too long. The 38bp NNNWS barcode we propose does not hit these limits.

Do you use DNA barcodes to track lineages? Ever wondered how to design random barcodes and process sequencing data? @_miloj, @s_venkataram and I have a new pre-print for you! Best practices in designing, sequencing and identifying random DNA barcodes ecoevorxiv.org/t58xw/

@skryazhi Very useful! I wonder if you have thoughts on paired-end sequencing? With Hi-Fi PCR, it can theoretically square sequencing errors without costing double. However in Fig. 3, a 60-bit barcode more than doubles the average hamming distance between barcodes relative to 30 bits.

We hope people find this work useful! And we love to get any feedback on the manuscript, here or by email.

Thank you to Slava Tkachenko for helping us address all the reviewer concerns!

Susanne, Christina Curtis and Dmitri recently characterized the proteotoxic response mechanisms to mutational load and experimentally-validated this model: biorxiv.org/content/10.110…

Very Excited to *finally* publish, with @SusanneTilk @PetrovADmitri, our article explaining why deleterious passengers accumulate in genomically-unstable tumors: elifesciences.org/articles/67790