Volume 11; Issue 1

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Biology Direct
Volume 11; Issue 1

Biology Direct

Volume 11; Issue 1

1

The mysterious orphans of Mycoplasmataceae

Tatarinova, Tatiana V., Lysnyansky, Inna, Nikolsky, Yuri V., Bolshoy, Alexander

Journal:

Year:

2016

Language:

english

File:

PDF, 1.68 MB

english, 2016

2

Onset, timing, and exposure therapy of stress disorders: mechanistic insight from a mathematical model of oscillating neuroendocrine dynamics

Kim, Lae U., D’Orsogna, Maria R., Chou, Tom

Journal:

Year:

2016

Language:

english

File:

PDF, 3.10 MB

english, 2016

3

A mathematical approach to virus therapy of glioblastomas

de Rioja, Victor Lopez, Isern, Neus, Fort, Joaquim

Journal:

Year:

2016

Language:

english

File:

PDF, 902 KB

english, 2016

4

Characterizing exons and introns by regularity of nucleotide strings

Woods, Tonya, Preeprem, Thanawadee, Lee, Kichun, Chang, Woojin, Vidakovic, Brani

Journal:

Year:

2016

Language:

english

File:

PDF, 2.07 MB

english, 2016

5

Just how Lamarckian is CRISPR-Cas immunity: the continuum of evolvability mechanisms

Koonin, Eugene V., Wolf, Yuri I.

Journal:

Year:

2016

Language:

english

File:

PDF, 725 KB

english, 2016

6

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data

Jang, Yeongjun, Yu, Namhee, Seo, Jihae, Kim, Sun, Lee, Sanghyuk

Journal:

Year:

2016

Language:

english

File:

PDF, 2.37 MB

english, 2016

7

Preservation of methylated CpG dinucleotides in human CpG islands

Panchin, Alexander Y., Makeev, Vsevolod J., Medvedeva, Yulia A.

Journal:

Year:

2016

Language:

english

File:

PDF, 883 KB

english, 2016

8

Nucleic acids delivery methods for genome editing in zygotes and embryos: the old, the new, and the old-new

Sato, Masahiro, Ohtsuka, Masato, Watanabe, Satoshi, Gurumurthy, Channabasavaiah B.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.39 MB

english, 2016

9

Conservation and divergence of the histone code in nucleomorphs

Marinov, Georgi K., Lynch, Michael

Journal:

Year:

2016

Language:

english

File:

PDF, 3.58 MB

english, 2016

10

Infinitely long branches and an informal test of common ancestry

de Oliveira Martins, Leonardo, Posada, David

Journal:

Year:

2016

Language:

english

File:

PDF, 3.29 MB

english, 2016

11

The cyclin D1 carboxyl regulatory domain controls the division and differentiation of hematopoietic cells

Chaves-Ferreira, Miguel, Krenn, Gerald, Vasseur, Florence, Barinov, Aleksandr, Gonçalves, Pedro, Azogui, Orly, Cumano, Ana, Li, Zhi, Pellegrini, Sandra, Rocha, Benedita, Laderach, Diego

Journal:

Year:

2016

Language:

english

File:

PDF, 3.16 MB

english, 2016

12

Ribosome reinitiation at leader peptides increases translation of bacterial proteins

Korolev, Semen A., Zverkov, Oleg A., Seliverstov, Alexandr V., Lyubetsky, Vassily A.

Journal:

Year:

2016

Language:

english

File:

PDF, 544 KB

english, 2016

13

Beyond Turing: mechanochemical pattern formation in biological tissues

Mercker, Moritz, Brinkmann, Felix, Marciniak-Czochra, Anna, Richter, Thomas

Journal:

Year:

2016

Language:

english

File:

PDF, 2.25 MB

english, 2016

14

Viroids: “living fossils” of primordial RNAs?

Diener, Theodor O.

Journal:

Year:

2016

Language:

english

File:

PDF, 372 KB

english, 2016

15

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development

Mészáros, Bálint, Zeke, András, Reményi, Attila, Simon, István, Dosztányi, Zsuzsanna

Journal:

Year:

2016

Language:

english

File:

PDF, 2.75 MB

english, 2016

16

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

Li, Dingchen, Li, Zongwei, Zhou, Zhe, Li, Zhen, Qu, Xinyan, Xu, Peisong, Zhou, Pingkun, Bo, Xiaochen, Ni, Ming

Journal:

Year:

2016

Language:

english

File:

PDF, 2.96 MB

english, 2016

17

A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

Eliáš, Marek, Klimeš, Vladimír, Derelle, Romain, Petrželková, Romana, Tachezy, Jan

Journal:

Year:

2016

Language:

english

File:

PDF, 3.21 MB

english, 2016

18

Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology

Vianello, Angelo, Passamonti, Sabina

Journal:

Year:

2016

Language:

english

File:

PDF, 542 KB

english, 2016

19

Numerical simulation of vascular tumour growth under antiangiogenic treatment: addressing the paradigm of single-agent bevacizumab therapy with the use of experimental data

Argyri, Katerina D., Dionysiou, Dimitra D., Misichroni, Fay D., Stamatakos, Georgios S.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.84 MB

english, 2016

20

A web server for analysis, comparison and prediction of protein ligand binding sites

Singh, Harinder, Srivastava, Hemant Kumar, Raghava, Gajendra P. S.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.01 MB

english, 2016

21

The Columbian Exchange as a source of adaptive introgression in human populations

Jordan, I. King

Journal:

Year:

2016

Language:

english

File:

PDF, 803 KB

english, 2016

22

Estimation of ribosome profiling performance and reproducibility at various levels of resolution

Diament, Alon, Tuller, Tamir

Journal:

Year:

2016

Language:

english

File:

PDF, 2.69 MB

english, 2016

23

BLAST-based structural annotation of protein residues using Protein Data Bank

Singh, Harinder, Raghava, Gajendra P. S.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.88 MB

english, 2016

24

Altools: a user friendly NGS data analyser

Camiolo, Salvatore, Sablok, Gaurav, Porceddu, Andrea

Journal:

Year:

2016

Language:

english

File:

PDF, 820 KB

english, 2016

25

Optimal treatment and stochastic modeling of heterogeneous tumors

Badri, Hamidreza, Leder, Kevin

Journal:

Year:

2016

Language:

english

File:

PDF, 1.77 MB

english, 2016

26

Stem-like features of cancer cells on their way to metastasis

Gkountela, Sofia, Aceto, Nicola

Journal:

Year:

2016

Language:

english

File:

PDF, 1.56 MB

english, 2016

27

Profuse evolutionary diversification and speciation on volcanic islands: transposon instability and amplification bursts explain the genetic paradox

Craddock, Elysse M.

Journal:

Year:

2016

Language:

english

File:

PDF, 552 KB

english, 2016

28

Cpf1 nucleases demonstrate robust activity to induce DNA modification by exploiting homology directed repair pathways in mammalian cells

Tóth, Eszter, Weinhardt, Nóra, Bencsura, Petra, Huszár, Krisztina, Kulcsár, Péter I., Tálas, András, Fodor, Elfrieda, Welker, Ervin

Journal:

Year:

2016

Language:

english

File:

PDF, 1.11 MB

english, 2016

29

Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis

Markov, Alexander V., Kaznacheev, Ilya S.

Journal:

Year:

2016

Language:

english

File:

PDF, 4.03 MB

english, 2016

30

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics

List, Johann-Mattis, Pathmanathan, Jananan Sylvestre, Lopez, Philippe, Bapteste, Eric

Journal:

Year:

2016

Language:

english

File:

PDF, 1.74 MB

english, 2016

31

Cancer heterogeneity and multilayer spatial evolutionary games

Świerniak, Andrzej, Krześlak, Michał

Journal:

Year:

2016

Language:

english

File:

PDF, 1.93 MB

english, 2016

32

The essence of life

Journal:

Year:

2016

Language:

english

File:

PDF, 467 KB

english, 2016

33

Comparative genomic analysis of retrogene repertoire in two green algaeVolvox carteriandChlamydomonas reinhardtii

Jąkalski, Marcin, Takeshita, Kazutaka, Deblieck, Mathieu, Koyanagi, Kanako O., Makałowska, Izabela, Watanabe, Hidemi, Makałowski, Wojciech

Journal:

Year:

2016

Language:

english

File:

PDF, 1.08 MB

english, 2016

34

xHMMER3x2: Utilizing HMMER3’s speed and HMMER2’s sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

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

Journal:

Year:

2016

Language:

english

File:

PDF, 2.65 MB

english, 2016

35

Tracking the evolution of cancer cell populations through the mathematical lens of phenotype-structured equations

Lorenzi, Tommaso, Chisholm, Rebecca H., Clairambault, Jean

Journal:

Year:

2016

Language:

english

File:

PDF, 1.79 MB

english, 2016

36

The struggle byCaenorhabditis elegansto maintain proteostasis during aging and disease

Kikis, Elise A.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.36 MB

english, 2016

37

Should tissue structure suppress or amplify selection to minimize cancer risk?

Hindersin, Laura, Werner, Benjamin, Dingli, David, Traulsen, Arne

Journal:

Year:

2016

Language:

english

File:

PDF, 819 KB

english, 2016

38

ZFAS1:a long noncoding RNA associated with ribosomes in breast cancer cells

Hansji, Herah, Leung, Euphemia Y., Baguley, Bruce C., Finlay, Graeme J., Cameron-Smith, David, Figueiredo, Vandre C., Askarian-Amiri, Marjan E.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.74 MB

english, 2016

39

Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group

Tice, Alexander K., Shadwick, Lora L., Fiore-Donno, Anna Maria, Geisen, Stefan, Kang, Seungho, Schuler, Gabriel A., Spiegel, Frederick W., Wilkinson, Katherine A., Bonkowski, Michael, Dumack, Kenneth,

Journal:

Year:

2016

Language:

english

File:

PDF, 2.36 MB

english, 2016

40

Essential functions linked with structural disorder in organisms of minimal genome

Pancsa, Rita, Tompa, Peter

Journal:

Year:

2016

Language:

english

File:

PDF, 1.44 MB

english, 2016

41

Compartmentalization in PVC super-phylum: evolution and impact

Pinos, Sandrine, Pontarotti, Pierre, Raoult, Didier, Baudoin, Jean Pierre, Pagnier, Isabelle

Journal:

Year:

2016

Language:

english

File:

PDF, 2.42 MB

english, 2016

42

Gene overlapping and size constraints in the viral world

Brandes, Nadav, Linial, Michal

Journal:

Year:

2016

Language:

english

File:

PDF, 3.13 MB

english, 2016

43

Biochemical and biophysical characterization of cell-free synthesized Rift Valley fever virus nucleoprotein capsids enables in vitro screening to identify novel antivirals

Broce, Sean, Hensley, Lisa, Sato, Tomoharu, Lehrer-Graiwer, Joshua, Essrich, Christian, Edwards, Katie J., Pajda, Jacqueline, Davis, Christopher J., Bhadresh, Rami, Hurt, Clarence R., Freeman, Beverly

Journal:

Year:

2016

Language:

english

File:

PDF, 2.08 MB

english, 2016

44

Neurogenomics and the role of a large mutational target on rapid behavioral change

Stanley, Craig E., Kulathinal, Rob J.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.16 MB

english, 2016

45

Inter-platform concordance of gene expression data for the prediction of chemical mode of action

Siriwardhana, Chathura, Datta, Susmita, Datta, Somnath

Journal:

Year:

2016

Language:

english

File:

PDF, 710 KB

english, 2016

46

IPC – Isoelectric Point Calculator

Kozlowski, Lukasz P.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.11 MB

english, 2016

47

Intrinsic protein disorder in histone lysine methylation

Lazar, Tamas, Schad, Eva, Szabo, Beata, Horvath, Tamas, Meszaros, Attila, Tompa, Peter, Tantos, Agnes

Journal:

Year:

2016

Language:

english

File:

PDF, 2.68 MB

english, 2016

48

Unexpected links reflect the noise in networks

Anatoly Yambartsev,Michael A. Perlin,Yevgeniy Kovchegov…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.10 MB

english, 2016

49

The role of the backbone torsion in protein folding

Irina Sorokina,Arcady Mushegian

Journal:

Year:

2016

Language:

english

File:

PDF, 386 KB

english, 2016

50

Exploring the importance of cancer pathways by meta-analysis of differential protein expression networks in three different cancers

Sinjini Sikdar,Somnath Datta,Susmita Datta

Journal:

Year:

2016

Language:

english

File:

PDF, 701 KB

english, 2016

51

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls

Paweł P. Łabaj,David P. Kreil

Journal:

Year:

2016

Language:

english

File:

PDF, 1.55 MB

english, 2016

52

Prognostic value of cross-omics screening for kidney clear cell renal cancer survival

Slavica Dimitrieva,Ralph Schlapbach,Hubert Rehrauer

Journal:

Year:

2016

Language:

english

File:

PDF, 2.28 MB

english, 2016

53

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes

Suyan Tian,Howard H. Chang,Chi Wang

Journal:

Year:

2016

Language:

english

File:

PDF, 1.85 MB

english, 2016

54

Long range personalized cancer treatment strategies incorporating evolutionary dynamics

Chen-Hsiang Yeang,Robert A. Beckman

Journal:

Year:

2016

Language:

english

File:

PDF, 1.47 MB

english, 2016

55

Emergence of heterogeneity in acute leukemias

Thomas Stiehl,Christoph Lutz,Anna Marciniak-Czochra

Journal:

Year:

2016

Language:

english

File:

PDF, 2.40 MB

english, 2016

56

Evolution of the Tim17 protein family

Vojtěch Žárský,Pavel Doležal

Journal:

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

57

CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments

Benjamin Hur,Sangsoo Lim,Heejoon Chae,Seokjun Seo,Sunwon Lee…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.17 MB

english, 2016

58

Identification of microRNAs regulatingEscherichia coliF18 infection in Meishan weaned piglets

Zhengchang Wu,Weiyun Qin,Seng Wu,Guoqiang Zhu,Wenbin Bao…

Journal:

Year:

2016

Language:

english

File:

PDF, 3.17 MB

english, 2016

59

Importins promote high-frequency NF-κB oscillations increasing information channel capacity

Zbigniew Korwek,Karolina Tudelska,Paweł Nałęcz-Jawecki,Maciej Czerkies…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.99 MB

english, 2016

60

Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable

Alena Orlenko,Ashley I. Teufel,Peter B. Chi,David A. Liberles

Journal:

Year:

2016

Language:

english

File:

PDF, 1.45 MB

english, 2016

61

Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Mauro Degli Esposti,Diego Cortez,Luis Lozano,Simon Rasmussen…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.44 MB

english, 2016

62

The multiple evolutionary origins of the eukaryoticN-glycosylation pathway

Jonathan Lombard

Journal:

Year:

2016

Language:

english

File:

PDF, 8.09 MB

english, 2016

63

Primary and metastatic tumor dormancy as a result of population heterogeneity

Journal:

Year:

2016

Language:

english

File:

PDF, 2.54 MB

english, 2016

64

The role of cell location and spatial gradients in the evolutionary dynamics of colon and intestinal crypts

Leili Shahriyari,Natalia L. Komarova,Alexandra Jilkine

Journal:

Year:

2016

Language:

english

File:

PDF, 1.83 MB

english, 2016

65

Computational inference of a genomic pluripotency signature in human and mouse stem cells

Esra Kurum,Bérénice A. Benayoun,Ankit Malhotra,Joshy George…

Journal:

Year:

2016

Language:

english

File:

PDF, 1.34 MB

english, 2016

66

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks

Neetu Sain,Debasisa Mohanty

Journal:

Year:

2016

Language:

english

File:

PDF, 2.95 MB

english, 2016

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