BioMicroCenter:News

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{{BioMicroCenter}}
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== Welcome to the MIT BIOMICRO CENTER ==
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== BioMicro Center News ==
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=== Aug 9, 2010 ===
 
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Dear Users,<br>
 
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There have been a number of significant changes in the BioMicro Center in the past few months and there will be more to come.  To keep you up to date, I will again be sending out a newsletter every month or two with highlights of what is going on. Unlike previous newsletters, these will only be sent to those who have used the facility within the past year or so, so be sure to spread the word if you see items that might be of interest to others in your lab!
 
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====New equipment====
 
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A number of pieces of new equipment have been added to the BioMicro Center, particularly in the area of high throughput screening. First, through an equipment grant sponsored by Wendy Gilbert, we have added a second robotic fluidics machine that is specifically geared for screening 96 and 384 well plates.  Unlike the older robot, this [[BioMicroCenter:Tecan_Freedom_Evo|Tecan]] has a plate manipulating arm that allows it to handle much larger experiments. We also have added the [[BioMicroCenter:RTPCR|Fluidigm Biomark]] which has been relocated from E17 and we are also in the evaluation phase for the [[BioMicroCenter:Nanostring|Nanostring nCounter]]. Both of these machines allow you to look at a large number of genes / SNPs across a large number of samples. The [[BioMicroCenter:RTPCR|Biomark]] is a nanofluidic RT-PCR machine that creates large matrices (either 48x48 or 96x96) of samples and primers, allowing you to do close to 10,000 RT-PCR reactions on a plate. The [[BioMicroCenter:Nanostring|nCounter]] uses a [[BioMicroCenter:Nanostring|“code set”]] of up to 800 genes to hybridize to dozens or hundreds of samples, then visualizes the single molecule interactions. The [[BioMicroCenter:Nanostring|nCounter]] is particularly interesting in that it does not require conversion of the sample to cDNA, or even purification of the RNA. Information about all of these instruments can be found on our website.
 
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====New services====
 
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We are happy to announce the beginning of sample preparation services for Illumina sequencing. We are introducing this service starting with double stranded DNA fragments (>100bp) such as de novo genomic sequencing, resequencing, ChIP-seq and RNA-seq that has been converted to cDNA. The service includes QC, end-repair, adaptor ligation, size selection and enrichment. Once samples are prepared, they are validated and added directly to the Illumina sequencing queue. Right now, this service is limited, but we are hoping to introduce multiplexing and RNA samples in the near future.
 
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====Upcoming Events====
 
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With so many changes both in new equipment and upgrades to current equipment we wanted to create an opportunity for you to learn more about the assays available in the facility. To help with this, we will be sponsoring a “Technology Seminar Series” this fall. The weekly seminars will be at noon on Mondays (lunch will be provided). Each week we will showcase a different technology in the facility and bring you up to date on the latest advances and future directions of the technology. We have asked the companies we have invited to bring their scientists to speak (not the sales team) so you have a chance to interact with them directly.
 
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I hope you are having a great summer!<br>
 
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-Stuart
 
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=== May 13, 2010 ===
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=== JANUARY 9, 2013 ===
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In order to increase the space available for equipment in the BioMicro Center, we are doing a little more remodeling. Please note the following changes:
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Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of. <BR><BR>
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* The freezers have been relocated to the 304 hallway
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First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.  <BR><BR>
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* The RT-PCR machines will be moving to the 316 entry.
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During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.  <BR><BR>
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We hope this change will make accessing the [[BioMicroCenter:RTPCR|RT-PCR]] machines easier and will also create room for the [[BioMicroCenter:Tecan_Freedom_Evo|new Tecan EVO 150]], scheduled to arrive in early June. Keep an eye on this page for future updates!
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Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting  how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week.
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If you have any concerns, please do not hesitate to contact me.
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=== April 19, 2010 ===
 
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Starting next month, the [http://mit.edu/ki/index.html Koch Institute] and the MIT BioMicro Center will be hosting a [http://www.nanostring.com/ Nanostring] nCounter system on a trial basis. The [http://www.nanostring.com/products/ncounter/ nCounter system] is a [http://www.nanostring.com/applications/technology/ single molecule visualizer] that quantitatively detects RNA and other nucleic acids using a hybridization system in a highly multiplex manner. The system uses color-coded molecular barcodes to digitally count nucleic acid molecules in solution. The system does not use enzymes for detecting the nucleic acids, allowing direct measurements of mRNA from a variety of input materials including degraded RNA or crude cell lysates.
 
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The instruments will be located in the BioMicro Center and will be available to all members of the MIT community. We will be using this time to gauge the level of interest in the nCounter and whether it would be a viable system to purchase.
 
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If you are interested in learning more, we will be hosting a seminar with [http://www.nanostring.com/ Nanostring] representatives on April 30th. The seminar will be at 11am in 68-181. Nanostring representatives will be available after the talk to discuss the instruments and specific applications. More information is in the [[Media:Nanostring_abstract.pdf‎|ABSTRACT]] for the talk.
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=== April 1, 2010 ===
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== ABOUT THE BIOMICRO CENTER ==
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Thanks to the generosity of a grant from the [http://www.moore.org/ Moore Foundation] to Dr. Penny Chisholm and ARRA funding to Dr. Chris Burge the BioMicro Center will be significantly expanding our sequencing capacity over the next 4-6 months. The first step of this expansion begins today with the addition of a new [http://www.illumina.com/systems/genome_analyzer_iix.ilmn GAIIx] and [http://www.illumina.com/systems/genome_analyzer/cbot.ilmn cBot] from Illumina. We are working hard to get ''"Ryland"'' and ''"Agustus Gloop"'' up and running and we hope to be able to shorten our queue times very soon!
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The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [Department of Biology], the [Koch Institute], the [Department of Biological Engineering] and the [Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina Genome Analyzer (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms continues to be a significant portion of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Instistute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core<BR><BR>
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=== March 2010 ===
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== PUBLICATIONS ==
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Due to an increase in the cost of Illumina reagents, increase in data file size, and the complexity of sample preps, we have had to increase, slightly, the cost of Illumina sequencing. These new rates will be effective on samples submitted after April 1, 2010. Samples already in the queue will use the current rates.
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'''2013'''<BR><BR>
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'''2012'''<BR><BR>
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<biblio>
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#Paper1 pmid=22981692 <!-SL Boyer: Heart->
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#Paper2 pmid=22847430 <!-SL Saeij->
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#Paper3 pmid=22102570 <!-HD Chisholm->
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</biblio>
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'''2011'''<BR><BR>
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<biblio>
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#Paper1 pmid=21892155 <!-SL Sur->
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</biblio>
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'''2010'''<BR><BR>
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<biblio>
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#Paper1 pmid=20720539 <!-SL Young->
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#Paper2 pmid=20581084 <!-SL Zwaka->
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</biblio>
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'''2009'''<BR><BR>
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<biblio>
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#Paper1 pmid=19531355 <!-SL Amon->
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</biblio>
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{| border=1 align="right"
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== PREVIOUS NEWSLETTERS ==
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! ILLUMINA SEQUENCING
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!width=100| MIT - current
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!width=100| MIT - April 1, 2010
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!width=100| unit
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! Notes
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| Single End (36nt)
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|align="right"| $805
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|align="right"| $860
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|align="center"| per lane
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| inlcudes quality control (RT-PCR or BioAnalyzer), sequencing, genome alignment and data storage of Firecrest files for 2 yrs.
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| Paired End (36+36nt)
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|align="right"| $1,385
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|align="right"| $1,450
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|align="center"| per lane
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| Add'l 36nt
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|align="right"| $295
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|align="right"| $300
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|align="center"| per lane
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| Sample Multiplexing
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|align="right"| $0
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|align="right"| $50
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|align="center"| per 10 samples combined
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| Combined over the whole order. Only applies to samples combined by BCM technicians.
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| Repriming
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|align="right"| $200
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|align="right"| $300
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|align="center"| per flow cell
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| Uses 6nt. Cost is divided by number of lanes requiring repriming. Repriming is required for standard Illumina multiplexing.
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Non-MIT rates are 30% higher for academic institutions and 50% highers for non-academic institutions. Priority is given to samples from CORE facilities.
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'''[[BioMicroCenter:News2012|2012]]'''<BR>
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'''[[BioMicroCenter:News2011|2011]]'''<BR>
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'''[[BioMicroCenter:News2010|2010]]'''
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== RECENT CHANGES TO THE WEBSITE ==
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===RECENT & UPCOMING CHANGES===
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{{BioMicroCenter:News/Changes/Content}}
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<B><BIG>PREVIOUS NEWSLETTERS </BIG></B>
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{|
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|'''[[BioMicroCenter:News/2009|2009]]'''
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|{{BioMicroCenter:News/2009/Content}}
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|-
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|'''[[BioMicroCenter:News/2008|2008]]'''
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|-
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|{{BioMicroCenter:News/2008/Content}}
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|}
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<br>
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<B><BIG>RECENT CHANGES TO THE WEBSITE <\BIG><\B>
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{{BioMicroChanges}}
{{BioMicroChanges}}
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Revision as of 12:54, 30 January 2013

Image:BioMicroCenter-header6.jpg

.

Contents

Welcome to the MIT BIOMICRO CENTER

BioMicro Center News

JANUARY 9, 2013

Happy new years to everyone. A couple new things happening in BioMicro that we want to make everyone aware of.

First, this month begins a year long experiment in joining the BioMicro Center Informatics team and the KI Bioinformatics and Computing Core in to a single team. Our two teams have been collaborating for several years, sharing computational infrastructure, etc. but this year we will be formalizing and expanding the relationship with the goal of creating a more efficient unified core. Informatics analysis requests should still be sent to Charlie Whittaker or to myself as usual, but will be spread across the joint team based on expertise and on availability. You are also, as always, welcome to contact any of the informatics scientists directly. We hope this will allow us to reduce waiting times and to keep costs under control.

During the trial period (and hopefully going forward), pricing for informatics will be available in two flavors. First, for projects needing routine work, the subsidized rate will be $70/h for all CORE members (Biology, BE, KI, CEHS). For more involved projects, we have second option to purchase a “share” of the informatics team. This is an annual commitment for a fraction of an informaticist and will cost $960/mo for an average of 4h/week of informatics support. The monthly usage levels do not have to be exact and can be used in large blocks. The hours in the share can be used with any member of the team and the informaticist can vary from project to project.

Finally, and importantly, we will be changing the way we are storing Illumina sequencing data long term. In the past, we have saved the fastq, sam and bam files, along with the quality control data, in a zipped file. These zipped files now occupy over 50TB of storage which is limiting how we are able to handle new sequencing runs. To address this, we will be deleting the fastq and sam files from the archive and storing only the binary bam and quality control files. The fastq and sam files can be regenerated rapidly from the bam files using Picard and SamTools (though reads may not be in the same order). As always, we strongly encourage you to keep your own copy of the Illumina data and use our version only as a backup. We will begin this conversion next week. If you have any concerns, please do not hesitate to contact me.



ABOUT THE BIOMICRO CENTER

The MIT BioMicro Center was founded in 2000 as the core bio-fabrication and microarray processing facility at MIT. The Center is a joint endeavor between the [Department of Biology], the [Koch Institute], the [Department of Biological Engineering] and the [Center for Environmental Health Sciences.] The BioMicro Center offers a wide range of genomic services to researchers at MIT. The majority of services rendered pertain to massively parallel sequencing using the Illumina Genome Analyzer (both library preparation and sequencing). Commercial array processing and include both the Affymetrix Gene Chip and Agilent DNA array platforms continues to be a significant portion of our portfolio. Real-time PCR and Agilent BioAnalyzer services are available in the facility both as services available to researchers, as well as for quality control of microarray and sequencing samples. In addition, the Center has a presence in high-throughput screening with robotics and plate reading as well as informatics and computational support. The BioMicro Center serves the Koch Instistute as the MicroArray Technologies Core and as part of the Bioinformatics and Computing Core and the MIT Center for Environmental Health Sciences as part of the Genomics and Imaging Core

PUBLICATIONS

2013

2012

  1. Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, and Bruneau BG. . pmid:22981692. PubMed HubMed [Paper1]
  2. Minot S, Melo MB, Li F, Lu D, Niedelman W, Levine SS, and Saeij JP. . pmid:22847430. PubMed HubMed [Paper2]
  3. Kelly L, Huang KH, Ding H, and Chisholm SW. . pmid:22102570. PubMed HubMed [Paper3]
All Medline abstracts: PubMed HubMed

2011

  1. Mellios N, Sugihara H, Castro J, Banerjee A, Le C, Kumar A, Crawford B, Strathmann J, Tropea D, Levine SS, Edbauer D, and Sur M. . pmid:21892155. PubMed HubMed [Paper1]

2010

  1. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, and Young RA. . pmid:20720539. PubMed HubMed [Paper1]
  2. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, and Zwaka TP. . pmid:20581084. PubMed HubMed [Paper2]
All Medline abstracts: PubMed HubMed

2009

  1. Boselli M, Rock J, Unal E, Levine SS, and Amon A. . pmid:19531355. PubMed HubMed [Paper1]

PREVIOUS NEWSLETTERS

2012
2011
2010

RECENT CHANGES TO THE WEBSITE

22 July 2014

+      15:16 BioMicroCenter:Software‎ (3 changes) . . (+744) . . (Page history) [Jingzhi Zhu‎ (3×)]
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