Cbcb:Pop-Lab:Niranjan-Report - Revision history

Niranjan: /* March 2nd, 2009 */

2009-04-06T14:00:48Z

March 2nd, 2009

← Older revision		Revision as of 14:00, 6 April 2009
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	~~==March 2nd, 2009==~~

	~~===Tasks===~~

	~~# Made more updates to my webpage~~
	~~# Started making a presentation for my job talk~~
	~~# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.~~

	~~===Papers Read===~~

	~~# [[Media:rabadan2007.pdf\|Non-random reassortment in human influenza A viruses]]. R. Rabadan, A.J. Levine and M. Krasnitz.~~

	~~The basic idea in this paper is that if you assume constant~~
	~~rate of mutational drift in different segments of the same strain (an~~
	~~assumption that seems to be true on a coarse level for some segments, but~~
	~~not for others), then given two non-reassorted strains, the nucleotide~~
	~~differences between their NA segments should be roughly proportional to~~
	~~that from the HA segments and they use that as a test to identify putative~~
	~~reassortments. They use a vaguely described idea to figure out which~~
	~~combination of segments have reassorted (probably done manually) and they~~
	~~seem to make no attempt to figure out if a set of taxa have reassorted~~
	~~based on a common event. Finally, there is no evaluation of the capability~~
	~~of this method - just a list of results which seem to clearly miss the~~
	~~reassortments we already know of. In fact, in the abstract, they make the~~
	~~claim that they find all the reassortments from earlier works.~~

Niranjan: /* Papers Read */

2009-02-16T15:22:11Z

Papers Read

← Older revision		Revision as of 15:22, 16 February 2009
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	===Papers Read===		===Papers Read===

	# [[Media:rabadan2007.pdf\|Non-random reassortment in human influenza A viruses]]		# [[Media:rabadan2007.pdf\|Non-random reassortment in human influenza A viruses]]. R. Rabadan, A.J. Levine and M. Krasnitz.
	R. Rabadan, A.J. Levine and M. Krasnitz.

	The basic idea in this paper is that if you assume constant		The basic idea in this paper is that if you assume constant
	rate of mutational drift in different segments of the same strain (an		rate of mutational drift in different segments of the same strain (an
	assumption that seems to be true on a coarse level for some segments, but		assumption that seems to be true on a coarse level for some segments, but
	not for others) then given two non-reassorted strains the nucleotide		not for others), then given two non-reassorted strains, the nucleotide
	differences between their NA segments should be roughly proportional to		differences between their NA segments should be roughly proportional to
	that from the HA segments and they use that as a test to identify putative		that from the HA segments and they use that as a test to identify putative
Line 22:		Line 21:
	seem to make no attempt to figure out if a set of taxa have reassorted		seem to make no attempt to figure out if a set of taxa have reassorted
	based on a common event. Finally, there is no evaluation of the capability		based on a common event. Finally, there is no evaluation of the capability
	of this method, just a list of results which seem to clearly miss the		of this method - just a list of results which seem to clearly miss the
	reassortments we already know of! In fact they make the claim that they		reassortments we already know of. In fact, in the abstract, they make the
	find all the reassortments from earlier works~~, in the abstract!~~		claim that they find all the reassortments from earlier works.

Niranjan: /* Papers Read */

2009-02-16T15:19:16Z

Papers Read

← Older revision		Revision as of 15:19, 16 February 2009
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	===Papers Read===		===Papers Read===

	# [Media:rabadan2007.pdf\|Non-random reassortment in human influenza A viruses]		# [[Media:rabadan2007.pdf\|Non-random reassortment in human influenza A viruses]]
	R. Rabadan, A.J. Levine and M. Krasnitz.		R. Rabadan, A.J. Levine and M. Krasnitz.

Niranjan: /* Papers Read */

2009-02-16T15:18:51Z

Papers Read

← Older revision		Revision as of 15:18, 16 February 2009
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	===Papers Read===		===Papers Read===

	# [rabadan2007.pdf\| Non-random reassortment in human influenza A viruses]		# [Media:rabadan2007.pdf\|Non-random reassortment in human influenza A viruses]
	R. Rabadan, A.J. Levine and M. Krasnitz.		R. Rabadan, A.J. Levine and M. Krasnitz.

Niranjan: /* Papers Read */

2009-02-16T15:17:02Z

Papers Read

← Older revision		Revision as of 15:17, 16 February 2009
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	===Papers Read===		===Papers Read===

	# [~~http://www3~~.~~interscience.wiley.com/cgi-bin/fulltext/119423402/PDFSTART~~\|Non-random reassortment in human influenza A viruses]		# [rabadan2007.pdf\| Non-random reassortment in human influenza A viruses]
	R. Rabadan, A.J. Levine and M. Krasnitz.		R. Rabadan, A.J. Levine and M. Krasnitz.

Niranjan at 15:14, 16 February 2009

2009-02-16T15:14:56Z

← Older revision		Revision as of 15:14, 16 February 2009
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	~~Report for~~ March 2nd, 2009		==March 2nd, 2009==

	[[Tasks]]		===Tasks===

	1) Made more updates to my webpage		# Made more updates to my webpage
			# Started making a presentation for my job talk
			# Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

	~~2) Started making a presentation for my job talk~~		===Papers Read===

	~~3) Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome~~.		# [http://www3.interscience.wiley.com/cgi-bin/fulltext/119423402/PDFSTART\|Non-random reassortment in human influenza A viruses]

	~~[[Papers Read]]~~

	1. [Non-random reassortment in human influenza A viruses]
	R. Rabadan, A.J. Levine and M. Krasnitz.		R. Rabadan, A.J. Levine and M. Krasnitz.

Niranjan at 15:08, 16 February 2009

2009-02-16T15:08:36Z

← Older revision		Revision as of 15:08, 16 February 2009
Line 4:		Line 4:

	1) Made more updates to my webpage		1) Made more updates to my webpage

	2) Started making a presentation for my job talk		2) Started making a presentation for my job talk
	3) Assisted Carl in writing a grant proposal to extend on our
	work on reassortments in the Flu genome.		3) Assisted Carl in writing a grant proposal to extend on our work on reassortments in the Flu genome.

	[[Papers Read]]		[[Papers Read]]

Niranjan at 15:07, 16 February 2009

2009-02-16T15:07:43Z

← Older revision		Revision as of 15:07, 16 February 2009
Line 1:		Line 1:
	Report for March 2nd, 2009		Report for March 2nd, 2009

			[[Tasks]]

			1) Made more updates to my webpage
			2) Started making a presentation for my job talk
			3) Assisted Carl in writing a grant proposal to extend on our
			work on reassortments in the Flu genome.

			[[Papers Read]]

			1. [Non-random reassortment in human influenza A viruses]
			R. Rabadan, A.J. Levine and M. Krasnitz.

			The basic idea in this paper is that if you assume constant
			rate of mutational drift in different segments of the same strain (an
			assumption that seems to be true on a coarse level for some segments, but
			not for others) then given two non-reassorted strains the nucleotide
			differences between their NA segments should be roughly proportional to
			that from the HA segments and they use that as a test to identify putative
			reassortments. They use a vaguely described idea to figure out which
			combination of segments have reassorted (probably done manually) and they
			seem to make no attempt to figure out if a set of taxa have reassorted
			based on a common event. Finally, there is no evaluation of the capability
			of this method, just a list of results which seem to clearly miss the
			reassortments we already know of! In fact they make the claim that they
			find all the reassortments from earlier works, in the abstract!

Niranjan at 20:24, 11 February 2009

2009-02-11T20:24:22Z

New page

Report for March 2nd, 2009