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102. Surviving, enjoying, and excelling in your PhD

Author

Krishnan, Arjun

Subjects
phd, ComputingMilieux_COMPUTERSANDEDUCATION, professional-development, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), GeneralLiterature_MISCELLANEOUS, ComputingMilieux_MISCELLANEOUS
Abstract

These are slides from a workshop conducted for graduate students in the Michigan State UniversityBroadening Experiences in Scientific Training (MSU BEST) programbest.msu.eduon Monday, February 26 at 5:00 PM. The session was attended by over 25 students and consisted of three parts: Discussion about 9 things you can do as a student that will set you up for a great PhD experience. Demo of a few practices we have in place at the Krishnan Lab at MSU ( www.arjun-krishnan.net | @KrishnanLab ) for well-rounded professional development. Launch the "career development week” to define and measure a bunch of immediate, tangible growth opportunities.

Published
2018
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104. Indian Academy of Sciences, Bengaluru – 87th annual meeting.

Author

Krishnan, Arjun R., Pawar, Pratik, and Priya, S.

Subjects
*PHILOSOPHY of science, *ANNUAL meetings, *RANDOM walks, *ATOMIC force microscopy, *POTATOES
Abstract

The article presents the discussion on 87th annual meeting of the Indian Academy of Sciences, Bengaluru held virtually between 12 and 14 November 2021. Topics include comprising of several talks in the form of inaugural lectures by fellows/associates, special lectures, public lectures, and symposium; and discussing the interface of cancer biology and computational systems modelling.

Published
2022

106. Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster

Author

Iyer, Janani, primary, Singh, Mayanglambam Dhruba, additional, Jensen, Matthew, additional, Patel, Payal, additional, Pizzo, Lucilla, additional, Huber, Emily, additional, Koerselman, Haley, additional, Weiner, Alexis T., additional, Lepanto, Paola, additional, Vadodaria, Komal, additional, Kubina, Alexis, additional, Wang, Qingyu, additional, Talbert, Abigail, additional, Yennawar, Sneha, additional, Badano, Jose, additional, Manak, J. Robert, additional, Rolls, Melissa M., additional, Krishnan, Arjun, additional, and Girirajan, Santhosh, additional

Published
2018
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108. Rare variants in the genetic background modulate the expressivity of neurodevelopmental disorders

Author

Pizzo, Lucilla, primary, Jensen, Matthew, additional, Polyak, Andrew, additional, Rosenfeld, Jill A., additional, Mannik, Katrin, additional, Krishnan, Arjun, additional, McCready, Elizabeth, additional, Pichon, Olivier, additional, Le Caignec, Cedric, additional, Van Dijck, Anke, additional, Pope, Kate, additional, Voorhoeve, Els, additional, Yoon, Jieun, additional, Stankiewicz, Paweł, additional, Cheung, Sau Wai, additional, Pazuchanics, Damian, additional, Huber, Emily, additional, Kumar, Vijay, additional, Kember, Rachel, additional, Mari, Francesca, additional, Curró, Aurora, additional, Castiglia, Lucia, additional, Galesi, Ornella, additional, Avola, Emanuela, additional, Mattina, Teresa, additional, Fichera, Marco, additional, Mandarà, Luana, additional, Vincent, Marie, additional, Nizon, Mathilde, additional, Mercier, Sandra, additional, Bénéteau, Claire, additional, Blesson, Sophie, additional, Martin-Coignard, Dominique, additional, Mosca-Boidron, Anne-Laure, additional, Caberg, Jean-Hubert, additional, Bucan, Maja, additional, Zeesman, Susan, additional, Nowaczyk, Małgorzata J.M., additional, Lefebvre, Mathilde, additional, Faivre, Laurence, additional, Callier, Patrick, additional, Skinner, Cindy, additional, Keren, Boris, additional, Perrine, Charles, additional, Prontera, Paolo, additional, Marle, Nathalie, additional, Renieri, Alessandra, additional, Reymond, Alexandre, additional, Kooy, R Frank, additional, Isidor, Bertrand, additional, Schwartz, Charles, additional, Romano, Corrado, additional, Sistermans, Erik, additional, Amor, David J., additional, Andrieux, Joris, additional, and Girirajan, Santhosh, additional

Published
2018
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110. Indian Academy of Sciences, Bengaluru – 34th Mid-Year Meeting.

Author

Krishnan, Arjun R.

Subjects
*LIFE sciences, *LANGUAGE models, *WATER management, *CAREER development, *MEMBRANE proteins
Abstract

The article offers information on the 34th Mid-Year Meeting of the Indian Academy of Sciences in Bengaluru, India. Topics include defluoridation techniques for drinking water; algebra's role in computation; electrochemical synthesis of green ammonia; insights into cosmology, among others; and also discusses on antimicrobial peptides, mathematical morphology in geosciences, neuroinflammation in multiple sclerosis, ribosomal methyltransferase-mediated antibiotic resistance and space weather.

Published
2023

111. RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response

Author

Krishnan, Arjun, Gupta, Chirag, Ambavaram, Madana M. R., Pereira, Andy, Krishnan, Arjun, Gupta, Chirag, Ambavaram, Madana M. R., and Pereira, Andy

Abstract

Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 abiotic stress-specific gene modules covering 28,421 rice genes (> 72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.

Published
2017
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113. Pervasive epistasis modulates neurodevelopmental defects of the autism-associated 16p11.2 deletion

Author

Iyer, Janani, primary, Singh, Mayanglambam Dhruba, additional, Jensen, Matthew, additional, Patel, Payal, additional, Pizzo, Lucilla, additional, Huber, Emily, additional, Koerselman, Haley, additional, Weiner, Alexis T., additional, Lepanto, Paola, additional, Vadodaria, Komal, additional, Kubina, Alexis, additional, Wang, Qingyu, additional, Talbert, Abigail, additional, Yennawar, Sneha, additional, Badano, Jose, additional, Manak, J. Robert, additional, Rolls, Melissa M., additional, Krishnan, Arjun, additional, and Girirajan, Santhosh, additional

Published
2017
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115. Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress

Author

Ambavaram, Madana M. R., Basu, Supratim, Krishnan, Arjun, Ramegowda, X., Batlang, Utlwang, Rahman, L., Baisakh, Niranjan, and Pereira, Andy

Subjects
Plant Roots/growth & development, Hot Temperature, fungi, Transcription Factors/genetics, food and beverages, Oryza/genetics, Adaptation, Physiological, Plant Proteins/genetics, Droughts, Gene Expression Regulation, Plant, Plants, Genetically Modified/growth & development, Stress, Physiological, Gene Regulatory Networks, Biomass, Edible Grain/growth & development, Photosynthesis
Abstract

Improving photosynthetic efficiency to increase crop yield is an important goal of plant breeders. Here, Ambavaram et al. identify a transcription factor that is a key regulator of photosynthetic carbon metabolism in rice and show that its overexpression enhances grain yield.

Published
2014

120. Multiscale Characterization of Microstructure in Near-Surface Regions of a 16MnCr5 Gear Wheel After Cyclic Loading.

Author

Salomon, Steffen, Basir Parsa, Alireza, Eggeler, Gunther, Medghalchi, Setareh, Pfetzing, Janine, Li, Tong, Jamebozorgi, Vahid, Bala Krishnan, Arjun, Vincent, Smobin, Kostka, Aleksander, and Li, Yujiao

Subjects
MICROSTRUCTURE, CYCLIC loads, X-ray diffraction, ATOM-probe tomography, CEMENTITE
Abstract

The dependence of the microstructure on the degree of deformation in near-surface regions of a 16MnCr5 gear wheel after 2.1 × 106 loading cycles has been investigated by x-ray diffraction analysis, transmission electron microscopy, and atom probe tomography. Retained austenite and large martensite plates, along with elongated lamella-like cementite, were present in a less deformed region. Comparatively, the heavily deformed region consisted of a nanocrystalline structure with carbon segregation up to 2 at.% at grain boundaries. Spheroid-shaped cementite, formed at the grain boundaries and triple junctions of the nanosized grains, was enriched with Cr and Mn but depleted with Si. Such partitioning of Cr, Mn, and Si was not observed in the elongated cementite formed in the less deformed zone. This implies that rolling contact loading induced severe plastic deformation as well as a pronounced annealing effect in the active contact region of the toothed gear during cyclic loading. [ABSTRACT FROM AUTHOR]

Published
2018
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121. A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data.

Author

Rangan, Aaditya V., McGrouther, Caroline C., Kelsoe, John, Schork, Nicholas, Stahl, Eli, Zhu, Qian, Krishnan, Arjun, Yao, Vicky, Troyanskaya, Olga, Bilaloglu, Seda, Raghavan, Preeti, Bergen, Sarah, Jureus, Anders, Landen, Mikael, and null, null

Subjects
HUMAN genome, GENE expression, MOLECULAR biology, SINGLE nucleotide polymorphisms, BIOLOGICAL evolution
Abstract

A common goal in data-analysis is to sift through a large data-matrix and detect any significant submatrices (i.e., biclusters) that have a low numerical rank. We present a simple algorithm for tackling this biclustering problem. Our algorithm accumulates information about 2-by-2 submatrices (i.e., ‘loops’) within the data-matrix, and focuses on rows and columns of the data-matrix that participate in an abundance of low-rank loops. We demonstrate, through analysis and numerical-experiments, that this loop-counting method performs well in a variety of scenarios, outperforming simple spectral methods in many situations of interest. Another important feature of our method is that it can easily be modified to account for aspects of experimental design which commonly arise in practice. For example, our algorithm can be modified to correct for controls, categorical- and continuous-covariates, as well as sparsity within the data. We demonstrate these practical features with two examples; the first drawn from gene-expression analysis and the second drawn from a much larger genome-wide-association-study (GWAS). [ABSTRACT FROM AUTHOR]

Published
2018
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122. Coordinated Activation of Cellulose and Repression of Lignin Biosynthesis Pathways in Rice1[C][W][OA]

Author

Ambavaram, Madana M.R., Krishnan, Arjun, Trijatmiko, Kurniawan R., and Pereira, Andy

Subjects
Genotype, Arabidopsis Proteins, fungi, food and beverages, Down-Regulation, Oryza, Plants, Genetically Modified, complex mixtures, Lignin, Systems Biology, Molecular Biology, and Gene Regulation, Up-Regulation, Cell Wall, Gene Expression Regulation, Plant, RNA, Plant, Gene Regulatory Networks, Cellulose, Promoter Regions, Genetic, Transcription Factors
Abstract

Cellulose from plant biomass is the largest renewable energy resource of carbon fixed from the atmosphere, which can be converted into fermentable sugars for production into ethanol. However, the cellulose present as lignocellulosic biomass is embedded in a hemicellulose and lignin matrix from which it needs to be extracted for efficient processing. Here, we show that expression of an Arabidopsis (Arabidopsis thaliana) transcription factor, SHINE (SHN), in rice (Oryza sativa), a model for the grasses, causes a 34% increase in cellulose and a 45% reduction in lignin content. The rice AtSHN lines also exhibit an altered lignin composition correlated with improved digestibility, with no compromise in plant strength and performance. Using a detailed systems-level analysis of global gene expression in rice, we reveal the SHN regulatory network coordinating down-regulation of lignin biosynthesis and up-regulation of cellulose and other cell wall biosynthesis pathway genes. The results thus support the development of nonfood crops and crop wastes with increased cellulose and low lignin with good agronomic performance that could improve the economic viability of lignocellulosic crop utilization for biofuels.

Published
2010

123. Systems analysis of stress response in plants

Author

Krishnan, Arjun, Genetics, Bioinformatics, and Computational Biology, Pereira, Andy, Dickerman, Allan W., Grene, Ruth, and Murali, T. M.

Subjects
networks, modules, rice, mutant resource, gene expression profiling, Arabidopsis, food and beverages, drought response, bioenergy, regulatory programs
Abstract

The response of plants to environmental stress spans several orders of magnitude in time and space, causing system-wide changes. These changes comprise of both protective responses and adverse reactions in the plant. Stresses like water deficit or drought cause a drastic effect in crop yield, while concomitantly agriculture consumes 1/3rd of the fresh water available to us and there is widespread water scarcity around the world. It is, hence, a fundamental goal of modern biology and applied biotechnology to unravel this complex stress response in laboratory model plants like Arabidopsis and crop models like rice. Such an understanding, especially at the cellular level, will aid in informed engineering of stress tolerance in plants. We have developed and used integrative functional genomics approaches to characterize environmental stress response at various levels of organization including genes, modules and networks in Arabidopsis and rice. We have also applied these methods in problems concerning bioenergy. Since the poor knowledge of the cellular roles of a large portion of plant genes remains a fundamental barrier to using such approaches, we have further explored the problem of 'gene function prediction'. And, finally, as a contribution to the community, we have curated a large mutant resource for the crop model, rice, and established a web resource for exploratory analysis of abiotic stress in this model. All together, this work presents insights into several facets of stress response, offers numerous novel predictions for experimental validation, and provides principled analysis frameworks for systems level analysis of environmental stress response in plants. Ph. D.

Published
2010

127. Understanding multicellular function and disease with human tissue-specific networks

Author

Greene, Casey S, primary, Krishnan, Arjun, additional, Wong, Aaron K, additional, Ricciotti, Emanuela, additional, Zelaya, Rene A, additional, Himmelstein, Daniel S, additional, Zhang, Ran, additional, Hartmann, Boris M, additional, Zaslavsky, Elena, additional, Sealfon, Stuart C, additional, Chasman, Daniel I, additional, FitzGerald, Garret A, additional, Dolinski, Kara, additional, Grosser, Tilo, additional, and Troyanskaya, Olga G, additional

Published
2015
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128. Targeted exploration and analysis of large cross-platform human transcriptomic compendia

Author

Zhu, Qian, primary, Wong, Aaron K, additional, Krishnan, Arjun, additional, Aure, Miriam R, additional, Tadych, Alicja, additional, Zhang, Ran, additional, Corney, David C, additional, Greene, Casey S, additional, Bongo, Lars A, additional, Kristensen, Vessela N, additional, Charikar, Moses, additional, Li, Kai, additional, and Troyanskaya, Olga G, additional

Published
2015
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129. Indian Academy of Sciences, Bengaluru – 33rd Mid-Year Meeting.

Author

Priya, S. and Krishnan, Arjun R.

Subjects
*SCIENCE education, *WOMEN in science, *LIFE sciences, *MATERIALS science, *INDIAN women (Asians)
Abstract

The article gives information on the 33rd Mid-Year Meeting of the Indian Academy of Sciences, Bengaluru was held at the New Biological Sciences Auditorium, Indian Institute of Science (IISc), Bengaluru, 8 and 9 July, 2022.

Published
2022

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