Article
Green & Sustainable Science & Technology
Ashmita Ghosh, Sambit Sarkar, Kalyan Gayen, Tridib K. Bhowmick
ENVIRONMENTAL PROGRESS & SUSTAINABLE ENERGY
(2020)
Review
Biotechnology & Applied Microbiology
Sambit Sarkar, Mriganka Sekhar Manna, Tridib Kumar Bhowmick, Kalyan Gayen
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2020)
Article
Immunology
Satoshi Fukuyama, Kiyoko Iwatsuki-Horimoto, Maki Kiso, Noriko Nakajima, Robert W. Gregg, Hiroaki Katsura, Yuriko Tomita, Tadashi Maemura, Tiago Jose da Silva Lopes, Tokiko Watanabe, Jason E. Shoemaker, Hideki Hasegawa, Seiya Yamayoshi, Yoshihiro Kawaoka
JOURNAL OF INFECTIOUS DISEASES
(2020)
Article
Biochemistry & Molecular Biology
Sambit Sarkar, Mriganka Sekhar Manna, Tridib Kumar Bhowmick, Kalyan Gayen
PROCESS BIOCHEMISTRY
(2020)
Article
Engineering, Chemical
Jordan J. A. Weaver, Jason E. Shoemaker
Article
Virology
Emily E. Ackerman, Jason E. Shoemaker
Article
Biochemical Research Methods
Robert W. Gregg, Fathima Shabnam, Jason E. Shoemaker
Summary: The study revealed that cell heterogeneity can enhance IFN beta responses during infection. Only 20-30% of cells need to respond during infection, beyond which no additional protection against cell death or reduction of viral load is provided.
Article
Polymer Science
Satyajit Bhattacharjee, Dibyajyoti Haldar, Mriganka Sekhar Manna, Kalyan Gayen, Tridib Kumar Bhowmick
Summary: The study focused on utilizing waste biomass of pineapple to produce an edible coating for improving the storage capacity of banana fruit. Physicochemical analysis of extracted cellulose was conducted to formulate carboxymethyl cellulose coating, which showed an increased shelf-life period of bananas up to 8 days. This sustainable process demonstrated the potential of waste biomass transformation into functional coatings to enhance fruit storage.
JOURNAL OF APPLIED POLYMER SCIENCE
(2021)
Article
Biochemical Research Methods
Heeju Noh, Ziyi Hua, Panagiotis Chrysinas, Jason E. Shoemaker, Rudiyanto Gunawan
Summary: Understanding the molecular targets of diseases and drugs is crucial for drug discovery and treatment formulation. High-throughput gene transcription profiling technology provides whole-genome data, but identifying direct gene targets can be challenging due to the complexity of gene regulatory networks. DeltaNeTS+ is a powerful network analysis tool that can infer direct gene targets from gene expression profiles, combining steady-state and time-course data and leveraging gene network structure information.
BMC BIOINFORMATICS
(2021)
Correction
Biochemistry & Molecular Biology
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristobal Monraz Gomez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Drager, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Bornigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gokce Yagmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, D. A. B. Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Groues, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Pena-Chilet, Kinza Rian, Tomas Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Auge, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Willighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristobal Monraz Gomez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Draeger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Boernigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gokce Yagmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W. Overall, Dieter Maier, Angela Bauch, Benjamin M. Gyori, John A. Bachman, Carlos Vega, Valentin Groues, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Pena-Chilet, Kinza Rian, Tomas Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurelien Dugourd, Aurelien Naldi, Vincent Noel, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Auge, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L. Wilighagen, Alexander R. Pico, Chris T. Evelo, Marc E. Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider
Summary: The C19DMap is an open, interoperable and computable repository of COVID-19 molecular mechanisms, serving as a computational resource for network analysis and disease modeling. This framework provides tools, platforms and guidelines for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sambit Sarkar, Mriganka Sekhar Manna, Tridib Kumar Bhowmick, Kalyan Gayen
Summary: Different lighting patterns have significant impacts on the growth and biomolecular synthesis of microalgae, with fixed lighting mode resulting in higher biomass concentration, variable lighting mode leading to the highest protein content, and continuous lighting mode showing the highest levels of carotenoids and carbohydrates. The study also found that the light/dark period plays a crucial role in the growth and synthesis of biomolecules in microalgae.
PROCESS BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Josua O. Aponte-Serrano, Jordan J. A. Weaver, T. J. Sego, James A. Glazier, Jason E. Shoemaker
Summary: Respiratory viruses pose significant public health challenges, and understanding the immune response mechanisms and developing effective treatments are crucial. A spatialized multicellular computational model of RNA virus infection and antiviral response mediated by type-I interferon was presented, showing that modifying signaling molecules or diffusion lengths could affect viral plaque growth. The model suggests that cytokine assay measurements may be most informative under conditions leading to arrested plaque growth.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Virology
Emily E. Ackerman, Jordan J. A. Weaver, Jason E. Shoemaker
Summary: The timing and magnitude of the innate immune response to viral infection vary across different influenza A virus subtypes. This study uses computational modeling and immunologic data to identify the immune interactions that differ in mice infected with low-pathogenic H1N1 or high-pathogenic H5N1 influenza viruses. The production rate of interferon is found to be the major driver of strain-specific immune responses.
Article
Immunology
Ryota Sato, Chieko Makino-Okamura, Quingshun Lin, Muying Wang, Jason E. Shoemaker, Tomohiro Kurosaki, Hidehiro Fukuyama
INTERNATIONAL IMMUNOLOGY
(2020)