Nithya Ramakrishnan
@nitkal
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Assistant Professor at Institute of Bioinformatics and Applied Biotechnology.
Bengaluru, India
Joined December 2007
Elated that our work is in the cover of NAR!Grateful to Tobias Karakach for the opportunity! Excellent water-color work @Jasmine_Barra_K
We are on the Cover of #NucleicAcidsResearch, Volume 53, ISSUE 17, 2025 https://t.co/8iBmVXNauJ This is a watercolour by my mom, Iudi Simon. A self-taught painter and living proof that it’s never too late to uncover new beauty within ourselves. 🙏#NAR for showcasing her art.
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This work investigates the role of histone post-translational modifications (PTMs) in gene regulation during DNA replication. We show that the fidelity of maintaining a primary PTM pattern can be significantly enhanced by the presence of an additional antagonistic PTM sequence.
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The first paper from our group - modeling the impact of antagonism in epigenetic inheritance :
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Mini Research Symposium on Quantum and AI/ML at @official_ibab . Registration has been extended to Oct 5. Exciting line of talks ahead : https://t.co/HT1R4YYM0a
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Our work on kurtosis based projection pursuit for inferring biological significance even from low-count multi-omic datasets is published in Nucleic Acids Research : https://t.co/jWyduYiBwg Great learning and collaboration with Tobias Karakach,@Jasmine_Barra_K
academic.oup.com
Abstract. Due to the heterogeneity of multi-omics data, exacting their maximum information potential remains a challenge. Whereas some solutions have been
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Quantum and AI/ML mini-symposium at IBAB: The last date for abstract submission has been extended to Sep 20, 2025 : https://t.co/sy0VGUnBaa Alternatively you can register directly here:
Quantum and AI/ML symposium at IBAB - Please register for an exciting line of talks. Abstracts for flash talks are invited (before Sep 11)
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Quantum and AI/ML symposium at IBAB - Please register for an exciting line of talks. Abstracts for flash talks are invited (before Sep 11)
🚀 Join us at IBAB’s Research Minisymposium on Quantum and AI/ML! 📅 11 Oct 2025 | 📍 IBAB Auditorium, Bengaluru Engaging talks, flash sessions & networking! 🔗 Register by 30 Sept: https://t.co/tuezKSeX1Q
#IBAB25 #Quantum #AI #ML
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IBAB is looking for a computer scientist to aid with the internal software solutions and infrastructure . Details are here: https://t.co/gseKRKtbdy Today is the last date for applications!
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Here's the online version of my talk at the BDBio symposium 2025 at IISc on "Decoding chromatin biology using Learning algorithms".
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Our latest preprint- How Multivariate Mutual Information (MMI) can identify principal features in high dimensional datasets - illustrated with histone PTM's
biorxiv.org
Mutual information (MI) has been traditionally employed in many areas including biology to identify the non-linear relationships between features. This technique is particularly useful in the...
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Happy to have participated and spoken at this wonderful conference on Algorithms for Big Data Biology- https://t.co/upk6oTWHnT. Exciting talks and posters on interdisciplinary science and great company.
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Can you recognize the physicist standing between Dirac and SN Bose in this picture? She is Purnima Sinha, one of the first women PhDs from India. Sinha was Bose's PhD student. Although Bose was famous for his theoretical work(Bose statistics), he was also a keen experimenter.
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Looking forward to sharing our work in this wonderful series.
🎄🔔Ho Ho ho!😆 Our final #FragileNucleosome seminar of the year! We are excited to host @juliamr418 and @nitkal , two amazing ECR scientists! 🗓️Don't forget to register: https://t.co/sRSFZhQViR
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Introductory workshop on ML in Genomics - at @official_ibab . Registration is free for students and researchers in academia. https://t.co/IQFDtay5Hj
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🚀 Beyond excited to announce our release of the #Cell2Sentence (C2S) API and new foundation models! 🎉 Our C2S API makes it incredibly easy to convert #singlecell data into cell sentences, perform inference with LLM-based C2S models, fine-tune them, and convert cell sentences
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It was wonderful to be a part of this workshop on using AI/ML on epigenetics. Thanks to @icmrnirrch and Dr Susan Thomas
The second session of ICMR-DHR sponsored workshop on “Applications of #ArtificialIntelligence and #MachineLearning in Disease Informatics” was taken online by Dr Nithya Ramakrishnan (IBAB Bangalore) on using machine learning for epigenetic studies in science.
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The Viterbi algorithm behaves as a threshold filling algorithm in certain statistical regions of the chromatin. We show in this work that the presence of the antagonistic modifications impacts the threshold for filling the chromatin to improve the fidelity of inheritance.
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We model the mother chromatin with antagonistic histone modifications as a HMM and the DNA replication fork as a noisy communication channel. We employ the Viterbi decoding algorithm to retrieve the mother's PTM pattern in the daughter sequences
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Our work modeling how the presence of antagonistic histone modifications help in improving epigenetic fidelity is now on bioRxiv :
biorxiv.org
Histone Post-Translational Modifications (PTMs) are important epigenetic marks regulating gene expression. The specific pattern of histone PTMs across the gene is critical for turning on/off the...
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Graph clustering merges similar items into groups to better understand relationships in data. Today, read about our recent works, including key techniques that enabled us to scale a high-quality algorithm that can cluster trillion-edge graphs. Read more → https://t.co/9pYF1xUEJ7
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