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Public: Bio551Past

Spring Quarter 2018

Lab meeting consisting of :___________ . Link to add to the meeting agenda

When: Fridays, 9:00 - 10:30 AM. Where: Kincaid 502 (except April 6, BEACON space)

March 30: Peter - soliciting feedback on a draft of the phenotypic plasticity manuscript.

April 6: Byran - practice talk

April 13: Journal club Rodriguez-Beltran et al. 2018 Δ

April 20: Alison Feder (guest presentation!)

April 27: Graduate Student Symposium, lab meeting cancelled

May 4: Journal club Gifford et al. 2018 Δ

May 11: Peter

May 18: Reilly Poster Practice (Undergraduate Research Symposium)

May 25 "CANCELLED"

June 1: Katrina Research Update

Winter Quarter 2018

Lab meetings are Fridays from 8:00-9:30 in KIN A049

January 5: No lab meeting

January 12: Ryan McGee

January 19: Josh Borin

January 26: Recruitment Day

February 2: Sonia Singhal

February 9: Katrina van Raay

February 16: Reilly

February 23: Olivia

March 2: Hannah

March 9: Brian

March 16:' Olivia


Fall Quarter 2017

Lab meetings are Fridays from 8:00-9:30 in KIN 502

September 29: Benjamin Kerr

October 6: All Kerr lab members

October 13: Olivia Kosterlitz

October 20: Katrina van Raay & Alwyn Mouton

October 27: Hannah Jordt

November 3: Olivia Kosterlitz

November 10: Cancelled for Veterans' Day

November 17: Peter Conlin

November 24: Cancelled for Thanksgiving

December 1: Peter Conlin

December 8: Katie Dickinson

Summer Quarter 2017

Lab meetings are Fridays from 10:30-12:00 in KIN 502

June 16: Katrina van Raay

June 23: Luis Zaman & Katrina van Raay

June 30: Robin Green & Kerr lab members

July 7: Cancelled

July 14: Cancelled for Microbial Population Biology GRC

July 21: Bryan Andrews

July 28: Hannah Jordt

August 4 Cancelled for BEACON Congress 2017

August 11: Cancelled

August 18: Mitchell Pesesky

August 24 (THURSDAY, 11:00-12:00pm): Ishay Ben-Zion

September 1: Benjamin Kerr

September 8: Olivia Kosterlitz & Hannah Jordt

September 15: Cancelled for the Biology departmental retreat

September 22: Katrina van Raay & special guest


Spring Quarter 2017

Lab meetings were Fridays from 10:30-12:00 in PAA A023D

March 31: Katie and Brian

April 7: Ryan McGee

April 14: Liv Kosterlitz

April 21: Cancelled for the Biology Graduate Student Symposium (GSS)

April 28: Sonia Singhal

May 5: Luis Zaman

May 12: Erin McClure

May 19: Cancelled for the Undergraduate Research Symposium

May 26: Sonia Singhal

June 2: Cancelled for Sonia's Defense! 11:30am

June 9: Peter Conlin

Winter Quarter 2017

Lab meetings were Fridays from 9:30-11:00 in KIN 502

January 6: Katie

January 13: Hannah

January 20: Hannah

January 27: Peter

February 3: Sonia - paper for PRESS

February 10: BEACON Proposal Party

February 17: Katrina

February 24: Peter

March 3: Katrina

March 10: Carrie and Sonia

March 17: Peter


Fall Quarter 2016

Lab meetings are Fridays from 9:30-11:00 in KIN 502

September 30: Quarterly lab update

October 7: Research Update - Carrie

October 14: Paper Queue

October 21: Research Update - Mitch

October 28: Paper Queue

November 4: Research Update - Brian

November 11: Canceled for Veterans Day

November 18: Paper Queue

December 2: Research Update - Sonia

December 9: Canceled

Queue

PaperTotal VotesNum Votes
Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities3.805
Parasite diversity drives rapid host dynamics and evolution of resistance in a bacteria-phage system3.405
A competitive trade-off limits the selective advantage of increased antibiotic production2.906
A Quick Introduction to Version Control with Git and GitHub2.704
Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli1.304
Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations1.303
Spatiotemporal microbial evolution on antibiotic landscapes1.004
How Good Are Statistical Models at Approximating Complex Fitness Landscapes?0.953
Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes0.853
Forecasting Epidemiological and Evolutionary Dynamics of Infectious Diseases0.703
Biological invasions and host–parasite coevolution: different coevolutionary trajectories along separate parasite invasion fronts0.501
The Ecology and Evolution of Microbial Competition0.401
Laboratory Evolution of Microbial Interactions in Bacterial Biofilms0.201
Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast0.000
The fitness landscape of a tRNA gene0.000
Rapid and widespread de novo evolution of kin discrimination0.000

Summer Quarter 2016

Lab meetings are Fridays from 10:00-11:30 in KIN 502

June 24: Lab meeting organization

July 1: Paper

July 8: Research Updates

July 15: Paper

July 22: Research Updates

July 29: Paper

August 5: Research Updates

August 12: Canceled for BEACON Congress

August 26: Paper

September 2: Paper

September 9: Research Update

September 16: Paper

Spring Quarter 2016

Unless otherwise noted, lab meetings are on Fridays from 10:00-11:30 in PAA049.

If you are presenting, send information to the lab mailing list before Wednesday at noon.

April 1: Lab meeting organization

April 8: Canceled: Evolution: Making Sense of Biology (MCB Symposium)

April 15: Canceled: EVO-WIBO 2016!

April 22: Research Update

April 29: Paper:

May 6: Research Updates:

May 13: Guest:

May 20: Canceled: Undergraduate Research Symposium

May 27: Paper:

June 3: Research Updates:

Winter Quarter 2016

Lab meeting consisting of research update, literature queue or queue-jumping.
When: Fridays, 10.00-11.30am. Where: Kincaid 502 (except Jan 8, PAA A049D)

Paper queue and lab meeting schedule: https://docs.google.com/spreadsheets/d/1vl4eHTq_lvFDvhNugp9W99ZkFGeaIR8asrsbal-VSyw/edit?usp=sharing

Jan 8: Hannah & Sylvie : Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
Jan 15: research update ( Josh )
Jan 22: Luis & Katrina: Evolutionary Rationale for Phages as Complements of Antibiotics
Jan 29: Sylvie & Ben: Engineering microbiomes to improve plant and animal health
Feb 5: Sarah: The ecology of the microbiome: Networks, competition, and stability
Feb 12: research update ( Sarah & Katie )
Feb 19: Ben: Breaking evolutionary constraint with a tradeoff ratchet
Feb 26: Queue Jump ( Jake )
Mar 4: (GSS is all day)
Mar 11: research update ( Peter )
Mar 18: Robin: Single gene locus changes perturb complex microbial communities as much as apex predator loss

Fall Quarter 2015

Lab meeting consisting of research update, literature queue or queue-jumping.
Time: 11.00-12.20pm. Place: Kincaid A023D

Oct 2: Brian & Jake : Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations
Oct 9: research update (Hannah)
Oct 16: Katie & Robin : Evolutionary limits to cooperation in microbial communities
Oct 23: research update (Joya)
Oct 30: Sonia & _ : Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
Nov 6: research update (Sarah re: Oxford work)
Nov 13: Katrina & Katie : Contrasted coevolutionary dynamics between a bacterial pathogen and its bacteriophages
Nov 20: queue jump: Katrina & Ben: Background reading Additional reading to be posted Wed evening (Nov 18).
Nov 27: Thanksgiving! (canceled)
Dec 4: research update (Peter)
Dec 11: lab goals (Katrina)


Summer 2015- Lab meeting

Research updates only. Place: Kin 502. Time: 9.00-10.30

Summer 2015

Weekly goal (please update as you go along) can be updated on the spreadsheet here: https://docs.google.com/a/uw.edu/spreadsheets/d/1MHcCunzaAFxFIFswIkcuMm_EBOuog1PtYdLw3mdAgEY/edit?usp=sharing

Group name: HACK (Currently: Hannah, Amanda, Carrie, Katrina, Katie)

Mission: This group is for beginner programmers. We will work on learning R or Python. Totally ok if you've never opened up Python or R, as Carrie said it's "no scientist left behind".

HACK Wiki

Meeting day and time: Thursdays, 11:00 in KIN 502.

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Group name: Tea with SQuEE (Brian and Katie, sometimes Luis)

Mission: Eco & Evo of QS journal club

Meeting day and time: Friday's usually around 4pm at a pub

Papers: SQuEE Zotero Group

Additional Discussion: #squee channel on Slack, also updated on Kerr Lab Meeting calendar (at least for summer)

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Group name: Methods to our Madness

Mission: Introduce each other to a new tool (technique, device, software, etc.) at each meeting

Meeting day and time: First meeting Tuesday June 16 at 11:00. Meetings added to Kerr Lab Meeting calendar.

Discussion: #methods channel on Slack

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Group name: Breakfast Club

Mission: To stay abreast of evidence-based pedagogy, focusing on higher ed STEM teaching.

Meeting day and time: Wed 8am, KIN 502

Contact Jake or Hannah for more information

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Group name: Phage Club

Mission: Read and discuss papers related to bacteriophage evolution and ecology. Impromptu brainstorming sessions encouraged.

Meeting day and time: Thurs. 11am, but please note we sometimes reschedule (and sometimes meet off campus). The Phage Club reading list and schedule will be updated regularly, but please e-mail Katrina, Sonia, or Luis to confirm time and location of meeting, just in case we forget to update something.

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Group name: pOP (aka plasmid group with Hannah and Sylvie)

Mission: Read and discuss papers related to plasmid eco/evo and horizontal gene transfer.

Meeting day and time: Fridays at 11am.

Reading list:

July 17- Frost & Koraimann (2010) Regulation of bacterial conjugation: balancing opportunity with adversity

July 2- Lau et al (2013) New quantitative methods for measuring plasmid loss rates reveal unexpected stability

June 26- Turner et al (2014) Antibiotic resistance correlates with transmission in plasmid evolution

June 19- San Millan et al (2014) Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

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Spring Quarter 2015

Revamped lab meeting.
Queues, queue-jumping, & research updates.
9-10:30 in KIN 502, unless otherwise noted.



Spring


Queue:

  1. Brian & Jake : Shape matters: lifecycle of cooperative patches promotes cooperation in bulky populations
  2. Katie & Robin : Evolutionary limits to cooperation in microbial communities
  3. Sonia & _ : Multiple Fitness Peaks on the Adaptive Landscape Drive Adaptive Radiation in the Wild
  4. Katrina & Katie : The costs of evolving resistance in heterogeneous parasite environments
  5. Hannah & Sylvie : Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids
  6. Sylvie & _ :
  7. Peter & _ :
  8. Carrie & _ :
  9. Ben & Peter : The genetical theory of multilevel selection
  10. Amanda & _ :
  11. Robin & _ :
  12. Jake & _ :

Paper Suggestions:

Winter Quarter 2014

This quarter is the first of a revamped lab meeting, in which we have a paper queue (with pilot & copilot), queue-jumping for emergent lab fun, and once-a-month research updates. We are meeting 9-10:30, in KIN 502.

Fall Quarter 2014

This quarter we are doing a pairwise journal club of current papers, with once a month research updates. We are meeting 11-12, in the BEACON space.

Summary: Two populations of deer mice – high and low elevation – differ in hemoglobin by 12aa in three clusters. Mix ‘n match of these three clusters show epistasis in O2-binding ability.

Summer Quarter 2014

This quarter we are working through Sex & Death (Sterelny & Griffiths 1999), which is an intro to the philosophy of biology. We are meeting 10-11, in KIN 502.

Spring Quarter 2014

This quarter we are doing a pairwise journal club of classic papers, with once a month research updates. We are meeting 10-11, in KIN 502.

Bonus papers
(papers submitted but not chosen this quarter)

Winter Quarter 2014

This quarter we are doing a pairwise journal club (2 "hosts" per week!), with once a month research updates. We are meeting 10:30-11:30, in basement room A023D.

Bonus papers
(papers submitted but not chosen this quarter)


Fall Quarter 2013

This quarter we are having a journal club, with special guest Ben Skyping in from sabbatical once a month for research updates. We are meeting 11:30-12:30, in HCK 312.


Summer Quarter 2013

This quarter we are going to be reviewing basic computational skills (using the shell, using the wiki, basic programing using python and R, data analysis, figure generation, using cloud computing, object-oriented concepts, etc.).


Spring Quarter, 2013

This quarter we are reading the primary literature. We are discussing the following papers:

Spring 2013 Lab Meeting Papers


Winter Quarter, 2013

This quarter we are giving progress reports on the various on-going projects in the lab as well as discussing one paper in each lab meeting.

Sign-up to present at lab meeting

Note: Remember that this is a public page. Do not attach published works, only links. Password-protected uploads are can be put here.


Fall Quarter, 2012

This quarter we are giving progress reports on the various on-going projects in the lab.

Sept 28: Lab Orientation (meet in the lab), SQuEE, and Brian Connelly

Sign-up to present at a lab meeting

Sign-up for one-on-one meetings


Spring Quarter, 2012

This quarter we are reading Robustness and Evolvability in Living Systems by Andreas Wagner.

Click here for scanned pdfs of every chapter in the book

March 30th: Chapters 1 & 2 (Josh)

April 6th: Chapters 3 & 4 (Jake)

April 13: Chapters 5 & 6 (Carrie)

April 20: Chapters 7 & 8 (OPEN)

April 27: Chapters 9 & 10 (Ben)

May 4th: Chapters 11 & 12 (OPEN)

May 11th: Chapters 13 & 14 (Peter)

May 25th: Chapters 15 & 16 (Sonia)

June 1st: Chapters 17 & 18 (Frazer)

June 8th: Chapters 19 & 20 & Epilogue (Katie)


Winter Quarter, 2012

This quarter we are reading Only A Theory: Evolution and the Battle for America's Soul. Please sign up for a week and link to an supplemental material paper.

Jan 13th: Chapter 1 and Wiki Tutorial (Josh Nahum)

Jan 20th: Cancelled due to weather

Jan 27th: Chapter 2 & 3 and The Evolutionary Origin of Complex Features (Ben Kerr)

Feb 3rd: Chapter 4 and A Draft Sequence of the Neandertal Genome (Neem)

Feb 10th: Chapter 5 and Oxygen and the Evolution of Complex Life (Sonia)

Feb 17th: Chapter 6 (Carrie)

Feb 24th: Cancelled

Mar 2nd: Chapter 7 (Peter)

Mar 9th: Chapter 8 and Using Avida-ED for Teaching and Learning About Evolution in Undergraduate Introductory Biology Courses (Josh Nahum)


Ben's Meeting Schedules


Beacon Schedule

BEACON Meeting Schedule

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Page last modified on June 08, 2018, at 12:28 AM