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1

Prediction-based fingerprints of protein–protein interactions

Aleksey Porollo, Jarosław Meller

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 400 KB

english, 2007

2

Control of Nutrient Stress-Induced Metabolic Reprogramming by PKCζ in Tumorigenesis

Ma, Li, Tao, Yongzhen, Duran, Angeles, Llado, Victoria, Galvez, Anita, Barger, Jennifer F., Castilla, Elias A., Chen, Jing, Yajima, Tomoko, Porollo, Aleksey, Medvedovic, Mario, Brill, Laurence M., Pla

Journal:

Year:

2013

Language:

english

File:

PDF, 2.52 MB

english, 2013

3

Prediction of Antimicrobial Resistance in Gram-Negative Bacteria From Whole-Genome Sequencing Data

Van Camp, Pieter-Jan, Haslam, David B., Porollo, Aleksey

Journal:

Frontiers in Microbiology

Year:

2020

File:

PDF, 8.18 MB

2020

4

Accurate prediction of solvent accessibility using neural networks–based regression

Rafał Adamczak, Aleksey Porollo, Jarosław Meller

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 327 KB

english, 2004

5

Combining prediction of secondary structure and solvent accessibility in proteins

Rafał Adamczak, Aleksey Porollo, Jarosław Meller

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 140 KB

english, 2005

6

Interleukin-6 receptor enhances early colonization of the murine omentum by upregulation of a mannose family receptor, LY75, in ovarian tumor cells

Premkumar Vummidi Giridhar, Holly M. Funk, Catherine A. Gallo, Aleksey Porollo, Carol A. Mercer, David R. Plas, Angela F. Drew

Journal:

Clinical and Experimental Metastasis

Year:

2011

Language:

english

File:

PDF, 551 KB

english, 2011

7

Large-Scale Characterization of Introns in the Pneumocystis carinii Genome

BRADLEY E. SLAVEN, ALEKSEY POROLLO, THOMAS SESTERHENN, A. GEORGE SMULIAN, MELANIE T. CUSHION, JAROSLAW MELLER

Journal:

Journal of Eukaryotic Microbiology

Year:

2006

Language:

english

File:

PDF, 121 KB

english, 2006

8

Draft Assembly and Annotation of the Pneumocystis carinii Genome

BRADLEY E. SLAVEN, JAROSLAW MELLER, ALEKSEY POROLLO, THOMAS SESTERHENN, A. GEORGE SMULIAN, MELANIE T. CUSHION

Journal:

Journal of Eukaryotic Microbiology

Year:

2006

Language:

english

File:

PDF, 65 KB

english, 2006

9

Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D

Aleksey Porollo, Jaroslaw Meller

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 453 KB

english, 2007

10

p62 Is a Key Regulator of Nutrient Sensing in the mTORC1 Pathway

Angeles Duran, Ramars Amanchy, Juan F. Linares, Jayashree Joshi, Shadi Abu-Baker, Aleksey Porollo, Malene Hansen, Jorge Moscat, Maria T. Diaz-Meco

Journal:

Year:

2011

Language:

english

File:

PDF, 2.14 MB

english, 2011

11

Diary of the Week

Subramanian Vignesh, Kavitha, Landero Figueroa, Julio A., Porollo, Aleksey, Caruso, Joseph A., Deepe, George S.

Journal:

Year:

1950

Language:

english

File:

PDF, 208 KB

english, 1950

12

Granulocyte Macrophage-Colony Stimulating Factor Induced Zn Sequestration Enhances Macrophage Superoxide and Limits Intracellular Pathogen Survival

Subramanian Vignesh, Kavitha, Landero Figueroa, Julio A., Porollo, Aleksey, Caruso, Joseph A., Deepe, George S.

Journal:

Year:

2013

Language:

english

File:

PDF, 4.13 MB

english, 2013

13

EC2KEGG: a command line tool for comparison of metabolic pathways

Aleksey Porollo

Journal:

Source Code for Biology and Medicine

Year:

2014

Language:

english

File:

PDF, 248 KB

english, 2014

14

MutaCYP: Classification of missense mutations in human cytochromes P450

Kenneth Fechter,Aleksey Porollo

Journal:

BMC Medical Genomics

Year:

2014

Language:

english

File:

PDF, 574 KB

english, 2014

15

Linear Regression Models for Solvent Accessibility Prediction in Proteins

Wagner, Michael, Adamczak, Rafaℓ, Porollo, Aleksey, Meller, Jarosℓaw

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 106 KB

english, 2005

16

Zinc Sequestration: Arming Phagocyte Defense against Fungal Attack

Vignesh, Kavitha Subramanian, Landero Figueroa, Julio A., Porollo, Aleksey, Caruso, Joseph A., Deepe, George S., Heitman, Joseph

Journal:

Year:

2013

Language:

english

File:

PDF, 499 KB

english, 2013

17

Phenome-wide association study (PheWAS) in EMR-linked pediatric cohorts, genetically links PLCL1 to speech language development and IL5-IL13 to Eosinophilic Esophagitis

Namjou, Bahram, Marsolo, Keith, Caroll, Robert J., Denny, Joshua C., Ritchie, Marylyn D., Verma, Shefali S., Lingren, Todd, Porollo, Aleksey, Cobb, Beth L., Perry, Cassandra, Kottyan, Leah C., Rothenb

Journal:

Frontiers in Genetics

Year:

2014

Language:

english

File:

PDF, 2.14 MB

english, 2014

18

An XRCC4 Splice Mutation Associated With Severe Short Stature, Gonadal Failure, and Early-Onset Metabolic Syndrome

de Bruin, Christiaan, Mericq, Verónica, Andrew, Shayne F., van Duyvenvoorde, Hermine A., Verkaik, Nicole S., Losekoot, Monique, Porollo, Aleksey, Garcia, Hernán, Kuang, Yi, Hanson, Dan, Clayton, Peter

Journal:

Journal of Clinical Endocrinology & Metabolism

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

19

Comparative Genomics of Pneumocystis Species Suggests the Absence of Genes for myo- Inositol Synthesis and Reliance on Inositol Transport and Metabolism

Porollo, Aleksey, Sesterhenn, Thomas M., Collins, Margaret S., Welge, Jeffrey A., Cushion, Melanie T.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.31 MB

english, 2014

20

CoeViz: a web-based tool for coevolution analysis of protein residues

Baker, Frazier N., Porollo, Aleksey

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 2.24 MB

english, 2016

21

IL-4 Induces Metallothionein 3- and SLC30A4-Dependent Increase in Intracellular Zn2+ that Promotes Pathogen Persistence in Macrophages

Subramanian Vignesh, Kavitha, Landero Figueroa, Julio A., Porollo, Aleksey, Divanovic, Senad, Caruso, Joseph A., Deepe, George S.

Journal:

Year:

2016

Language:

english

File:

PDF, 4.98 MB

english, 2016

22

Survey of public domain software for docking simulations and virtual screening

Biesiada, Jacek, Porollo, Aleksey, Velayutham, Prakash, Kouril, Michal, Meller, Jaroslaw

Journal:

Year:

2011

Language:

english

File:

PDF, 521 KB

english, 2011

23

Functional Characterization of Pneumocystis carinii Inositol Transporter 1

Cushion, Melanie T., Collins, Margaret S., Sesterhenn, Thomas, Porollo, Aleksey, Vadukoot, Anish Kizhakkekkara, Merino, Edward J.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.43 MB

english, 2016

24

A fast and robust protocol for metataxonomic analysis using RNAseq data

Cox, Jeremy W., Ballweg, Richard A., Taft, Diana H., Velayutham, Prakash, Haslam, David B., Porollo, Aleksey

Journal:

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

25

Calpain-14 and its association with eosinophilic esophagitis

Litosh, Vladislav A., Rochman, Mark, Rymer, Jeffrey K., Porollo, Aleksey, Kottyan, Leah C., Rothenberg, Marc E.

Journal:

Journal of Allergy and Clinical Immunology

Year:

2017

Language:

english

File:

PDF, 4.34 MB

english, 2017

26

The Epstein-Barr virus B-ZIP protein Zta recognizes specific DNA sequences containing 5-methylcytosine and 5-hydroxymethylcytosine

Tillo, Desiree, Ray, Sreejana, Syed, Khund Sayeed, Gaylor, Mary Rose, He, Ximiao, Wang, Jun, Assad, Nima, Durell, Stewart, Porollo, Aleksey, Weirauch, Matthew T., Vinson, Charles

Journal:

Year:

2017

Language:

english

File:

PDF, 4.50 MB

english, 2017

27

“Ultrastructure of highly ordered granules in alveolar type II cells in several species”

Miller, Marian L, Porollo, Aleksey, Wert, Susan

Journal:

The Anatomical Record

Year:

2018

Language:

english

File:

PDF, 7.16 MB

english, 2018

28

Congenital heart disease and aortic arch variants associated with mutation in PHOX2B

Lombardo, Rachel C, Porollo, Aleksey, Cnota, James F, Hopkin, Robert J

Journal:

Genetics in Medicine

Year:

2018

Language:

english

File:

PDF, 490 KB

english, 2018

29

The 14 th International Workshops on Opportunistic Protists (IWOP 14)

Cushion, Melanie T., Limper, Andrew H., Porollo, Aleksey, Saper, Vivian, Sinai, Anthony P., Weiss, Louis M.

Journal:

Journal of Eukaryotic Microbiology

Year:

2018

Language:

english

File:

PDF, 174 KB

english, 2018

30

Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation

Cushion, Melanie T., Ashbaugh, Alan, Hendrix, Keeley, Linke, Michael J., Tisdale, Nikeya, Sayson, Steven G., Porollo, Aleksey

Journal:

Antimicrobial Agents and Chemotherapy

Year:

2018

Language:

english

File:

PDF, 1.10 MB

english, 2018

31

Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA

Ray, Sreejana, Tillo, Desiree, Assad, Nima, Ufot, Aniekanabasi, Deppmann, Christopher, Durell, Stewart R., Porollo, Aleksey, Vinson, Charles

Journal:

Biochemical and Biophysical Research Communications

Year:

2018

Language:

english

File:

PDF, 1.77 MB

english, 2018

32

A Fungal P450 (CYP5136A3) Capable of Oxidizing Polycyclic Aromatic Hydrocarbons and Endocrine Disrupting Alkylphenols: Role of Trp129 and Leu324

Syed, Khajamohiddin, Porollo, Aleksey, Lam, Ying Wai, Yadav, Jagjit S., Lee, Yin-Won

Journal:

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

33

Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae

Udatha, D. B. R. K. Gupta, Mapelli, Valeria, Panagiotou, Gianni, Olsson, Lisbeth, Porollo, Aleksey

Journal:

Year:

2012

Language:

english

File:

PDF, 3.04 MB

english, 2012

34

Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms

Tsai, Keng-Chang, Jian, Jhih-Wei, Yang, Ei-Wen, Hsu, Po-Chiang, Peng, Hung-Pin, Chen, Ching-Tai, Chen, Jun-Bo, Chang, Jeng-Yih, Hsu, Wen-Lian, Yang, An-Suei, Porollo, Aleksey

Journal:

Year:

2012

Language:

english

File:

PDF, 3.31 MB

english, 2012

35

SVMTriP: A Method to Predict Antigenic Epitopes Using Support Vector Machine to Integrate Tri-Peptide Similarity and Propensity

Yao, Bo, Zhang, Lin, Liang, Shide, Zhang, Chi, Porollo, Aleksey

Journal:

Year:

2012

Language:

english

File:

PDF, 238 KB

english, 2012

36

Interaction Signatures Stabilizing the NAD(P)-Binding Rossmann Fold: A Structure Network Approach

Bhattacharyya, Moitrayee, Upadhyay, Roopali, Vishveshwara, Saraswathi, Porollo, Aleksey

Journal:

Year:

2012

Language:

english

File:

PDF, 823 KB

english, 2012

37

A Quantitative Model to Estimate Drug Resistance in Pathogens

Baker, Frazier, Cushion, Melanie, Porollo, Aleksey

Journal:

Journal of Fungi

Year:

2016

Language:

english

File:

PDF, 446 KB

english, 2016

38

CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices

Baker, Frazier, Porollo, Aleksey

Journal:

Year:

2018

Language:

english

File:

PDF, 8.53 MB

english, 2018

39

The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1

Ray, Sreejana, Ufot, Aniekanabasi, Assad, Nima, Singh, Jocelyn, Durell, Stewart R., Porollo, Aleksey, Tillo, Desiree, Vinson, Charles

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Year:

2019

File:

PDF, 2.13 MB

2019

40

The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1

Ray, Sreejana, Ufot, Aniekanabasi, Assad, Nima, Singh, Jocelyn, Durell, Stewart R., Porollo, Aleksey, Tillo, Desiree, Vinson, Charles

Journal:

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms

Year:

2019

Language:

english

File:

PDF, 2.13 MB

english, 2019

41

Metallothionein 3 Controls the Phenotype and Metabolic Programming of Alternatively Activated Macrophages

Chowdhury, Debabrata, Alrefai, Hani, Landero Figueroa, Julio A., Candor, Kathleen, Porollo, Aleksey, Fecher, Roger, Divanovic, Senad, Deepe, George S., Subramanian Vignesh, Kavitha

Journal:

Year:

2019

Language:

english

File:

PDF, 3.76 MB

english, 2019

42

Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance

Van Camp, Pieter-Jan, Haslam, David B., Porollo, Aleksey

Journal:

International Journal of Molecular Sciences

Year:

2020

Language:

english

File:

PDF, 599 KB

english, 2020

43

DEVELOPMENT OF AN ONLINE DATABASE OF LABORATORIES FOR MEASUREMENT OF EXPOSURE BIOMARKERS (MEB-Lab)

Pinney, Susan M., Porollo, Aleksey

Journal:

ISEE Conference Abstracts

Year:

2011

File:

PDF, 54 KB

2011