Genome Analysis Wiki - User contributions [en]

User talk:Cdobski

2019-05-01T20:50:33Z

SCaron: Welcome!

'''Welcome to ''Genome Analysis Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents help pages].
Again, welcome and have fun! [[User:SCaron|SCaron]] ([[User talk:SCaron|talk]]) 16:50, 1 May 2019 (EDT)

User:Cdobski

2019-05-01T20:50:33Z

SCaron: Creating user page for new user.

Chrissy Dobski is an Administrative Specialist for the Center for Statistical Genetics. She has four years with the University of Michigan, and three years prior supporting Northwestern University's Drucker Virology Lab. Her office is located in the tower of SPH1, room 4619. Please contact her by phone at 734-763-0424 or by email at cdobski@umich.edu.

User talk:Yukt

2019-05-01T20:49:58Z

SCaron: Welcome!

User:Yukt

2019-05-01T20:49:58Z

SCaron: Creating user page for new user.

Ketian Yu is a Ph.D. student in the Department of Biostatistics at the University of Michigan. She is interested in computational and statistical models for human genetics. She got her master's degree in Statistics from the University of Michigan in 2017 and her bachelor's degree in Statistics from the University of Science and Technology of China in 2015. She loves outdoors and going on adventures.

User talk:Sarahgag

2016-07-19T16:45:11Z

SCaron: Welcome!

'''Welcome to ''Genome Analysis Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:SCaron|SCaron]] ([[User talk:SCaron|talk]]) 12:45, 19 July 2016 (EDT)

User:Sarahgag

2016-07-19T16:45:11Z

SCaron: Creating user page for new user.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

User talk:Chriclrk

2016-05-12T19:55:13Z

SCaron: Welcome!

User:Chriclrk

2016-05-12T19:55:13Z

SCaron: Creating user page for new user.

Senior Application Programmer / Analyst at the Center for Statistical Genetics
Hired in August of 2015

Formerly Director of Software Engineering and Information Technology at SparkFun Electronics, a hobbyist electronics startup in Boulder, CO
Formerly Image Processor / Web Developer for the Imaging Team of the Cassini mission to Saturn at the Space Science Institute in Boulder, CO

User talk:Liugroup

2015-04-08T23:52:11Z

SCaron: Welcome!

User:Liugroup

2015-04-08T23:52:11Z

SCaron: Creating user page for new user.

This is Dajiang. How are you?
This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you? This is Dajiang. How are you?

Sean Caron

2014-07-31T19:11:41Z

SCaron:

[[Image:Sean_head.jpg|200px|right]]

Sean is responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to Center faculty, students and staff. Sean earned his B.S.E. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.
<P>
[http://wildflower.diablonet.net/~scaron Sean's personal page]

Sean Caron

2014-07-31T19:09:07Z

SCaron:

[[Image:Sean_head.jpg|200px|right]]

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to Center faculty, students and staff. Sean earned his B.S.E. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.
<P>
[http://wildflower.diablonet.net/~scaron Sean's personal page]

Sean Caron

2014-07-31T19:08:23Z

SCaron:

[[Image:Sean_head.jpg|200px|right]]

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to Center faculty, students and staff. Sean earned his B.S.E. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.
<P>
<A HREF="http://wildflower.diablonet.net/~scaron">Sean's personal page</A>

Main Page

2014-01-13T19:50:37Z

SCaron:

<div id="mf-mainpage">


{| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;"
|-
| style="width:100%; text-align:center; white-space:nowrap; color:#000;" | <div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div>
|}

[[Image:Abecasis_group_photo_cropped.jpg|900px|center|Group Photo 2013]]




== Welcome! ==

Welcome to our brand new wiki!

If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|request an account]]. We recommend using your e-mail address or Michigan uniqname as your user id.

For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].

== Sequence Analysis Tools ==

We are developing [[Software|software tools]] for the analysis of next generation sequence data.

These tools include:

#Variant Calling with [[GlfSingle]] and [[GlfMultiples]]
#Variant Calling and De Novo Mutation Detection in Families with [[Polymutt]]
#Variant Annotations using [[VcfCodingSnps]]
#Rare Variant Analysis using [[RvTests]]
#Rare Variant Association Analysis in family samples [[FamRvTest]]
#Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
#C++ APIs for sequence analsysis using [[C++ Library: libStatGen]]
#Meta-analysis of single variant or gene-level associations [[RAREMETAL-SOFTWARE]]
#Sequencing study design helper [[Rarefy]]
#Local ancestry inference (ancestry painting) using off-targeted sequence data [[SEQMIX]]

These tools and additional tools can be found on the [[Software]] page.

We are developing Genome/Sequencing Processing Pipelines for anyone to use: [[GotCloud]]

== High Level Tutorials ==

Some high-level tutorials on the analysis of next generation sequence data:

#[[Evaluating a Read Mapper on Simulated Data]]
#[[SNP Call Set Properties]]
#[[Generic Exome Analysis Plan]]

== Projects ==

[[SardiNIA]] - The SardiNIA longitudinal study of aging.

[[1000 Genomes Project Pilot 1 SNP Calling]]

[[EMADS|Exome Meta-analysis of Drinking and Smoking (EMADS)]]

== Learn Genetics ==

Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.

== General Resources ==

*[[Computer How-Tos]]
</div>

Sean Caron

2013-06-15T03:22:56Z

SCaron:

Sean Caron

2013-06-15T03:14:27Z

SCaron:

[[Image:Sean_head.jpg|200px|right]]

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to Center faculty, students and staff. Sean earned his B.S. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.

Sean Caron

2013-06-15T03:07:31Z

SCaron:

[[Image:Sean_head.jpg|200px|right]]

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to faculty, students and staff. Sean earned his B.S. in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.

Sean Caron

2013-06-15T01:40:36Z

SCaron:

[[Image:Sean_head.jpg|200px|right]]

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to faculty, students and staff. Sean earned his BSE in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.

Sean Caron

2013-06-15T01:39:48Z

SCaron:

[[Image:Sean_head.jpg|300px|right]]

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to faculty, students and staff. Sean earned his BSE in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.

File:Sean head.jpg

2013-06-15T01:38:16Z

SCaron:

Sean Caron

2013-06-15T01:35:33Z

SCaron:

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to faculty, students and staff. Sean earned his BSE in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.

Sean Caron

2013-06-15T01:34:45Z

SCaron:

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to faculty, students and staff as required. Sean earned his BSE in Electrical Engineering from the University of Michigan with a concentration in digital signal processing and control systems.

Sean Caron

2013-06-15T01:33:54Z

SCaron: Created page with 'Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to facu…'

Sean is the UNIX systems administrator responsible for the operation and maintenance of the Center's high performance computing cluster. He also provides end-user support to faculty, students and staff as required. Sean earned his BSE in Electrical Engineering from the University of Michigan.

Abecasis Lab

2013-06-15T01:31:57Z

SCaron:

[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]

== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

* Goo Jun
* Christian Fuchsberger
* Alex Tsoi
* [[Dajiang Liu]]
* Lars Fritsche
* [[Scott Vrieze]]

=== International Visitors ===

* Andrea Maschio
* Giorgio Pistis
* Eleanora Porcu

=== Graduate Students ===

* Su Chu

* Sayantan Das

* Shuang Feng

* Dan Hovelson

* [[Alan Kwong]]

* Ben Lerch

* Sara Rashkin

* Sebanti Sengupta

* Vivian Wang

* Xiaowei Zhan

* Tingting Zhou

=== Staff ===

* Laura Baker

* Tom Blackwell

* [[Sean Caron]]

* Jennifer Bragg-Gresham

* Kevin Li

* Mary Kate Wing

== Alumni ==

=== Former Research Faculty ===

Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

Weimin Chen (graduated 2007), now Assistant Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

Bingshan Li (graudated 2011), now Assistant Professor at the [https://medschool.vanderbilt.edu/cqs/people/Bingshan/Li/cqs-faculty-members Center for Quantitative Sciences, Vanderbilt University]

Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

Paul Scheet (graduated 2008), now Assistant Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

Carlo Sidore (graduated 2012), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

William Stewart (graduated 2008), now Assistant Professor at [http://www.mathmed.org/#William_Stewart Battelle Center for Computational Medicine, Departments of Statistics and Pediatrics, National Children's Hospital and Ohio State University]

=== Former Doctoral Students ===

Wei Chen (graduated 2011), now Assistant Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD Department of Pediatrics, University of Pittsburgh Medical Center]

Jun Ding (graduate 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

Youna Hu (graduated 2012), now a Research Fellow [http://cteg.berkeley.edu/members/hu.html working with Rasmus Nielsen at Berkeley]

Mingyao Li (graduated 2005), now Associate Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

Liming Liang (graduated 2009), now Assistant Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://www.ucdenver.edu/academics/colleges/PublicHealth/departments/Epidemiology/About/Faculty/Pages/FingerlinT.aspx Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/339/FacultyPro/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

Jin Zhen (graduated 2009), now working in the Pharmaceutical Industry.

=== Former Masters Students ===

Melinda Curran

Vesela Gateva

Xijing Han

Elizabeth Jewell

Yanming Li

Heather Munro

Theresa Scott (nee Daigneault)

Matthew Snyder

Yuan Wei

Abigail Woodroffe

Zaojun Ye

Matthew Zawitowski

Anita Yu Zhao

=== Visitors ===

Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Abecasis Lab

2012-02-16T20:52:43Z

SCaron:

[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]

== Mission Statement ==

We are developing and applying computational and statistical tools to further understanding of complex human diseases, such as cardiovascular disease and diabetes.

== Leadership ==

[[Goncalo Abecasis]] is currently the Felix Moore Collegiate Professor of Biostatistics at the University of Michigan School of Public Health.

== Current Members ==

=== Research Fellows ===

* Goo Jun
* Christian Fuchsberger
* Alex Tsoi
* Dajiang Liu

=== International Visitors ===

* Fabio Busonero
* Carlo Sidore
* Andrea Maschio

=== Graduate Students ===

* Su Chu

* Melinda Curran

* Sayantan Das

* Dan Hovelson

* Youna Hu

* Alan Kwong

* Sara Rashkin

* Shuang Feng

* Xiaowei Zhan

=== Staff ===

* Paul Anderson

* Laura Baker

* Tom Blackwell

* Sean Caron

* Jennifer Bragg-Gresham

* Mary Kate Trost

== Alumni ==

=== Former Research Faculty ===

Hyun Min Kang (''graduated in 2011''), now Assistant Professor at the [http://www.sph.umich.edu/biostat/ University of Michigan School of Public Health, Department of Biostatistics].

=== Former Research Fellows ===

Weimin Chen (graduated 2007), now Assistant Professor at the [http://people.virginia.edu/~wc9c/ Department of Public Health Sciences & Center for Public Health Genomics, University of Virginia]

Bingshan Li (graudated 2011), now Assistant Professor at the [http://chgr.mc.vanderbilt.edu Center for Human Genetics Research, Vanderbilt University]

Serena Sanna (graduated 2007), now an investigator at the [http://www.serenasanna.com/ Istituto di Neurogenetica e Neurofarmacologia in Sardinia, Italy]

Paul Scheet (graduated 2008), now Assistant Professor at [http://faculty.mdanderson.org/Paul_Scheet/Default.asp?SNID=221605974 Department of Epidemiology, University of Texas MD Anderson Cancer Center]

William Stewart (graduated 2008), now Assistant Professor at [http://www.columbia.edu/~ws2267/ Department of Biostatistics, Columbia University]

=== Former Doctoral Students ===

Wei Chen (graduated 2011), now Assistant Research Professor at the [http://www.chp.edu/CHP/Chen%2C+Wei%2C+PhD University of Pittsburgh Medical Center]

Jun Ding (graduate 2010), now Staff Scientist / Facility Head at the [http://www.grc.nia.nih.gov/branches/lg/lg.htm Laboratory of Genetics, National Institute on Aging (NIH)].

Yun Li (graduated 2009), now Assistant Professor at the [http://www.sph.unc.edu/?option=com_profiles&Itemid=6138&profileAction=ProfDetail&pid=708777879 Department of Biostatistics, University of North Carolina].

Mingyao Li (graduated 2005), now Assistant Professor at the [http://www.cceb.upenn.edu/faculty/index.php?id=159 Department of Biostatistics and Epidemiology, University of Pennsylvania]

Liming Liang (graduated 2009), now Assistant Professor at the [http://www.hsph.harvard.edu/faculty/liming-liang/ Departments of Biostatistics and Epidemiology, Harvard University]

Tasha Fingerlin (graduated 2003), now Associate Professor at the [http://pmb.uchsc.edu/faculty/Fingerlin/index.html Section of Epidemiology and Community Health, University of Colorado Health Sciences Center]

Andrew Skol (graduated 2006), now Assistant Professor at the [http://med-www02.bsd.uchicago.edu/FacultyProfile/faculty_profile.aspx?empl_id=10164 Section of Genetic Medicine, University of Chicago]

Jin Zhen (graduated 2009), now working in the Pharmaceutical Industry.

=== Former Masters Students ===

Vesela Gateva

Xijing Han

Elizabeth Jewell

Yanming Li

Heather Munro

Theresa Scott (nee Daigneault)

Matthew Snyder

Yuan Wei

Abigail Woodroffe

Zaojun Ye

Matthew Zawitowski

Anita Yu Zhao

=== Visitors ===

Toshiko Tanakato

== Really Useful Stuff ==

* [[Abecasis Group Awards]]
* [https://calendars.office.microsoft.com/pubcalstorage/m3n2kr0z1470909/Goncalo_Abecasis_Calendar(1).ics Goncalo's Calendar]

Main Page

2011-02-15T19:48:54Z

SCaron: /* Welcome! */

{| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" |
| style="width:100%; text-align:center; white-space:nowrap; color:#000;" |
<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div>
|}

[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]

== Welcome! ==

Welcome to our brand new wiki!

If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|request an account]]. We recommend using your e-mail address or Michigan uniqname as your user id.

For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].

== Sequence Analysis Tools ==

We are developing [[Software|software tools]] for the analysis of next generation sequence data.

# Variant Calling with [[glfSingle]], [[glfTrio]] and [[glfMultiples]]
# Variant Annotations using [[vcfCodingSnps]]
# Rare Variant Analysis using [[rvTests]]
# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
# File Readers using [[C++ Library: libbam|BamFile]] and [[C++ Library: libfqf|FastQFile]]
# File Conversions using [[bam2FastQ]]

== High Level Tutorials ==

Some high-level tutorials on the analysis of next generation sequence data:

# [[Evaluating a Read Mapper on Simulated Data]]
# [[SNP Call Set Properties]]
# [[Generic Exome Analysis Plan]]

== Projects ==

[[SardiNIA]] - The SardiNIA longitudinal study of aging.

[[1000 Genomes Project Pilot 1 SNP Calling]]

== Learn Genetics ==

Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.

==Abecasis Group Meeting==

3:00-4:30 p.m. on Mondays, room 2610, SPH I.

Main Page

2011-02-15T19:48:40Z

SCaron: /* Welcome! */

{| style="width:100%; background:#fcfcfc; margin-top:1.2em; border:1px solid #ccc;" |
| style="width:100%; text-align:center; white-space:nowrap; color:#000;" |
<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">Abecasis Group Wiki</div>
|}

[[Image:2009.08_Group_Retreat_Photo.jpg|400px|center|Group Photo]]

== Welcome! ==

Welcome to our brand new wiki!

If you would like to contribute, [[Special:UserLogin|log-in]] or [[Special:RequestAccount|create an account]]. We recommend using your e-mail address or Michigan uniqname as your user id.

For basic instructions, see [http://en.wikipedia.org/wiki/Wikipedia:Tutorial the Wikipedia Tutorial].

== Sequence Analysis Tools ==

We are developing [[Software|software tools]] for the analysis of next generation sequence data.

# Variant Calling with [[glfSingle]], [[glfTrio]] and [[glfMultiples]]
# Variant Annotations using [[vcfCodingSnps]]
# Rare Variant Analysis using [[rvTests]]
# Quality control using [[C++ Executable: fastQValidator|FastQValidator]], [[VerifyBamID]], and [[BamValidator]]
# File Readers using [[C++ Library: libbam|BamFile]] and [[C++ Library: libfqf|FastQFile]]
# File Conversions using [[bam2FastQ]]

== High Level Tutorials ==

Some high-level tutorials on the analysis of next generation sequence data:

# [[Evaluating a Read Mapper on Simulated Data]]
# [[SNP Call Set Properties]]
# [[Generic Exome Analysis Plan]]

== Projects ==

[[SardiNIA]] - The SardiNIA longitudinal study of aging.

[[1000 Genomes Project Pilot 1 SNP Calling]]

== Learn Genetics ==

Faculty in the group teach in a variety of formal and informal settings. [[Class Notes|Class notes]] and relevant discussion are archived here.

==Abecasis Group Meeting==

3:00-4:30 p.m. on Mondays, room 2610, SPH I.

User:SCaron

2011-02-15T19:47:46Z

SCaron:

I am a UNIX Systems Administrator at the Center for Statistical Genetics at the University of Michigan School of Public Health.