Please join us next Friday at 3pm for the next working group meeting, where Jennifer Deger and Colleen Strohlein will present on:
In vivo functional dissection of Alzheimer’s disease genetic risk
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LUKE PARKITNY, PhD, MSMed(PainMgt), BPhysio Research Operations Lead Center for Alzheimer's and Neurodegenerative Diseases (Director: Joshua M. Shulman, MD PhD) Baylor College of Medicine Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital 1250 Moursund St., Suite 1150.30, Houston, TX 77030 E: [log in to unmask]<mailto:[log in to unmask]> W: CAND Website<https://www.bcm.edu/research/research-centers/center-for-alzheimers-and-neurodegenerative-diseases>
This is a gentle reminder that we will meet tomorrow (Friday) at 3pm in 0725.01.
Best,
[Text Description automatically generated with low confidence]
LUKE PARKITNY, PhD, MSMed(PainMgt), BPhysio Research Operations Lead Center for Alzheimer's and Neurodegenerative Diseases (Director: Joshua M. Shulman, MD PhD) Baylor College of Medicine Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital 1250 Moursund St., Suite 1150.30, Houston, TX 77030 E: [log in to unmask]<mailto:[log in to unmask]> W: CAND Website<https://www.bcm.edu/research/research-centers/center-for-alzheimers-and-neurodegenerative-diseases>
Looking forward to your participation in this meeting. We plan to (i) review draft figures for the planned manuscript detailing the results of our functional screening of AD genes, we will also (ii) introduce a beta version of the AD Locus Cross-species Explorer tool, which we would love to have feedback on. Lastly, we should (iii) touch briefly on the imminent U01 “data release” and what we want to share.
We hope that everyone in the community has been recovering well from the recent visit by Beryl.
We are going ahead with our monthly functional genomics working group meeting tomorrow and will discuss exciting new work conducted by Shabab Hannan from the Shulman lab
"Investigating the role of novel genetic risk factor SNX32 (sorting nexin 32) in the aging brain"
Owing to the lack of availability of some individuals and that the originally scheduled meeting falls on a Friday after a holiday, we would like to reschedule our Functional Genomics Working Group meeting for the following Friday, July 12 at 3pm.
We will send additional information shortly.
Thank you for your understanding and we look forward to meeting again to discuss exciting new and ongoing projects.
I was reminded that at our last meeting, we ran out of time, and Keyang never had a chance to present her update on the ClinGen Allele registry and Linked Data Hub. I propose that we have an extended meeting this Friday so that we have time to hear this update in addition to progress on CD2AP. If you are able, I suggest that we meet from 3-4:30
I apologize to those who attempted to join the meeting today via zoom, however we were not able to host the virtual component as indicated.
We have decided that, moving forward, the working group meeting will be exclusively held in-person. Today's discussion stimulated great discussions and we hope to continue this throughout the year.
It was brought to my attention that some missed the original email with today's topics.
Please join us for some great presentations and discussions on work from Hugo Bellen's lab:
A short introduction from Hugo Bellen
An update on The LD pathway in AD from Matthew Moulton (20min)
The role of Tau in LD formation from Lindsey Goodman (20min) In vivo functional dissection of Alzheimer's disease genetic risk from Jennifer Deger (10min) WHEN: 01 MARCH 2024 WHERE: N.0725.01 at the Dan and Jan Duncan NRI (and zoom): 3pm
Gentle reminder that the Functional Genomics working group will meet tomorrow, Friday 01 March at 3pm.
I hope to see you all there.
Luke Parkitny, PhD, MSMed(PainMgt), BPhysio Research Operations Lead The Laboratory for Integrative Functional Genomics (PI: Joshua M. Shulman, MD PhD) Baylor College of Medicine Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital 1250 Moursund St., Suite 1150.30, Houston, TX 77030
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_91773308032-3Fpwd-3DM25qWXBTcnVDNnBUSnJTOERnV1RRZz09&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=xnZsRISf0bbLhE8y86dAfWRk332saq0BHS14RprTlQXKROoz81GZCFJnIouKV_Eb&s=F27-1EjvAy2-Sseq4gZL6Eu3jOrxtEX12iks3mnypXE&e=
Reminder that we will resume our Functional Genomics working group meetings today at 3PM. Please join us in person at NRI in RM 725.01. I can’t guarantee that we will be able to offer a zoom option, as this often has caused delays and glitches. We will have a special presentation from Hui Ye (Shulman Lab) on “An evolutionarily conserved role of the retromer subunit, VPS29, in synaptic transmission and lysosomal homeostasis”. We are excited to have your feedback on this developing story.
Our Functional Genomics working group will meet again on Friday 1/5 at 3PM Please join us in person at NRI in RM 725.01. I can’t guarantee that we will be able to offer a zoom option, as this often has caused delays and glitches. We will have a special presentation from Hui Ye (Shulman Lab) on “An evolutionarily conserved role of the retromer subunit, VPS29, in synaptic transmission and lysosomal homeostasis”.
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_91773308032-3Fpwd-3DM25qWXBTcnVDNnBUSnJTOERnV1RRZz09&d=DwIFAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=E6KPadnXY0zUfwVkc04pGfq21hXWstu5ZlcUNfmhlSBpPp4LlLNo3VLtHI-w1uB6&s=uQU5VOO8FyrCnlTFLzPll3Mxyn8_9cdUfNTM_WpOtXU&e=
Our AD Functional Genomics working group will meet today at 3PM. Please join us in person at NRI in RM 725.01. I can’t guarantee that we will be able to offer a zoom option, as this often has caused delays and glitches.
Agenda:
-Update on loss-of-function screening for CNS requirements of AD genes (Jennifer Deger)
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_91773308032-3Fpwd-3DM25qWXBTcnVDNnBUSnJTOERnV1RRZz09&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=6IRkdlGTOeU4RaUyjLMz8mGXE6P1PCj8AzGqHOcaehYQ4tOf22DHUL8iPt9fKSiu&s=RifbU3tnk4Cf9_0FNiFC9gzIvSk6LcwTNQEBWGcE1MA&e=
From: Shulman, Joshua M. <[log in to unmask]> Date: Wednesday, August 30, 2023 at 9:14 AM To: Listserv - CAND-FUNCTION <[log in to unmask]> Subject: AD Functional Genomics meeting: Friday 9/1 @ 3PM Dear all,
we will resume our AD Functional Genomics working group meetings this Friday at 3PM. Please join us in person at NRI in Rm 725.01. I can’t guarantee that we will be able to offer a zoom option, as this often has caused delays and glitches.
we will resume our AD Functional Genomics working group meetings this Friday at 3PM. Please join us in person at NRI in Rm 725.01. I can’t guarantee that we will be able to offer a zoom option, as this often has caused delays and glitches.
For the next couple gatherings, we will try to shift to discussion of biological pathways and ongoing / planned mechanistic followup studies, which fits with AIM 4 of our ADSP U01. If there are specific pathways that you’d like to present on or discuss, please let me know. Discussion of “dark targets” with
We will meet tomorrow at 3PM at N.0725.20. Francois St-Pierre’s team will present on their incipient studies of Alzheimer’s genes and related targets using cell-based assays.
I’ve decided that the hybrid format is not feasible anymore—it leads to too many delays, glitches, and other frustrations. I hope you all can join in person!
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_91773308032-3Fpwd-3DM25qWXBTcnVDNnBUSnJTOERnV1RRZz09&d=DwIFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=CZ9qH-0NJXZzUKDPzbMHxTgddM5WShM8UQUlkRq7Q4kANA_520qImBSL7czPcyrl&s=vLHIfWgrBLj4P8XkvXGwsj5vuHl8t1J41P99dPNF3AU&e=
We will resume meeting today for our AD Functional Genomics workgroup. We will hear from Olivier Lichtarge and team (Danny) as well as Ismail Al-Ramahi on their computational and functional follow-up of AD targets.
To encourage productive exchange, we hope that most will attend In person at NRI, room N.0725.01, but if this is not possible, we will attempt a hybrid:
Dear all, Apologies, due to travel obligations we will have our next AD functional genomics meeting on June 9 at 3pm. Olga, please adjust the calendar invite. Thanks, Josh
From: Rybina- Willis, Olga <[log in to unmask]> Date: Tuesday, May 16, 2023 at 9:54 AM To: Listserv - CAND-FUNCTION <[log in to unmask]> Cc: PETROSYAN, Varduhi <[log in to unmask]>, Gu, Mingxue <[log in to unmask]>, Veeraragavan, Surabi <[log in to unmask]>, Hannan, Shabab Bin <[log in to unmask]>, Hamdan, Mohammed <[log in to unmask]>, Shulman, Joshua M. <[log in to unmask]>, Milosavljevic, Aleksandar <[log in to unmask]>, Bellen, Hugo J <[log in to unmask]>, Barros De Paula, Ruth <[log in to unmask]>, Deger, Jennifer Marie <[log in to unmask]>, Al-Ramahi, Ismael <[log in to unmask]>, Kanca, Oguz <[log in to unmask]>, Lee, Tom Van <[log in to unmask]>, Moulton, Matthew <[log in to unmask]>, Zhao, Pinghan <[log in to unmask]>,
We have our recurring U01 / internal AD Functional Genomics meeting today at 3PM. The proposed agenda:
Update on cell model studies from Tom and Alex Review of Year 2 milestones, as we need to soon prepare our progress report Discussion of agenda for in person FunGen consortium meeting at BCM May 2-3
We will meet today at 3PM in the NRI 7th floor conference room and by zoom. We will continue our discussion of selected targets, focusing in further on the ADAM10 locus (below) which as 2 interesting / viable candidates: ADAM10 and AQP9. We will weigh the evidence in support of each and review data from our aims.
I’d like to propose that we move our next internal AD Functional Genomics meeting, the first of 2023, to Friday Jan 27 (at 3PM), as I will be away next week.
For this meeting, I would like to propose that we try something new, and focus discussion around targets. Mohammed has been reviewing results from the first ~300 targets, and we have prioritized the following 4 genes for initial discussion:
We will meet this coming Friday at 3PM for our next AD Functional Genomics meeting, using the planned meeting format below. We have a hybrid meeting both in NRI 725.01 and on zoom:
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_91773308032-3Fpwd-3DM25qWXBTcnVDNnBUSnJTOERnV1RRZz09&d=DwIF-g&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=hI3Vl5IMCQYJuhidHOV-osp1mexazugC8ooVaKaehIzsxRNHbj-adfqEuhLuaqgf&s=nvxoJDGksRVdpv6dxcORA2WjHvDEyOePpem1QLMzqMI&e= Password: 783224
For the discussion, we will discuss the following targets:
We will meet today at 3PM in N.0725.01 at NRI. Also, zoom link below if you are unable to come in person.
The goal of this meeting is to have “round-table” updates from all teams on U01 AIMs and related initiatives (cell-based models and mouse behavioral core). We should discuss if/how we can be more cohesive in our collaborations.
We have our internal monthly AD Functional Genomics Meeting this coming Friday (12/9) at 3PM. I’d like to try and begin meeting in person, if possible; we will reserve a room on the NRI 7th floor going forward. If necessary, we can implement a hybrid meeting if everyone is not able to join. Here is the zoom info:
We have our internal FGC/U01 meeting tomorrow at 3PM. We will hear an update from the Tom, Aleks, and Jin and the cell-based analysis pipeline. There will be time for us to have open discussion about other matters arising on the other aims.
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_97430342438-3Fpwd-3DZTdia05CTnpyd0Q2cUdFMStSaWcwdz09&d=DwIFAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=gakSkDrzeUo8FtLUKG6PG65BTQTKWx0SVjW3VkBOj_7cQfd1QwL8oAW21cR8zRSW&s=vgHXV9n2s_njcgit02w1b7iO6yG2j8lFeTT2OIj7L9o&e= Password: 584384
We will be meeting at 4PM tomorrow and we will hear presentations from Varduhi and Songmi from Aleks’ and Myriam’s teams, regarding the bioinformatic prioritization of AD targets for follow-up studies.
The change to 4PM is a 1-time accommodation from our usual meeting time, but should already be indicated on everyone’s calendar since the invite was circulated last month.
Hi everyone, reminder that we meet today at 3PM! Best, Josh
From: Shulman, Joshua M. <[log in to unmask]> Date: Wednesday, August 10, 2022 at 6:37 AM To: Listserv - CAND-FUNCTION <[log in to unmask]> Cc: Rybina- Willis, Olga <[log in to unmask]> Subject: FRIDAY @ 3PM: AD Functional Genomics Meetings Resume Hi Everyone,
We will resume with our functional genomics core working group meetings this Friday following the brief summer hiatus. You should have an invitation with zoom link already on your calendars, but here is the link just in case:
Hi Everyone, a little confusion came up today regarding the terms ortholog and paralog. I am attaching a review that talks about the relationship of genes in evolutionary biology by Koonin (Annu. Rev. Genet. 2005) that discusses the terms in detail. Note that it is not always straightforward determining which genes are orthologs and which are paralogs. It is also true that there does not have to be a one-to-one relationship of orthologs and that the terms do not imply conservation of function but only evolutionary relationships between genes. Since two gene duplication events followed the split that separates vertebrates
We will resume with our functional genomics core working group meetings this Friday following the brief summer hiatus. You should have an invitation with zoom link already on your calendars, but here is the link just in case:
Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_97430342438-3Fpwd-3DZTdia05CTnpyd0Q2cUdFMStSaWcwdz09&d=DwIFAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=CtRrz3Az77eLAoGra51j1_JbnruKoIP09DQFOCdGj54IbsuFXKH5jQC2CXsVWB68&s=EoZh_eI2tKFCh9PtpW3Vi-f9PxaOa62NECnOAeBKiAA&e= Password: 584384
Agenda: -brief review of FunGen EAB comments (Josh) -update on Year 1 high-throughput screen results (U01 Aim 2) and draft ADSP data release (Shabab, Jennifer) -Year 2 high-throughput screening plan (Josh will present proposal for discussion) -update on medium throughput screening (U01 Aim 3) (Jennifer, Shabab, Mingxue, Oguz) -time
We will meet today at 3PM for our AD Functional Genomics Meeting.
Here is the Agenda: ClinGen in FunGen-AD (Keyang) CD2AP in flies/mice (Matea) CD2AP in human cellular models (Tom / Tara) Mouse Neurobavioral Core (Surabi / Rodney)
Looking forward, Josh
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From: CAND Function <[log in to unmask]> on behalf of Shulman, Joshua M. <[log in to unmask]> Date: Tuesday, May 10, 2022 at 7:33 AM To: Listserv - CAND-FUNCTION <[log in to unmask]> Subject: Re: AD Functional Genomics Meeting Hi everyone,
Small note of clarification: we are STILL MEETING THIS FRIDAY at 3PM, and will hear from Matea and Tom about CD2AP, as well as an overview of the NRI rodent behavior core. We will then have a "summer break" from meeting and reconvene in August!
We were scheduled to meet today at 3pm, but I suggest we cancel this meeting as most of us participated in the ~4+ hour NIH FunGen consortium zoom yesterday. Our next meeting is May 13, and I will reach out to some of you regarding next steps on Aim 3 (medium throughput screening).
Friendly reminder that we will meet tomorrow, Friday at 3PM for our monthly AD Functional Genomics monthly meeting.
We will have several updates from the computational team, including from Keyang Yu, Cece Li, and Varduhi Petrosyan, on the U01 Aim 1 gene/variant prioritization analyses, pipeline, and tools.
Friendly reminder that we will meet tomorrow at 3PM for an “ectopic” AD Functional Genomics monthly meeting.
This is an add-on meeting following from last week, to continue our multiple short updates from on our ongoing collaborative analyses of new, longitudinal RNAseq datasets generated from multiple fly models of neurodegenerative disease (Abeta, Tau, Synuclein, and HTT). We can also begin to discuss scRNAseq data generated from these same models. While not formally part of our ADSP U01, this work will likely be of interest and relevant to all, so please feel free to join if you’d like. All
Friendly reminder that we will meet today at 3PM for our monthly AD Functional Genomics monthly meeting.
We will have multiple short updates from on our ongoing collaborative analyses of new, longitudinal RNAseq datasets generated from multiple fly models of neurodegenerative disease (Abeta, Tau, Synuclein, and HTT). We can also begin to discuss scRNAseq data generated from these same models. While not formally part of our ADSP U01, this work will likely be of interest and relevant to all, so please feel free to join if you’d like. These data our available to enhance and complement many of
We will meet on Friday at 3PM for our monthly AD Functional Genomics monthly meeting.
For this month, we are going to have updates on collaborative analyses of RNAseq datasets generated at NRI for neurodegenerative disease fly models (Abeta, Tau, Synuclein, and HTT), including short presentations from Megan, Justin, Pinghan, Justin, and possibly others. We can also discuss next steps for analyses of new scRNAseq data. While not formally part of our ADSP U01, this work will be of interest and relevant to all, so please feel free to join if you’d like.
Just a reminder that AD Functional Genomics meeting will be in hybrid format today, @3 pm
In person: NRI N.0725.01 and
on zoom: Join from PC, Mac, Linux, iOS or Android: https://urldefense.proofpoint.com/v2/url?u=https-3A__bcm.zoom.us_j_91773308032-3Fpwd-3DM25qWXBTcnVDNnBUSnJTOERnV1RRZz09&d=DwIFAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=BSIzjL4f6RGePXexwiOR6kUIu7Rikd96-JPwL6Z2MZY&m=jBxEa8sckUj2elWbKbvNN7XEF_llpi49ygJcN8BCRw3nOWG24cSOlJuIWPRPIMqV&s=GcCcOhIFYeuueJUy4JNSvbaZuMP_Kb3GyFUqWVzUfeY&e= Password: 783224
Thanks, Olga
From: CAND Function <[log in to unmask]> On Behalf Of Shulman, Joshua M. Sent: Monday, January 23, 2023 02:31 PM To: Listserv - CAND-FUNCTION <[log in to unmask]> Subject: Re: Next AD Functional Genomics Workgroup: Jan 27 @ 3PM
