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Functional grouping based on signatures in protein termini

Iris Bahir, Michal Linial
2006 Proteins: Structure, Function, and Bioinformatics  
The two ends of each protein are known as the amino (N-) and carboxyl (C-) termini. Short signatures in a protein's termini often carry vital cellular function. No systematic research has been conducted to address the importance of short signatures (3 to 10 amino acids) in protein termini at the proteomic level. Specifically, it is unknown whether such signatures are evolutionarily conserved, and if so, whether this conservation confers shared biological functions. Current signature detection
more » ... thods fail to detect such short signatures due to inadequate statistical scores. The findings presented in this study strongly support the notion that functional significance of protein sets may be captured by short signatures at their termini. A positional search method was applied to over one million proteins from the UniProt database. The result is a collection of about a thousand significant signature groups (SIGs) that include previously identified as well as many novel signatures in protein termini. These SIGs represent protein sets with minimal or no overall sequence similarity excepting the similarity at their termini. The most significant SIGs are assigned by their strong correspondence to functional annotations derived from external databases such as Gene Ontology. Each of the SIGs is associated with the statistical significance of its functional association. These SIGs provide a valuable source for testing previously overlooked signatures in protein termini and allow for the investigation of the role played by such signatures throughout evolution. The SIGs archive and advanced search options are available at http://www.proteus.cs.huji.ac.il.
doi:10.1002/prot.20903 pmid:16475191 fatcat:d7kj2khinzfqzgjewgiu7cvo3q

Pain Management – A Decade's Perspective of a New Subspecialty

Uri Hochberg, Haggai Sharon, Iris Bahir, Silviu Brill
2021 Journal of Pain Research  
Pain management is increasingly recognized as a formal medical subspecialty worldwide. Israel was among the first to offer a board-certified subspecialty, formalized by the Israeli Medical Association in 2010 which is open to all clinicians with a state-recognized specialization. This paper aims at evaluating the current program across several quality control measures. A survey among pain medicine specialists who graduated from the Israeli Pain Management subspecialty. All 43 graduates of the
more » ... ogram were sent a web-based questionnaire, each related to a different time in the participants' residency period - prior to, during and after training. Forty-one physicians responded to the survey (95% response rate). The most common primary specialty was Anesthesiology (44%), followed by Family Medicine (22%). One-third of the respondents applied to the program over five years after completing their initial residency. Two-thirds reported that they acquired all or most of the professional tools required by a pain specialist. Insufficient training was mentioned regarding addiction management (71%), special population needs (54%) and interventional treatment (37%). A high proportion (82%) responded that the examination contributed to their training and almost all perceived their period of subspecialty as having a positive value in their personal development. Two-thirds of respondents had not yet actively engaged beyond the clinical aspect with other entities responsible for formulating guidelines and other strategic decision-making. We hope the findings of this first-of-a-kind survey will encourage other medical authorities to construct formal training in pain medicine and enable this discipline to further evolve.
doi:10.2147/jpr.s303815 pmid:33859493 pmcid:PMC8044436 fatcat:p3naxmrhvfg7xdgniqsw74ma2a

Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Iris Bahir, Menachem Fromer, Yosef Prat, Michal Linial
2009 Molecular Systems Biology  
Source data is available for this figure at www.nature.com/msb.Viral adaptation to host I Bahir et al host; on the other hand, other mammalian viruses do not. ).  ...  Viral adaptation to host I Bahir et al The viral space displays enormous diversity but high redundancy In this study, we set out to analyze the overall potential adaptability of known virus families by  ... 
doi:10.1038/msb.2009.71 pmid:19888206 pmcid:PMC2779085 fatcat:2ozgofpqsncc3ppapsitbv3wfm

MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases

Noa Rappaport, Michal Twik, Noam Nativ, Gil Stelzer, Iris Bahir, Tsippi Iny Stein, Marilyn Safran, Doron Lancet
2014 Current Protocols in Bioinformatics  
Systems medicine provides insights into mechanisms of human diseases, and expedites the development of better diagnostics and drugs. To facilitate such strategies, we initiated MalaCards, a compendium of human diseases and their annotations, integrating and often remodeling information from 64 data sources. MalaCards employs, among others, the proven automatic data-mining strategies established in the construction of GeneCards, our widely used compendium of human genes. The development of
more » ... rds poses many algorithmic challenges, such as disease name unification, integrated classification, gene-disease association, and disease-targeted expression analysis. MalaCards displays a Web card for each of >19,000 human diseases, with 17 sections, including textual summaries, related diseases, related genes, genetic variations and tests, and relevant publications. Also included are a powerful search engine and a variety of categorized disease lists. This unit describes two basic protocols to search and browse MalaCards effectively.
doi:10.1002/0471250953.bi0124s47 pmid:25199789 fatcat:vowmssjxt5c5pnc56rviyj4ot4

In-silico human genomics with GeneCards

Gil Stelzer, Irina Dalah, Tsippi Stein, Yigeal Satanower, Naomi Rosen, Noam Nativ, Danit Oz-Levi, Tsviya Olender, Frida Belinky, Iris Bahir, Hagit Krug, Paul Perco (+4 others)
2011 Human Genomics  
Since 1998, the bioinformatics, systems biology, genomics and medical communities have enjoyed a synergistic relationship with the GeneCards database of human genes (http://www.genecards.org). This human gene compendium was created to help to introduce order into the increasing chaos of information flow. As a consequence of viewing details and deep links related to specific genes, users have often requested enhanced capabilities, such that, over time, GeneCards has blossomed into a suite of
more » ... s (including GeneDecks, GeneALaCart, GeneLoc, GeneNote and GeneAnnot) for a variety of analyses of both single human genes and sets thereof. In this paper, we focus on inhouse and external research activities which have been enabled, enhanced, complemented and, in some cases, motivated by GeneCards. In turn, such interactions have often inspired and propelled improvements in GeneCards. We describe here the evolution and architecture of this project, including examples of synergistic applications in diverse areas such as synthetic lethality in cancer, the annotation of genetic variations in disease, omics integration in a systems biology approach to kidney disease, and bioinformatics tools.
doi:10.1186/1479-7364-5-6-709 pmid:22155609 pmcid:PMC3525253 fatcat:szb36ui2mnbyzoup6jvadonurm

MalaCards: an integrated compendium for diseases and their annotation

Noa Rappaport, Noam Nativ, Gil Stelzer, Michal Twik, Yaron Guan-Golan, Tsippi Iny Stein, Iris Bahir, Frida Belinky, C. Paul Morrey, Marilyn Safran, Doron Lancet
2013 Database: The Journal of Biological Databases and Curation  
Citation details: Rappaport,N., Nativ,N., Stelzer,G., et al. MalaCards: an integrated compendium for diseases and their annotation.
doi:10.1093/database/bat018 pmid:23584832 pmcid:PMC3625956 fatcat:ju462m3cezgqtkai2jjrdvatuq

Single-cell level temporal profiling of tumour-reactive T cells under immune checkpoint blockade [article]

Jehanne Hassan, Elizabeth Appleton, Bahire Kalfaoglu, Malin Pedersen, José Almeida-Santos, Hisashi Kanemaru, Nobuko Irie, Shane Foo, Omnia Reda, Benjy J. Y. Tan, Il-mi Okazaki, Taku Okazaki (+4 others)
2022 bioRxiv   pre-print
The blockade of the immune checkpoints PD-1 and CTLA-4 enhances T cell response. However, it is largely unknown how antigen-reactive T cells regulate their checkpoint expression in vivo and whether and how the checkpoint blockade can change activation dynamics of tumour-reactive T cells. To address this, here we used Nr4a3-Timer-of-cell-kinetics-and-activity (Tocky), which allows analysis of temporal changes of activated T cells following TCR signalling in vivo. By analysing melanoma-bearing
more » ... a3 Tocky mice, we elucidate hidden dynamics of tumour-reactive T cells in the steady-state. The checkpoint blockade depleted highly activated effector Treg, while promoting unique effector T cell populations, and thus differentially modulating activation of tumour-reactive T cell populations. Furthermore, multidimensional analysis and seamless analysis of Tocky and scRNA-seq revealed a full spectrum of T cell dynamics in response to tumour burden and the checkpoint blockade. Lastly, we propose a rational design of combinatorial therapy to further enhance T cell activities.
doi:10.1101/2022.07.19.500582 fatcat:ftdxfzoksneihdedw6ea4gorbm

TEC prediction performance of the IRI-2012 model over Ethiopia during the rising phase of solar cycle 24 (2009–2011)

Yekoye Asmare Tariku
2015 Earth, Planets and Space  
Ground-based Global Positioning System (GPS) VTEC data, inferred from dual-frequency GPS receivers installed at Bahir Dar (geographic latitude 11.6°N and longitude 37.35°E, geomagnetic latitude 2.64°N  ...  This paper discusses the performance of the latest version of the International Reference Ionosphere (IRI-2012) model for estimating the vertical total electron content (VTEC) variation over Ethiopian  ...  Hence, the author is very grateful to UNAVCO, NOAA, and NASA for providing their GPS, daily sunspot number, and online IRI-2012 model data, respectively.  ... 
doi:10.1186/s40623-015-0312-1 fatcat:ghpjp4mw2zesnovzpuw75bo57e

Survey on diversity, relative abundance and hydrology of fishes in Ayima, Alatish and Gelegu Rivers, of Alatish National Park, Ethiopia

Tewabe Dereje
2020 International Journal of Aquaculture and Fishery Sciences  
These species have 23.9 % IRI, 20.8 % IRI and 18.7 % IRI, respectively (Table 3 ).  ...  There are also big pools which are not used for fi shing because of their extreme depth and related with religious fears (Tikur bahir in Aybeza).  ... 
doi:10.17352/2455-8400.000050 fatcat:kjnz4vode5bgjntbftfjasv6uu

A Phytolith Supported Biosphere-Hydrosphere Predictive Model for Southern Ethiopia: Insights into Paleoenvironmental Changes and Human Landscape Preferences since the Last Glacial Maximum

Markus L. Fischer, Felix Bachofer, Chad L. Yost, Ines J. E. Bludau, Christian Schepers, Verena Foerster, Henry Lamb, Frank Schäbitz, Asfawossen Asrat, Martin H. Trauth, Annett Junginger
2021 Geosciences  
we here present a new Predictive Vegetation Model that is linked with a Lake Balance Model and available vegetation-proxy records from southern Ethiopia including a new phytolith record from the Chew Bahir  ...  (B) Legend of potential vegetation arranged by altitude with (a to c) monthly temperature means in °C and precipitation in mm per month (IRI, last accessed 12/2020).  ...  (B) Legend of potential vegetation arranged by altitude with (a to c) monthly temperature means in • C and precipitation in mm per month (IRI, last accessed 12/2020).  ... 
doi:10.3390/geosciences11100418 fatcat:jze6mg3vq5c7viu2clj4kb5iou

Determining the Pace and Magnitude of Lake Level Changes in Southern Ethiopia Over the Last 20,000 Years Using Lake Balance Modeling and SEBAL

Markus L. Fischer, Monika Markowska, Felix Bachofer, Verena E. Foerster, Asfawossen Asrat, Christoph Zielhofer, Martin H. Trauth, Annett Junginger
2020 Frontiers in Earth Science  
The results suggest that an increase in precipitation of 20-30% throughout the southern Ethiopian Rift is necessary to fill paleo-lake Chew Bahir to its overflow level.  ...  Furthermore, it was demonstrated that paleo-lake Chew Bahir was highly dependent on the water supply from the upper lakes Abaya and Chamo and dries out within ∼40 years if the hydrological connection is  ...  The Kulfo River is also connected to Lake FIGURE 2 | Geographical features of the studied lake basins: (A) Modern catchment boundaries, monthly temperature means in • C and precipitation in mm/month (IRI  ... 
doi:10.3389/feart.2020.00197 fatcat:flxvg5gqtvbfvoi7skfjesmr7a

Predictors of mortality among TB-HIV Co-infected patients being treated for tuberculosis in Northwest Ethiopia: a retrospective cohort study

Balewgizie Sileshi, Negussie Deyessa, Belaineh Girma, Muluken Melese, Pedro Suarez
2013 BMC Infectious Diseases  
Patients are also referred to ART clinics for pre-ART and ART follow up from private health facilities within Bahir Dar and health facilities outside of Bahir Dar.  ...  Bahir Dar is located in Northwest Ethiopia, 565 kilometers from Addis Ababa.  ... 
doi:10.1186/1471-2334-13-297 pmid:23815342 pmcid:PMC3703293 fatcat:qfrk2uzfsvglzhd52nhi24zqzi

Environmental change and human occupation of southern Ethiopia and northern Kenya during the last 20,000 years

Verena Foerster, Ralf Vogelsang, Annett Junginger, Asfawossen Asrat, Henry F. Lamb, Frank Schaebitz, Martin H. Trauth
2015 Quaternary Science Reviews  
The pink circle marks the 642 site of the Chew Bahir record. Climate diagrams represent monthly temperature means in deg C and 643 precipitation in mm/month (IRI, last accessed 2/2014).  ...  Addis Ababa University for support in the realization of the Chew Bahir field campaign in difficult 405 terrain.  ... 
doi:10.1016/j.quascirev.2015.10.026 fatcat:oejqhmj7dffj3lxvf46e3tfdna

46 000 years of alternating wet and dry phases on decadal to orbital timescales in the cradle of modern humans: the Chew Bahir project, southern Ethiopia

V. Foerster, A. Junginger, A. Asrat, H. F. Lamb, M. Weber, J. Rethemeyer, U. Frank, M. C. Brown, M. H. Trauth, F. Schaebitz
2014 Climate of the Past Discussions  
Therefore, Chew Bahir is a perfect site to study and understand climatic variability on different timescales.</p>  ...  Here we present a high-resolution (~3–12 yr) and well-dated (32 AMS <sup>14</sup>C ages) lake-sediment record of the last 46 000 yr from the Chew Bahir basin in the southern Ethiopian Rift.  ...  Numbers refer to available precipitation and temperature data summarized in the climate diagrams (data: IRI, accessed October 2013). show variations within the Chew Bahir basin itself.  ... 
doi:10.5194/cpd-10-977-2014 fatcat:j2547cobnzao7bnk6pmljvym54
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