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### A Non-interactive Shuffle with Pairing Based Verifiability [chapter]

Jens Groth, Steve Lu
<i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g5tkfdmtlfgwfbpeepvyshdocu" style="color: black;">Advances in Cryptology – ASIACRYPT 2007</a> </i> &nbsp;
We give the first efficient non-interactive zero-knowledge proof for correctness of a shuffle.  ...  One way to make a shuffle verifiable is to give a zero-knowledge proof of correctness. All currently known practical zero-knowledge proofs for correctness of a shuffle rely on interaction.  ...  If a dishonest prover were to convince a verifier with a non-shuffle as well as produce a witness (decryption key) w co = (x, y), we can "decrypt" the equations checked by the verifier.  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-76900-2_4">doi:10.1007/978-3-540-76900-2_4</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/asiacrypt/GrothL07.html">dblp:conf/asiacrypt/GrothL07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/psnzsbojrvai5ofi2cq5dhpvxe">fatcat:psnzsbojrvai5ofi2cq5dhpvxe</a> </span>
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### A More Efficient Computationally Sound Non-Interactive Zero-Knowledge Shuffle Argument [chapter]

Helger Lipmaa, Bingsheng Zhang
<span title="">2012</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
We propose a new non-interactive (perfect) zero-knowledge (NIZK) shuffle argument that, when compared the only previously known efficient NIZK shuffle argument by Groth and Lu, has a small constant factor  ...  times smaller computation and communication, and is based on more standard computational assumptions.  ...  However, it is also important that the shuffle argument is non-interactive, due to the fact that non-interactive arguments are transferable (create once, verify many times without interacting with the  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-32928-9_27">doi:10.1007/978-3-642-32928-9_27</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n7jhiisz3zdkpkvh5kls3eedr4">fatcat:n7jhiisz3zdkpkvh5kls3eedr4</a> </span>
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### A more efficient computationally sound non-interactive zero-knowledge shuffle argument

Helger Lipmaa, Bingsheng Zhang, Ivan Visconti
<span title="2013-11-22">2013</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/spxf4rshtfhgvoxv3apocfge6m" style="color: black;">Journal of Computer Security</a> </i> &nbsp;
We propose a new non-interactive (perfect) zero-knowledge (NIZK) shuffle argument that, when compared the only previously known efficient NIZK shuffle argument by Groth and Lu, has a small constant factor  ...  times smaller computation and communication, and is based on more standard computational assumptions.  ...  However, it is also important that the shuffle argument is non-interactive, due to the fact that non-interactive arguments are transferable (create once, verify many times without interacting with the  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/jcs-130478">doi:10.3233/jcs-130478</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dachfvqsanf7jj63qhlhrhavzq">fatcat:dachfvqsanf7jj63qhlhrhavzq</a> </span>
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### Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

<span title="2014-02-19">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized.  ...  We find that the relationship between formal concepts provide a natural way for rare domains to elevate the rank of promiscuous domains, and enrich highly ranked domain-pairs with reliable DDIs.  ...  GDDIs are domain-pairs whose physical interaction has been verified experimentally. The GDDIs were obtained from [6] .  ...
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### Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay

Peng Jiang, Mona Singh, Hilary A. Coller, Mihaela Zavolan
<span title="2013-05-30">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The presence of both a PUM recognition site and a recognition site for preferentially co-occurring miRNAs was associated with faster decay of the associated transcripts.  ...  In sum, our computational analyses suggest that a specific set of RBPs and miRNAs work together to affect transcript decay, with the rescue of miRNA recognition sites via RBP binding as one possible mechanism  ...  (B, C) For each miRNA seed, a score was determined based on the extent of complementary base pairing with the reverse RBP recognition motifs [68] .  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1003075">doi:10.1371/journal.pcbi.1003075</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23737738">pmid:23737738</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3667768/">pmcid:PMC3667768</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/b6xgrqindnd6pd6trz7pjrje3q">fatcat:b6xgrqindnd6pd6trz7pjrje3q</a> </span>
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Melissa Chase, Markulf Kohlweiss, Anna Lysyanskaya, Sarah Meiklejohn
<span title="">2013</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
The notion of a verifiable shuffle describes how to satisfy both properties at the same time: ballots are submitted to a public bulletin board in encrypted form, verifiably shuffled by several mix servers  ...  Previous verifiable shuffle constructions had proofs of size O(kLM + kLN ), which, for elections with thousands of voters, mix servers, and decryption servers, meant that verifying an election on an ordinary  ...  Anna Lysyanskaya was supported by NSF grants 1012060, 0964379, 0831293, and by a Sloan Foundation fellowship, and Sarah Meiklejohn was supported by a MURI grant administered by the Air Force Office of  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-36362-7_29">doi:10.1007/978-3-642-36362-7_29</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hwdhegiih5al5aoczxrfzcxwhe">fatcat:hwdhegiih5al5aoczxrfzcxwhe</a> </span>
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### Shuffle-Seq: En masse combinatorial encoding for n-way genetic interaction screens [article]

Atray Dixit, Olena Kuksenko, David Feldman, Aviv Regev
<span title="2019-12-02">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Here, we develop Shuffle-Seq, a scalable method to assay genetic interactions.  ...  AbstractGenetic interactions, defined as the non-additive phenotypic impact of combinations of genes, are a hallmark of the mapping from genotype to phenotype.  ...  Pair-wise correlations in well occurrence profiles are calculated for each pair of sgRNA-UTBs, to identify significantly co-occurring barcode pairs (based on a permutation test associated with a randomly  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/861443">doi:10.1101/861443</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ywhumngy6rgwvjealplvp64crq">fatcat:ywhumngy6rgwvjealplvp64crq</a> </span>
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### Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds

Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I Shaw, Ying-Wai Li, Russell L Malmberg, Liming Cai
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: This paper shows that the measuring performance of base pairing entropy can be significantly improved with a constrained secondary structure ensemble in which only canonical base pairs are assumed  ...  Shannon base pairing entropy is an indicator for RNA secondary structure fold certainty in detection of structural, non-coding RNAs (ncRNAs).  ...  Illustration of the application of the generic production rule S aRbT that produces a base pair between positions i and j for the query sequence x, provided that the start non-terminal S 0 derives x 1  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-s5-s1">doi:10.1186/1471-2105-13-s5-s1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22537005">pmid:22537005</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3358654/">pmcid:PMC3358654</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mwcx3uyqxjh2feg3hyq7zu5yym">fatcat:mwcx3uyqxjh2feg3hyq7zu5yym</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830092723/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S5-S1?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d5/44/d5446038112f395e08bc20dabaf5ade2c5b6ac46.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-s5-s1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358654" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

### Stable stem enabled shannon entropies distinguish non-coding RNAs from random backgrounds

Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying-Wai Li, Russell L. Malmberg, Liming Cai
<span title="">2011</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rxuqxdg3hrb6zegvozp3e5t2v4" style="color: black;">2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)</a> </i> &nbsp;
Results: This paper shows that the measuring performance of base pairing entropy can be significantly improved with a constrained secondary structure ensemble in which only canonical base pairs are assumed  ...  Shannon base pairing entropy is an indicator for RNA secondary structure fold certainty in detection of structural, non-coding RNAs (ncRNAs).  ...  Illustration of the application of the generic production rule S aRbT that produces a base pair between positions i and j for the query sequence x, provided that the start non-terminal S 0 derives x 1  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/iccabs.2011.5729876">doi:10.1109/iccabs.2011.5729876</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/iccabs/WangMSSLMC11.html">dblp:conf/iccabs/WangMSSLMC11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2iovmk6qaffenfcbrniunba62a">fatcat:2iovmk6qaffenfcbrniunba62a</a> </span>
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### Malleable Proof Systems and Applications [chapter]

Melissa Chase, Markulf Kohlweiss, Anna Lysyanskaya, Sarah Meiklejohn
<span title="">2012</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
As our motivating application, we consider a shorter proof for verifiable shuffles.  ...  In this work, we examine notions of malleability for non-interactive zero-knowledge (NIZK) proofs.  ...  Acknowledgments Anna Lysyanskaya was supported by NSF grants 1012060, 0964379, 0831293, and by a Sloan Foundation fellowship, and Sarah Meiklejohn was supported in part by a MURI grant administered by  ...
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### Identifying microRNA targets in different gene regions

Wenlong Xu, Anthony San Lucas, Zixing Wang, Yin Liu
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Our model is based on both canonical seed matching and non-canonical seed pairing, which discovers targets that allow one bit GU wobble.  ...  method is developed that is solely based on canonical and non-canonical seed matches without requiring evolutionary conservation of the target sites.  ...  pair interaction.  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-s7-s4">doi:10.1186/1471-2105-15-s7-s4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25077573">pmid:25077573</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4110731/">pmcid:PMC4110731</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qsjd2dswkvg7nlfycp7sqewdru">fatcat:qsjd2dswkvg7nlfycp7sqewdru</a> </span>
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### D–Shuffle for Prêt à Voter [chapter]

<span title="">2014</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
This paper proposes a new verifiable shuffle "D-Shuffle" that is efficient. We provide a security proof for the D-Shuffle.  ...  Prêtà Voter is an end-to-end verifiable voting scheme, that uses paper based ballot forms that are turned into encrypted receipts.  ...  On the Efficiency of D-Shuffle The main advantage of the D-Shuffle is the fact that it is non-interactive.  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-662-44885-4_9">doi:10.1007/978-3-662-44885-4_9</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uw2j5bo5ejbipjuaa5u5c4pq3m">fatcat:uw2j5bo5ejbipjuaa5u5c4pq3m</a> </span>
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### PREDICTION OF DOWNSTREAM INTERACTION OF TRANSCRIPTION FACTORS WITH MAPK3 IN ARABIDOPSIS THALIANA USING PROTEIN SEQUENCE INFORMATION English

GOHAR TAJ, SUGANDHA SHARMA, VIKRAM S GAUR, ANIL KUMAR
<span title="2011-06-30">2011</span> <i title="Bioinfo Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2e6hogst2becdh3ezbyhjgrsuq" style="color: black;">International Journal of Bioinformatics Research</a> </i> &nbsp;
The approach here used is supervised learning based on physiochemical properties of protein sequences through which we predict whether the MAPK3 proteins interact with downstream transcription factor proteins  ...  The results of our study clearly revealed the complexity of MAPK3 interaction with several variants of different transcription factors and the same can be verified by different methodology of wet lab experimentation  ...  Based on examples of interacting pairs and non interacting pairs, we train a binary classifier to predict the class (interacting or non-interacting) of a set of protein sequences.  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.9735/0975-3087.3.1.167-177">doi:10.9735/0975-3087.3.1.167-177</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kb7273orpbgmzldweobplehys4">fatcat:kb7273orpbgmzldweobplehys4</a> </span>
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### Succinct Malleable NIZKs and an Application to Compact Shuffles [chapter]

Melissa Chase, Markulf Kohlweiss, Anna Lysyanskaya, Sarah Meiklejohn
<span title="">2013</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In this paper, we address these issues by providing a generic construction of controlled-malleable proofs using succinct non-interactive arguments of knowledge, or SNARGs for short.  ...  As an application, they construct the first compact verifiable shuffle, in which one such controlled-malleable proof suffices to prove the correctness of an entire multi-step shuffle.  ...  and in part by a graduate fellowship from the Charles Lee Powell Foundation.  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-36594-2_6">doi:10.1007/978-3-642-36594-2_6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/calwocpwjfbhrcw5atn5ewsffq">fatcat:calwocpwjfbhrcw5atn5ewsffq</a> </span>
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### The role of exon shuffling in shaping protein-protein interaction networks

Douglas V Cancherini, Gustavo S França, Sandro J de Souza
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Furthermore, we verified that a set of protein domains that are simultaneously promiscuous (known to interact to multiple types of other domains), selfinteracting (able to interact with another copy of  ...  Physical protein-protein interaction (PPI) is a critical phenomenon for the function of most proteins in living organisms and a significant fraction of PPIs are the result of domain-domain interactions  ...  A number of studies have tried to disclosure what pairs of domains establish physical interactions, either based on structural data [45, 46] , or based on statistical methods applied to PPI networks enriched  ...
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-11-s5-s11">doi:10.1186/1471-2164-11-s5-s11</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21210967">pmid:21210967</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3045794/">pmcid:PMC3045794</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gqlfl4rivjexpd5e74nwyyzqta">fatcat:gqlfl4rivjexpd5e74nwyyzqta</a> </span>
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