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Short Methionine Synthases [article]

Morgan N Price, Adam P. Arkin
2020 bioRxiv   pre-print
These methionine synthases are homologous to MetE, which uses 5-methyltetrahydrofolate, but they lack the N-terminal folate-binding domain of MetE.  ...  . 2018a; Price et al. 2020) , MetE, MesA, MesB, or MesD) .  ...  PYRFU_RS09465 contains the N-terminal domain (Meth_synt_1 in Pfam) and PYRFU_RS01495 contains the C-terminal domain (Meth_synt_2 in Pfam).  ... 
doi:10.1101/2020.04.21.054031 fatcat:rinllk233rgidbtua2reey6wwq

PaperBLAST: Text Mining Papers for Information about Homologs

Morgan N. Price, Adam P. Arkin, Morgan G. I. Langille
2017 mSystems  
Price and Arkin July/August 2017 Volume 2 Issue 4 e00039-17 msystems.asm.org 4 on April 28, 2019 by guest http://msystems.asm.org/ Downloaded from Price and Arkin July/August 2017 Volume 2 Issue 4  ...  b Price and Arkin July/August 2017 Volume 2 Issue 4 e00039-17 msystems.asm.org 8 on April 28, 2019 by guest http://msystems.asm.org/ (which is unique to CharProtDB) contained 7,636 sequences.  ... 
doi:10.1128/msystems.00039-17 pmid:28845458 pmcid:PMC5557654 fatcat:xpcwjz2qsnfarg5emlgnnwoyte

Interactive analysis of functional residues in protein families [article]

Morgan N Price, Adam P. Arkin
2022 bioRxiv   pre-print
Interactive analysis of functional residues in protein families Morgan N. Price and Adam P.  ...  Price, M. N., and A. P. Arkin. 2019. Curated BLAST for genomes. mSystems 4. doi:10.1128/mSystems.00072-19. Price, M. N., P. S. Dehal, and A. P. Arkin. 2010.  ... 
doi:10.1101/2022.06.30.498337 fatcat:rfcei3waqzhd7gam4vgmzbrwme

PaperBLAST: Text-mining papers for information about homologs [article]

Morgan N Price, Adam P. Arkin
2017 bioRxiv   pre-print
Examples While we were studying the utilization of various carbon sources by Pseudomonas fluorescens FW300-N2E3, we discovered that the AO353_07705 protein is required for the utilization of L-carnitine (Price  ...  example, Fitness BLAST (http://fit.genomics.lbl.gov/images/fitblast_example.html) identifies homologs that have mutant phenotypes in a collection of ~4,000 genome-wide mutant assays from diverse bacteria (Price  ... 
doi:10.1101/133041 fatcat:rti5csbjjbhtpmzxf37fgdrqsu

Curated BLAST for Genomes

Morgan N. Price, Adam P. Arkin, Casey S. Greene
2019 mSystems  
The two reading frames cover the N-and C-terminal portions of the protein (this can be seen by hovering on "62% id." or "59% id.").  ... 
doi:10.1128/msystems.00072-19 pmid:30944879 pmcid:PMC6435814 fatcat:ruuie43itrdnnjkfjkowt2yd3u

GapMind: Automated annotation of amino acid biosynthesis [article]

Morgan N Price, Adam M Deutschbauer, Adam P. Arkin
2019 biorxiv/medrxiv   pre-print
to encode N-succinylcitrulline carbamoyltransferase (28) .  ...  The specificity of the enzyme for N-succinylcitrulline or N-acetylcitrulline can be switched by mutating a single amino acid corresponding to position 90 of BT3717 (28) .  ... 
doi:10.1101/741918 fatcat:sbfi7immz5arpiq7urnoplbtlq

Collaborating over portable reading appliances

Catherine C. Marshall, Morgan N. Price, Gene Golovchinsky, Bill N. Schilit
1999 Personal Technologies  
Reading appliances or e-books are a new kind of personal technology that hold substantial promise as interpersonal technology, devices that help us collaborate. In this paper, we use a study of a group activity -a reading group that meets to discuss articles of mutual interest -to explore four scenarios for collaborating with e-books: (1) meeting room and face-to-face discussions; (2) serendipitous sharing of annotations, as when we borrow a document from a colleague or buy a used book; (3)
more » ... unity-wide use of anonymous annotations to guide future readers; and (4) e-books as a basis for initiating interaction between people. In so doing, we describe some methods for implementing these facilities, and introduce design guidelines.
doi:10.1007/bf01305319 fatcat:shcsuts3cvd53n67sgdpordrum

Digital library information appliances

Bill N. Schilit, Morgan N. Price, Gene Golovchinsky
1998 Proceedings of the third ACM conference on Digital libraries - DL '98  
Although digital libraries are intended to support education and knowledge work, current digital library interfaces are narrowly focused on retrieval. Furthermore, they are designed for desktop computers with keyboards, mice, and high-speed network connections. Desktop computers fail to support many key aspects of knowledge work, including active reading, free form ink annotation, fluid movement among document activities, and physical mobility. This paper proposes portable computers specialized
more » ... for knowledge work, or digital library information appliances, as a new platform for accessing digital libraries. We present a number of ways that knowledge work can be augmented and transformed by the use of such appliances. These insights are based on our implementation of two research prototype systems: XLibris, an "active reading machine," and Tele-Web, a mobile World Wide Web browser.
doi:10.1145/276675.276700 dblp:conf/dl/SchilitPG98 fatcat:os4pu3ybqbewrajgjdkix6vnn4

XLibris

Morgan N. Price, Bill N. Schilit, Gene Golovchinsky
1998 CHI 98 conference summary on Human factors in computing systems - CHI '98  
Active reading [1] is the combination of reading with critical thinking and learning, and involves not just reading per se, but also underlining, highlighting and commenting. We have built the XLibris "Active Reading Machine" to explore the premise that computation can enhance the active reading process. XLibris uses a high-resolution pen tablet display along with a paper-like user interface to emulate the physical experience of reading a document on paper: the reader can hold a scanned image
more » ... a page in his lap and mark on it with digital ink. XLibris monitors freeform ink annotations made while reading, and uses these to organize and to search for information. Readers can review, sort and filter clippings of their annotated text in a "Reader's Notebook." Finally, XLibris searches for material related to the annotated text, and displays links unobtrusively in the margin. XLibris demonstrates that computers can help active readers organize and find information while retaining many of the advantages of reading on paper.
doi:10.1145/286498.286510 dblp:conf/chi/PriceSG98 fatcat:bkuftfbc4zb3lkeq35t3vsqia4

The Life-Cycle of Operons

Morgan N. Price, Adam P. Arkin, Eric J. Alm
2006 PLoS Genetics  
Citation: Price MN, Arkin AP, Alm EJ (2006) The life-cycle of operons. PLoS Genet 2(6): e96.  ...  Á q Á X 4 i¼0 p 2 i ; ð1Þ and the number of adjacent new operon pairs would be N Á q Á ð X 4 i¼0 p i Þ 2 : ð2Þ Modifications to pre-existing operons.  ...  under completely random evolution, we used the fraction p i of operon pairs that have age i, the fraction q of operon pairs that are adjacent to the next (downstream) operon pair, and the total number N  ... 
doi:10.1371/journal.pgen.0020096 pmid:16789824 pmcid:PMC1480536 fatcat:gq44bswiwbgvxjzvtb2ms3c7gq

GapMind for Carbon Sources: Automated annotations of catabolic pathways [article]

Morgan N Price, Adam M Deutschbauer, Adam P. Arkin
2021 bioRxiv   pre-print
N. R. Srinivas, S. Madhu, R. Manorama, and S. Shivaji. 2010. Indibacter alkaliphilus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake.  ...  NagX is also distantly related to a putative N-acetylmuramate transporter (TfMurT) from Tannerella forsythia (Ruscitto et al. 2016 ).  ...  In four of the five bacteria, we found that N-acetylglucosamine 6-phosphate deacetylase NagA was also involved in glucosamine utilization .  ... 
doi:10.1101/2021.11.02.466981 fatcat:ghtdlbyhozcqjhwmitgwtwqac4

Printertainment

Jason Hong, Morgan N. Price, Bill N. Schilit, Gene Golovchinsky
1999 CHI '99 extended abstracts on Human factors in computing systems - CHI '99  
We explored a new type of user interface, interactive cover sheets: computer forms laid out on the banner pages of print jobs that people can mark on, scan back into a multifunction printer/scanner, and use as input to applications. Cover sheets are commonly strewn around printer rooms; with interactivity, they can let people see what others have to say, add their own comments, or play games, all while waiting for their print jobs. We designed three prototype applications and deployed them
more » ... ly in our research lab. We found that interactive cover sheets can be very appealing, that the sheets must be designed so that people can still identify these pages as cover sheets, and that the slow interaction cycle favors asynchronous applications.
doi:10.1145/632716.632865 dblp:conf/chi/HongPSG99 fatcat:yplgazq26zbnnajszywbbgbbay

Beyond paper

Bill N. Schilit, Gene Golovchinsky, Morgan N. Price
1998 Proceedings of the SIGCHI conference on Human factors in computing systems - CHI '98  
Reading frequently involves not just looking at words on a page, but also underlining, highlighting and commenting, either on the text or in a separate notebook. This combination of reading with critical thinking and learning is called active reading [2] . To explore the premise that computation can enhance active reading we have built the XLibris "active reading machine." XLibris uses a commercial high-resolution pen tablet display along with a paper-like user interface to support the key
more » ... dances of paper for active reading: the reader can hold a scanned image of a page in his lap and mark on it with digital ink. To go beyond paper, XLibris monitors the free-form ink annotations made while reading, and uses these to organize and to search for information. Readers can review, sort and filter clippings of their annotated text in a "Reader's Notebook." XLibris also searches for material related to the annotated text, and displays links to similar documents unobtrusively in the margin. XLibris demonstrates that computers can help active readers organize and find information while retaining many of the advantages of reading on paper.
doi:10.1145/274644.274680 dblp:conf/chi/SchilitGP98 fatcat:fgvrwpkm2jhqbfu5izg5gfcjkm

Digital libraries and mobility

Catherine C. Marshall, Gene Golovchinsky, Morgan N. Price
2001 Communications of the ACM  
Digital libraries offer the promise of anywhere, anytime access to vast online holdings. But what does this promise really mean? If we draw on studies of digital libraries in use, coupled with our development experience with the XLibris analytic reading software [9] on mobile pen-tablet hardware (shown in the accompanying figure), four potential advantages of mobile access to digital resources come to light. Digital library patrons can:
doi:10.1145/374308.374340 fatcat:jo72clypsbdzjhi4sdjy2rzeuy

Printertainment

Jason Hong, Morgan N. Price, Bill N. Schilit, Gene Golovchinsky
1999 CHI '99 extended abstracts on Human factors in computer systems - CHI '99  
We explored a new type of user interface, interactive cover sheets: computer forms laid out on the banner pages of print jobs that people can mark on, scan back into a multifunction printer/scanner, and use as input to applications. Cover sheets are commonly strewn around printer rooms; with interactivity, they can let people see what others have to say, add their own comments, or play games, all while waiting for their print jobs. We designed three prototype applications and deployed them
more » ... ly in our research lab. We found that interactive cover sheets can be very appealing, that the sheets must be designed so that people can still identify these pages as cover sheets, and that the slow interaction cycle favors asynchronous applications.
doi:10.1145/632863.632865 fatcat:pdo5zajhbfebvhlqpmytuz56ni
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