Volume 10; Issue 1

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Biology Direct
Volume 10; Issue 1

Biology Direct

Volume 10; Issue 1

1

Molecular complementarity between simple, universal molecules and ions limited phenotype space in the precursors of cells

Norris, Vic, Reusch, Rosetta N, Igarashi, Kazuei, Root-Bernstein, Robert

Journal:

Year:

2015

Language:

english

File:

PDF, 437 KB

english, 2015

2

Reviewer acknowledgement

Koonin, Eugene V, Landweber, Laura F, Lipman, David

Journal:

Year:

2015

Language:

english

File:

PDF, 271 KB

english, 2015

3

Mammalian Argonaute-DNA binding?

Smalheiser, Neil R, Gomes, Octavio L A

Journal:

Year:

2015

Language:

english

File:

PDF, 313 KB

english, 2015

4

Cooperation and selfishness both occur during molecular evolution

Journal:

Year:

2015

Language:

english

File:

PDF, 271 KB

english, 2015

5

Dynamics of social network structure for Alzheimer and Lymphoma scientific communities

Barbash, Shahar

Journal:

Year:

2015

Language:

english

File:

PDF, 1.03 MB

english, 2015

6

Microbes on the edge of Occam’s razor

Starokadomskyy, Petro

Journal:

Year:

2015

Language:

english

File:

PDF, 321 KB

english, 2015

7

A new ensemble coevolution system for detecting HIV-1 protein coevolution

Li, Guangdi, Theys, Kristof, Verheyen, Jens, Pineda-Peña, Andrea-Clemencia, Khouri, Ricardo, Piampongsant, Supinya, Eusébio, Mónica, Ramon, Jan, Vandamme, Anne-Mieke

Journal:

Year:

2015

Language:

english

File:

PDF, 2.59 MB

english, 2015

8

Genome-wide association study for posthitis in the free-living population of European bison (Bison bonasus)

Oleński, Kamil, Tokarska, Małgorzata, Hering, Dorota, Puckowska, Paulina, Ruść, Anna, Pertoldi, Cino, Kamiński, Stanisław

Journal:

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

9

The microbiome mutiny hypothesis: can our microbiome turn against us when we are old or seriously ill?

Rózsa, Lajos, Apari, Péter, Müller, Viktor

Journal:

Year:

2015

Language:

english

File:

PDF, 358 KB

english, 2015

10

“Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

Pliatsika, Venetia, Rigoutsos, Isidore

Journal:

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

11

Erratum to: Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes

Hooper, Scott L, Burstein, Helaine J

Journal:

Year:

2015

Language:

english

File:

PDF, 356 KB

english, 2015

12

Structure based approach for understanding organism specific recognition of protein-RNA complexes

Nagarajan, Raju, Chothani, Sonia, Ramakrishnan, Chandrasekaran, Sekijima, Masakazu, Gromiha, M

Journal:

Year:

2015

Language:

english

File:

PDF, 1.23 MB

english, 2015

13

Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool

Caputo, Aurélia, Dubourg, Grégory, Croce, Olivier, Gupta, Sushim, Robert, Catherine, Papazian, Laurent, Rolain, Jean-Marc, Raoult, Didier

Journal:

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

14

Global analyses of Chromosome 17 and 18 genes of lung telocytes compared with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes

Wang, Jian, Ye, Ling, Jin, Meiling, Wang, Xiangdong

Journal:

Year:

2015

Language:

english

File:

PDF, 3.74 MB

english, 2015

15

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae

Pagnier, Isabelle, Yutin, Natalya, Croce, Olivier, Makarova, Kira S, Wolf, Yuri I, Benamar, Samia, Raoult, Didier, Koonin, Eugene V, La Scola, Bernard

Journal:

Year:

2015

Language:

english

File:

PDF, 2.31 MB

english, 2015

16

Synthetic lethals in HIV: ways to avoid drug resistance

Petitjean, Michel, Badel, Anne, Veitia, Reiner A, Vanet, Anne

Journal:

Year:

2015

Language:

english

File:

PDF, 2.85 MB

english, 2015

17

An atlas of mouse CD4+ T cell transcriptomes

Stubbington, Michael JT, Mahata, Bidesh, Svensson, Valentine, Deonarine, Andrew, Nissen, Jesper K, Betz, Alexander G, Teichmann, Sarah A

Journal:

Year:

2015

Language:

english

File:

PDF, 2.48 MB

english, 2015

18

QSAR based model for discriminating EGFR inhibitors and non-inhibitors using Random forest

Singh, Harinder, Singh, Sandeep, Singla, Deepak, Agarwal, Subhash M, Raghava, Gajendra P S

Journal:

Year:

2015

Language:

english

File:

PDF, 1.49 MB

english, 2015

19

Plant viruses of the Amalgaviridae family evolved via recombination between viruses with double-stranded and negative-strand RNA genomes

Krupovic, Mart, Dolja, Valerian V, Koonin, Eugene V

Journal:

Year:

2015

Language:

english

File:

PDF, 781 KB

english, 2015

20

A new family of hybrid virophages from an animal gut metagenome

Yutin, Natalya, Kapitonov, Vladimir V, Koonin, Eugene V

Journal:

Year:

2015

Language:

english

File:

PDF, 510 KB

english, 2015

21

Sequence analysis reveals a conserved extension in the capping enzyme of the alphavirus supergroup, and a homologous domain in nodaviruses

Ahola, Tero, Karlin, David G

Journal:

Year:

2015

Language:

english

File:

PDF, 2.22 MB

english, 2015

22

The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications

Burroughs, A Maxwell, Zhang, Dapeng, Aravind, L

Journal:

Year:

2015

Language:

english

File:

PDF, 1.75 MB

english, 2015

23

Co-regulation of translation in protein complexes

Siwiak, Marlena, Zielenkiewicz, Piotr

Journal:

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

24

Test on existence of histology subtype-specific prognostic signatures among early stage lung adenocarcinoma and squamous cell carcinoma patients using a Cox-model based filter

Tian, Suyan, Wang, Chi, An, Ming-Wen

Journal:

Year:

2015

Language:

english

File:

PDF, 1.44 MB

english, 2015

25

Mitochondrial activity in gametes and transmission of viable mtDNA

Milani, Liliana, Ghiselli, Fabrizio

Journal:

Year:

2015

Language:

english

File:

PDF, 3.06 MB

english, 2015

26

Comparative genomic analysis of the WRKY III gene family inpopulus, grape,arabidopsisand rice

Wang, Yiyi, Feng, Lin, Zhu, Yuxin, Li, Yuan, Yan, Hanwei, Xiang, Yan

Journal:

Year:

2015

Language:

english

File:

PDF, 2.51 MB

english, 2015

27

Age-driven modulation of tRNA-derived fragments inDrosophilaand their potential targets

Karaiskos, Spyros, Naqvi, Ammar S., Swanson, Karl E., Grigoriev, Andrey

Journal:

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

28

“Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies”

Verma, Ved Vrat, Gupta, Rani, Goel, Manisha

Journal:

Year:

2015

Language:

english

File:

PDF, 2.73 MB

english, 2015

29

The human disease network in terms of dysfunctional regulatory mechanisms

Yang, Jing, Wu, Su-Juan, Dai, Wen-Tao, Li, Yi-Xue, Li, Yuan-Yuan

Journal:

Year:

2015

Language:

english

File:

PDF, 3.91 MB

english, 2015

30

RNA motif discovery: a computational overview

Achar, Avinash, Sætrom, Pål

Journal:

Year:

2015

Language:

english

File:

PDF, 1.64 MB

english, 2015

31

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Mudgal, Richa, Sandhya, Sankaran, Chandra, Nagasuma, Srinivasan, Narayanaswamy

Journal:

Year:

2015

Language:

english

File:

PDF, 3.24 MB

english, 2015

32

Modeling epigenetic regulation of PRC1 protein accumulation in the cell cycle

Dolbniak, Marzena, Kimmel, Marek, Smieja, Jaroslaw

Journal:

Year:

2015

Language:

english

File:

PDF, 2.89 MB

english, 2015

33

Why the Central Dogma: on the nature of the great biological exclusion principle

Koonin, Eugene V.

Journal:

Year:

2015

Language:

english

File:

PDF, 448 KB

english, 2015

34

KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation

Wang, Dapeng, Xu, Jiayue, Yu, Jun

Journal:

Year:

2015

Language:

english

File:

PDF, 1.46 MB

english, 2015

35

Microarray experiments and factors which affect their reliability

Jaksik, Roman, Iwanaszko, Marta, Rzeszowska-Wolny, Joanna, Kimmel, Marek

Journal:

Year:

2015

Language:

english

File:

PDF, 1.68 MB

english, 2015

36

Ancient origin of the biosynthesis of lignin precursors

Labeeuw, Leen, Martone, Patrick T, Boucher, Yan, Case, Rebecca J

Journal:

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

37

TMFoldWeb: a web server for predicting transmembrane protein fold class

Kozma, Dániel, Tusnády, Gábor E.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

38

PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

Singh, Sandeep, Singh, Harinder, Tuknait, Abhishek, Chaudhary, Kumardeep, Singh, Balvinder, Kumaran, S., Raghava, Gajendra P. S.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.43 MB

english, 2015

39

Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins

Shalaeva, Daria N., Galperin, Michael Y., Mulkidjanian, Armen Y.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.28 MB

english, 2015

40

Experiences with workflows for automating data-intensive bioinformatics

Spjuth, Ola, Bongcam-Rudloff, Erik, Hernández, Guillermo Carrasco, Forer, Lukas, Giovacchini, Mario, Guimera, Roman Valls, Kallio, Aleksi, Korpelainen, Eija, Kańduła, Maciej M, Krachunov, Milko, Kreil

Journal:

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

41

Emergence of life: Physical chemistry changes the paradigm

Spitzer, Jan, Pielak, Gary J., Poolman, Bert

Journal:

Year:

2015

Language:

english

File:

PDF, 1.73 MB

english, 2015

42

A principle of organization which facilitates broad Lamarckian-like adaptations by improvisation

Soen, Yoav, Knafo, Maor, Elgart, Michael

Journal:

Year:

2015

Language:

english

File:

PDF, 1.52 MB

english, 2015

43

Synthetic circuit designs for earth terraformation

Solé, Ricard V., Montañez, Raúl, Duran-Nebreda, Salva

Journal:

Year:

2015

Language:

english

File:

PDF, 1.31 MB

english, 2015

44

In silicoribozyme evolution in a metabolically coupled RNA population

Könnyű, Balázs, Szilágyi, András, Czárán, Tamás

Journal:

Year:

2015

Language:

english

File:

PDF, 1.93 MB

english, 2015

45

Imprecise intron losses are less frequent than precise intron losses but are not rare in plants

Ma, Ming-Yue, Zhu, Tao, Li, Xue-Nan, Lan, Xin-Ran, Liu, Heng-Yuan, Yang, Yu-Fei, Niu, Deng-Ke

Journal:

Year:

2015

Language:

english

File:

PDF, 943 KB

english, 2015

46

Design principles for cancer therapy guided by changes in complexity of protein-protein interaction networks

Benzekry, Sebastian, Tuszynski, Jack A., Rietman, Edward A., Lakka Klement, Giannoula

Journal:

Year:

2015

Language:

english

File:

PDF, 1.42 MB

english, 2015

47

The human transmembrane proteome

Dobson, László, Reményi, István, Tusnády, Gábor E.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.65 MB

english, 2015

48

Models of buffering of dosage imbalances in protein complexes

Veitia, Reiner A., Birchler, James A.

Journal:

Year:

2015

Language:

english

File:

PDF, 824 KB

english, 2015

49

The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales

Jay, Zackary J., Inskeep, William P.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

50

The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers

Kaur, Gurmeet, Subramanian, Srikrishna

Journal:

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

51

De novotranscriptome assembly and analysis ofSf21 cells using illumina paired end sequencing

Kakumani, Pavan Kumar, Shukla, Rohit, Todur, Vivek N., Malhotra, Pawan, Mukherjee, Sunil K., Bhatnagar, Raj K.

Journal:

Year:

2015

Language:

english

File:

PDF, 748 KB

english, 2015

52

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification

Badyaev, Alexander V., Morrison, Erin S., Belloni, Virginia, Sanderson, Michael J.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.35 MB

english, 2015

53

Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at “Evolution Canyon”, Mount Carmel, Israel

Beiles, Avigdor, Raz, Shmuel, Ben-Abu, Yuval, Nevo, Eviatar

Journal:

Year:

2015

Language:

english

File:

PDF, 3.56 MB

english, 2015

54

Lack of population differentiation patterns of previously identified putatively adaptive transposable element insertions at microgeographic scales

González, Josefa, Martínez, Jose, Makalowski, Wojciech

Journal:

Year:

2015

Language:

english

File:

PDF, 541 KB

english, 2015

55

Was the evolutionary road towards adaptive immunity paved with endothelium?

van Niekerk, Gustav, Davis, Tanja, Engelbrecht, Anna-Mart

Journal:

Year:

2015

Language:

english

File:

PDF, 648 KB

english, 2015

56

Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: theKlebsiellaparadigm

Caputo, Aurélia, Merhej, Vicky, Georgiades, Kalliopi, Fournier, Pierre-Edouard, Croce, Olivier, Robert, Catherine, Raoult, Didier

Journal:

Year:

2015

Language:

english

File:

PDF, 2.38 MB

english, 2015

57

Variation in the ribosome interacting loop of the Sec61α fromGiardia lamblia

Sinha, Abhishek, Ray, Atrayee, Ganguly, Sandipan, Ghosh Dastidar, Shubhra, Sarkar, Srimonti

Journal:

Year:

2015

Language:

english

File:

PDF, 2.11 MB

english, 2015

58

MicroRNA-derived network analysis of differentially methylated genes in schizophrenia, implicating GABA receptor B1 [GABBR1] and protein kinase B [AKT1]

Gumerov, Vadim, Hegyi, Hedi

Journal:

Year:

2015

Language:

english

File:

PDF, 2.76 MB

english, 2015

59

Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life

Lopez, Philippe, Halary, Sébastien, Bapteste, Eric

Journal:

Year:

2015

Language:

english

File:

PDF, 1.84 MB

english, 2015

60

Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease

Krupovic, Mart, Cvirkaite-Krupovic, Virginija, Prangishvili, David, Koonin, Eugene V.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

61

What can ecosystems learn? Expanding evolutionary ecology with learning theory

Power, Daniel A., Watson, Richard A., Szathmáry, Eörs, Mills, Rob, Powers, Simon T., Doncaster, C. Patrick, Czapp, BłaŻej

Journal:

Year:

2015

Language:

english

File:

PDF, 3.71 MB

english, 2015

62

Bacterial calpains and the evolution of the calpain (C2) family of peptidases

Rawlings, Neil D.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

63

The progene hypothesis: the nucleoprotein world and how life began

Altstein, Anatoly D.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

64

Quantitative proteomics signature profiling based on network contextualization

Goh, Wilson Wen Bin, Guo, Tiannan, Aebersold, Ruedi, Wong, Limsoon

Journal:

Year:

2015

Language:

english

File:

PDF, 3.34 MB

english, 2015

65

Evolutionary loss of peroxisomes – not limited to parasites

Žárský, Vojtěch, Tachezy, Jan

Journal:

Year:

2015

Language:

english

File:

PDF, 1.48 MB

english, 2015

66

Horizontally transferred genes cluster spatially and metabolically

Dilthey, Alexander, Lercher, Martin J.

Journal:

Year:

2015

Language:

english

File:

PDF, 480 KB

english, 2015

67

Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly

Shalaeva, Daria N., Dibrova, Daria V., Galperin, Michael Y., Mulkidjanian, Armen Y.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.73 MB

english, 2015

68

Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes

Yong, Chern Han, Wong, Limsoon

Journal:

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

69

Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon

Kapitonov, Vladimir V, Koonin, Eugene V

Journal:

Year:

2015

Language:

english

File:

PDF, 983 KB

english, 2015

70

A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

Campos, Marcelino, Llorens, Carlos, Sempere, José M., Futami, Ricardo, Rodriguez, Irene, Carrasco, Purificación, Capilla, Rafael, Latorre, Amparo, Coque, Teresa M., Moya, Andres, Baquero, Fernando

Journal:

Year:

2015

Language:

english

File:

PDF, 1.90 MB

english, 2015

71

The Lamarckian chicken and the Darwinian egg

Pilpel, Yitzhak, Rechavi, Oded

Journal:

Year:

2015

Language:

english

File:

PDF, 614 KB

english, 2015

72

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Wong, Wing-Cheong, Yap, Choon-Kong, Eisenhaber, Birgit, Eisenhaber, Frank

Journal:

Year:

2015

Language:

english

File:

PDF, 2.05 MB

english, 2015

73

Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer

Srihari, Sriganesh, Singla, Jitin, Wong, Limsoon, Ragan, Mark A.

Journal:

Year:

2015

Language:

english

File:

PDF, 3.82 MB

english, 2015

74

A novel RING finger in the C-terminal domain of the coatomer protein α-COP

Kaur, Gurmeet, Subramanian, Srikrishna

Journal:

Year:

2015

Language:

english

File:

PDF, 1.88 MB

english, 2015

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