Overview

Ovierview:

My research interests are to develop novel approaches for clinical diagnosis and prognosis of cancers (breast, colon, oesophagus, head and neck, skin) and other molecular diseases (Alzheimer's disease). For this, I am working at the forefront of cross disciplines by combining novel spectroscopic, molecular imaging technologies and machine learning approaches (conventional and High Power Computing) with clinical practices of histopathology, immunohistochemistry, etc, to investigate molecular changes in cells, tissue and biofluids.

Present research:

I am a Research Fellow in the £20M multinational Cancer Grand Challenge 'PRECISION' (https://www.dcisprecision.org/) project funded by the CRUK in which  my main aim is to identify prognostic biomarkers of ductal carcinoma insitu (DCIS), which is a precursor to invasive breast cancer. Currently, it is not known as to which women diagnosed with DCIS develop an invasive breast cancer and which women remain with DCIS without developing an invasive cancer. Because of this uncertain progression, all women diagnosed with DCIS are given a treatment (surgery, radiation therapy and chemotherapy) which in most cases might not be needed. To avoid the unnecessary 'overtreatment of DCIS', I am specifically investigating the molecular and physico-chemical features of breast tissue and breast microcalfications. On a large cohort of tissue samples, I am using a combination of vibrational spectroscopy imaging techniques, X-ray diffraction and novel data mining tools and corroborating imaging features to genetic data from the same patients to identify biomarkers of DCIS progression.

Past research:

1. I was a post-doctoral Research Fellow in the MINERVA project (http://minerva-project.eu/) funded by the European Union (FP7), in which I demonstrated a novel high-volume pathology screening approach for improved cancer diagnostics. I used a new generation infrared spectroscopic imaging based on spectral histopathology/cytology. I engaged with multi-national collaborations by bringing together concepts from optics, photonics, data mining tools, digital pathology and conventional clinical histopathology and immunohistochemistry.

2. I obtained my PhD from the Université de Reims Champagne-Ardenne, France during which the potentials of vibrational spectroscopy as a cancer diagnostic tool were demonstrated via the concepts of spectral histopathology and infrared spectral barcoding in clinical colon tissue and tissue arrays. 

3. My initial research activities at CCMB and ACTREC, India involved DNA sequencing and genotyping of single nucleotide and repeat length polymorphisms in specific genes and their association with breast, and head and neck cancers.

Education and Research Activities

2018-Ongoing     Post-doctoral Research Fellow, University of Exeter, United Kingdom (CRUK Cancer Grand Challenge-PRECISION)

2013-2017           Post-doc, University of Exeter, United Kingdom (MINERVA, EU FP7)

2009-2012           PhD, Université de Reims Champagne-Ardenne, France

2006-2008           Research Associate, Advanced Centre for Treatment Research and Education in Cancer (ACTREC),                                                                                Tata Memorial Centre, Mumbai, India

2005-2006           MSc Dissertation, Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India

2004-2006           MSc Biotechnology, Bharathidasan University, Trichy, India

1999-2004           BSc Biotechnology (Distinction), Osmania University, Hyderabad, India

Funded Research Projects/Grants

1. Co-Investigator: EPSRC CLIRPath-AI Pump-Prime Award, September 2022, £50,000

2. Principal Investigator: Wellcome Trust ISSF Translational Research Exchange Pump-Prime Award (WT105618MA), August 2022, £40,000

3. Principal Investigator: Wellcome Trust ISSF Seed-Corn Fund Round 5, April 2018, £10,000         

4. International travel grant from EPSRC CLIRPath-AI, April 2023, £2500                             

5. International travel grant from the Royal Society of Chemistry (RSC), September 2015, £800 

6. Co-Investigator: Researcher-Led Initiative grant '‘Negative results: not junk, but an opportunity to learn'’ funded by the University of Exeter Researcher Development and Research Culture team, 2018, £1000 

Invited talks

1. Invited speaker at SciX 2019, the annual meeting of the Federation of Analytical Chemistry and Spectroscopy Societies (FACSS), October 13-18, Palm Springs, California, USA       

2. Invited speaker at the Rajiv Gandhi University of Knowledge Technologies-RGUKT Basar (IIIT), January 3rd 2017, Telangana, India

3. Invited speaker at SciX 2016, the annual meeting of the Federation of Analytical Chemistry and Spectroscopy Societies (FACSS), September 18-23, Minneapolis, USA

4. Invited speaker at the GW4 Imaging Network Sandpit Event, 22nd January 2015, Exeter, UK

5. Invited speaker at the International Conference on Optical, Optoelectronic and Photonic Materials (ICOOPMA), 27th July-1st August 2014, Leeds, UK

Awards and Recognitions

1. Invited principal author themed “Prominent Young Spectroscopists” for the special issue of the journal Vibrational Spectroscopy, 2015
2. ‘Rambhau Kulkarni Young Scientist Award’ from the Indian Association for Cancer Research (IACR), February, 2008, Ahmedabad, India                                 

Professional Memberhsips:

1. American Assication for Cancer Research (AACR), USA - Associate member

2. The International Society for Clinial Spectroscopy (CLIRSPEC) - Member

National/Regional Facility User: 

1. User-Diamond Synchrotron Infrared Beamline, United Kingdom (B22: Multimode Infrared Imaging and Microspectroscopy Beamline (MIRIAM) 

2. User-Diamond Synchrotron X-ray micro-diffraction beamline, United Kingdom (I18: Microfocus Spectroscopy) 

3. User-CONTRAST Facility, Exeter. The UK Healthcare Coherent Raman Scattering facility

3. User-ISCA: Advanced High Power Computing (HPC), University of Exeter (https://www.exeter.ac.uk/researchcomputing/e-infrastructure/)

Other Professional Contributions:

Journal Board of Reviewers for 'Cancers'

Reviewer for international scientific journals: PLoS ONE, Journal of Raman Spectroscopy, Sensors, Biosensors, Molecules 

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Publications

_{Copyright Notice: Any articles made available for download are for personal use only. Any other use requires prior permission of the author and the copyright holder.}

| 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 |

2023

• Nallala J, Calabrese D, Gosling S, Lips E, Factor R, Hall A, Pinder S, Bouybayoune I, Sawyer E, King L. (2023) Molecular imaging of calcification and soft tissue defines prognosis of DCIS to invasive breast cancer, CANCER RESEARCH, volume 83, no. 7, DOI:10.1158/1538-7445.AM2023-5561. [PDF]
• Gosling SB, Arnold EL, Davies SK, Cross H, Bouybayoune I, Calabrese D, Nallala J, Pinder SE, Fu L, Lips EH. (2023) Microcalcification crystallography as a potential marker of DCIS recurrence, Sci Rep, volume 13, no. 1, DOI:10.1038/s41598-023-33547-8. [PDF]
• Nallala J, Calabrese D, Gosling S, Lips E, Factor R, Hall A, Pinder SE, Bouybayoune I, King L, Marks J. (2023) Abstract P4-02-22: Breast microcalcification chemistry predicts DCIS prognosis, Cancer Research, volume 83, no. 5_Supplement, DOI:10.1158/1538-7445.sabcs22-p4-02-22.

2022

• Bench C, Nallala J, Wang C-C, Sheridan H, Stone N. (2022) Unsupervised segmentation of biomedical hyperspectral image data: tackling high dimensionality with convolutional autoencoders, Biomedical Optics Express, volume 13, no. 12, pages 6373-6373, DOI:10.1364/boe.476233. [PDF]
• Bench C, Nallala J, Wang C-C, Sheridan H, Stone N. (2022) Unsupervised segmentation of biomedical hyperspectral image data: tackling high dimensionality with convolutional autoencoders. [PDF]
• Nallala J, Griggs R, Lloyd GR, Stone N, Shepherd NA. (2022) Infrared Spectroscopic Analysis in the Differentiation of Epithelial Misplacement From Adenocarcinoma in Sigmoid Colonic Adenomatous Polyps, Clinical Pathology, volume 15, pages 2632010X2210889-2632010X2210889, DOI:10.1177/2632010x221088960. [PDF]
• Nallala J, Calabrese D, Gosling S, Hall A, Pinder S, Bouybayoune I, King L, Marks J, Lips E, Lynch T. (2022) Abstract P2-08-07: Predicting DCIS prognosis using infrared and raman spectroscopy of breast calcifications and soft-tissue microstructure, Cancer Research, volume 82, no. 4_Supplement, DOI:10.1158/1538-7445.sabcs21-p2-08-07.
• Gosling S, Calabrese D, Nallala J, Greenwood C, Pinder S, King L, Marks J, Pinto D, Lynch T, Lyburn ID. (2022) A multi-modal exploration of heterogeneous physico-chemical properties of DCIS breast microcalcifications, ANALYST, volume 147, no. 8, pages 1641-1654, DOI:10.1039/d1an01548f. [PDF]

2021

• Popa D, Hopper R, Ali SZ, Cole M, Fan Y, Veigang-Radulescu V-P, Chikkaraddy R, Nallala J, Xing Y, Alexander-Webber J. (2021) A highly stable, nanotube-enhanced, CMOS-MEMS thermal emitter for mid-IR gas sensing, DOI:10.21203/rs.3.rs-772425/v1.
• Popa D, Hopper R, Ali SZ, Cole MT, Fan Y, Veigang-Radulescu VP, Chikkaraddy R, Nallala J, Xing Y, Alexander-Webber J. (2021) A highly stable, nanotube-enhanced, CMOS-MEMS thermal emitter for mid-IR gas sensing, Scientific Reports, volume 11, no. 1, DOI:10.1038/s41598-021-02121-5.
• Kansiz M, Spadea A, Nallala J, Lima C, Muhamadali H, Denbigh J, Lawrence J, Bakir G, Gardner P, Stone N. (2021) Review of life science applications using submicron O-PTIR and simultaneous Raman microscopy: a new paradigm in vibrational spectroscopy, Advanced Chemical Microscopy for Life Science and Translational Medicine 2021, DOI:10.1117/12.2578662.
• Gosling S, Calabrese D, Arnold E, Nallala J, Greenwood C, Stone N, Rogers K. (2021) Breast calcification chemistry as a biomarker for progression of in-situ breast cancer, Bone Reports, volume 14, pages 100787-100787, article no. 100787, DOI:10.1016/j.bonr.2021.100787. [PDF]

2020

• Nallala J, Jeynes C, Saunders S, Smart N, Lloyd G, Riley L, Salmon D, Stone N. (2020) Characterization of colorectal mucus using infrared spectroscopy: a potential target for bowel cancer screening and diagnosis, Laboratory Investigation, volume 100, no. 8, pages 1102-1110, DOI:10.1038/s41374-020-0418-3. [PDF]

2019

• Gosling S, Scott R, Greenwood C, Bouzy P, Nallala J, Lyburn I, Stone N, Rogers K. (2019) Breast Microcalcifications - Novel Biomarkers for Breast Tissue Pathology, BREAST CANCER RESEARCH, volume 21. [PDF]
• Rogers K, Lyburn I, Gosling S, Stone N, Krupakar N. (2019) Breast Cancer: Early diagnosis using materials immortalisation, BREAST CANCER RESEARCH, volume 21. [PDF]
• Stone N. (2019) Calcification Microstructure Reflects Breast Tissue Microenvironment, Journal of Mammary Gland Biology and Neoplasia, DOI:10.1007/s10911-019-09441-3.

2018

• Peñaranda F, Naranjo V, Lloyd GR, Kastl L, Kemper B, Schnekenburger J, Nallala J, Stone N. (2018) Discrimination of skin cancer cells using Fourier transform infrared spectroscopy, Comput Biol Med, volume 100, pages 50-61, DOI:10.1016/j.compbiomed.2018.06.023. [PDF]
• Petersen CR, Prtljaga N, Farries M, Ward J, Napier B, Lloyd GR, Nallala J, Stone N, Bang O. (2018) Mid-infrared fiber-coupled supercontinuum spectroscopic imaging using a tapered chalcogenide photonic crystal fiber, Optical Biopsy XVI: Toward Real-Time Spectroscopic Imaging and Diagnosis, volume 10489.
• Stone N, Petersen CR. (2018) Mid-infrared multispectral tissue imaging using a chalcogenide fiber supercontinuum source, Optics Letters, DOI:10.1364/OL.43.000999.
• Palombo F, Tamagnini F, Jeynes JCG, Mattana S, Swift I, Nallala J, Hancock J, Brown JT, Randall AD, Stone N. (2018) Detection of Aβ plaque-associated astrogliosis in Alzheimer’s disease brain by spectroscopic imaging and immunohistochemistry, Analyst, volume 143, pages 850-857, article no. 4, DOI:10.1039/c7an01747b.

2017

• Hermes M, Nallala J, Huot L, Tomko J, Junaid S, Tidemand-Lichtenberg P, Pedersen C, Stone N. (2017) Towards rapid high-resolution mid-ir imaging for molecular spectral histopathological diagnosis of oesophageal cancers, Optics InfoBase Conference Papers, volume Part F81-EQEC 2017.
• Kastl L, Kemper B, Lloyd GR, Nallala J, Stone N, Naranjo V, Penaranda F, Schnekenburger J. (2017) Mid-infrared spectroscopy in skin cancer cell type identification, Optics InfoBase Conference Papers, volume Part F61-ECBO 2017, DOI:10.1117/12.2287263.
• Peñaranda F, Naranjo V, Verdú-Monedero R, Lloyd GR, Nallala J, Stone N. (2017) Multimodal registration of optical microscopic and infrared spectroscopic images from different tissue sections: An application to colon cancer, Digital Signal Processing: A Review Journal, volume 68, pages 1-15, DOI:10.1016/j.dsp.2017.04.014.
• Farries M, Ward J, Lindsay I, Nallala J, Moselund P. (2017) Fast hyper-spectral imaging of cytological samples in the mid-infrared wavelength region, Progress in Biomedical Optics and Imaging - Proceedings of SPIE, volume 10060, DOI:10.1117/12.2250811.
• Kastl L, Kemper B, Lloyd GR, Nallala J, Stone N, Naranjo V, Penaranda F, Schnekenburger J. (2017) Performance of mid infrared spectroscopy in skin cancer cell type identification, Progress in Biomedical Optics and Imaging - Proceedings of SPIE, volume 10060, DOI:10.1117/12.2253314.
• Old OJ, Lloyd GR, Nallala J, Isabelle M, Almond LM, Shepherd NA, Kendall CA, Shore AC, Barr H, Stone N. (2017) Rapid infrared mapping for highly accurate automated histology in Barrett's oesophagus, ANALYST, volume 142, no. 8, pages 1227-1234, DOI:10.1039/c6an01871h. [PDF]
• Old OJ, Lloyd GR, Nallala J, Isabelle M, Almond LM, Shepherd NA, Kendall CA, Shore AC, Barr H, Stone N. (2017) Rapid infrared mapping for highly accurate automated histology in Barrett's oesophagus, Analyst, volume 142, no. 8, pages 1227-1234, DOI:10.1039/c6an01871h. [PDF]

2016

• Stone N, Nallala J, Lloyd GR. (2016) Identification of gastrointestinal cancers using rapid mid-IR spectral imaging, SPIE Newsroom, DOI:10.1117/2.1201605.006463.
• Peñaranda F, Naranjo V, Kastl L, Kemper B, Lloyd GR, Nallala J, Stone N, Schnekenburger J. (2016) Multivariate classification of Fourier transform infrared hyperspectral images of skin cancer cells, European Signal Processing Conference, volume 2016-November, pages 1328-1332, DOI:10.1109/EUSIPCO.2016.7760464.
• Kastl L, Kemper B, Lloyd GR, Nallala J, Stone N, Naranjo V, Penaranda F, Schnekenburger J. (2016) Potential of mid IR spectroscopy in the rapid label free identification of skin malignancies, OPTICAL BIOPSY XIV: TOWARD REAL-TIME SPECTROSCOPIC IMAGING AND DIAGNOSIS, volume 9703, DOI:10.1117/12.2208897. [PDF]
• Nallala J, Lloyd GR, Kendall C, Barr H, Shepherd N, Stone N. (2016) Identification of GI cancers utilising rapid mid-infrared spectral imaging, OPTICAL BIOPSY XIV: TOWARD REAL-TIME SPECTROSCOPIC IMAGING AND DIAGNOSIS, volume 9703, DOI:10.1117/12.2209363. [PDF]
• Penaranda F, Naranjo V, Verdu R, Lloyd GR, Nallala J, Stone N. (2016) A two-step framework for the registration of HE stained and FTIR images, OPTICAL BIOPSY XIV: TOWARD REAL-TIME SPECTROSCOPIC IMAGING AND DIAGNOSIS, volume 9703, DOI:10.1117/12.2208869. [PDF]
• Lindsay ID, Valle S, Ward J, Stevens G, Farries M, Huot L, Brooks C, Moselund PM, Vinella RM, Abdalla M. (2016) Towards supercontinuum-driven hyperspectral microscopy in the mid-infrared, OPTICAL BIOPSY XIV: TOWARD REAL-TIME SPECTROSCOPIC IMAGING AND DIAGNOSIS, volume 9703, DOI:10.1117/12.2210836. [PDF]
• Seddon AB, Benson TM, Sujecki S, Abdel-Moneim N, Tang Z, Furniss D, Sojka L, Stone N, Jayakrupakar N, Lloyd GR. (2016) Towards the mid-infrared optical biopsy, OPTICAL BIOPSY XIV: TOWARD REAL-TIME SPECTROSCOPIC IMAGING AND DIAGNOSIS, volume 9703, DOI:10.1117/12.2211584. [PDF]
• Lloyd GR, Nallala J, Stone N. (2016) Investigating the effect of pixel size on high spatial resolution FTIR imaging for detection of colorectal cancer, OPTICAL BIOPSY XIV: TOWARD REAL-TIME SPECTROSCOPIC IMAGING AND DIAGNOSIS, volume 9703, DOI:10.1117/12.2210844. [PDF]
• Nallala J, Lloyd GR, Shepherd N, Stone N. (2016) High-resolution FTIR imaging of colon tissues for elucidation of individual cellular and histopathological features, Analyst, volume 141, no. 2, pages 630-639, DOI:10.1039/c5an01871d. [PDF]

2015

• Griggs R, Nallala J, Lloyd G, Kendall C, Barr H, Stone N, Shepherd N. (2015) High resolution infrared spectroscopy: Reliable, rapid diagnosis of colorectal cancer in the colon, International Journal of Surgery, volume 23, DOI:10.1016/j.ijsu.2015.07.674.
• Griggs R, Nallala J, Lloyd G, Cook T, Kendall C, Barr H, Shepherd N, Stone N. (2015) HIGH RESOLUTION SPECTRAL IMAGING: NOVEL DIAGNOSTICS IN COLORECTAL CANCER, GUT, volume 64, pages A553-A554, DOI:10.1136/gutjnl-2015-309861.1214. [PDF]
• Griggs R, Nallala J, Lloyd G, Cook T, Kendall C, Barr H, Stone N, Shepherd N. (2015) EPITHELIAL MISPLACEMENT VERSUS POLYP CANCER: SHEDDING NEW LIGHT ON THE DIAGNOSTIC CONUNDRUM, GUT, volume 64, pages A553-A553, DOI:10.1136/gutjnl-2015-309861.1213. [PDF]
• Griggs RKL, Nallala J, Lloyd G, Kendall C, Barr H, Stone N, Shepherd NA. (2015) Differentiation of colonic polyp pathology using novel high resolution spectral imaging, BRITISH JOURNAL OF SURGERY, volume 102, pages 17-17. [PDF]
• Nallala J, Lloyd GR, Stone N. (2015) Evaluation of different tissue de-paraffinization procedures for infrared spectral imaging, Analyst, volume 140, no. 7, pages 2369-2375, DOI:10.1039/c4an02122c. [PDF]

2014

• Nallala J, Piot O, Diebold M-D, Gobinet C, Bouché O, Manfait M, Sockalingum GD. (2014) Infrared and Raman imaging for characterizing complex biological materials: a comparative morpho-spectroscopic study of colon tissue, Appl Spectrosc, volume 68, no. 1, pages 57-68, DOI:10.1366/13-07170. [PDF]

2013

• Nallala J, Diebold MD, Gobinet C, Bouche O, Sockalingum G-D, Piot O, Manfait M. (2013) Infrared spectral imaging: a new automated diagnostic tool for colon cancer, CANCER RESEARCH, volume 73, no. 8, DOI:10.1158/1538-7445.AM2013-733. [PDF]
• Nallala J. (2013) Label free technologies: infrared imaging applied to paraffinized tissue microarrays for colon cancer diagnosis. [PDF]
• Nallala J. (2013) Novel concepts in infrared spectral imaging as a cancer diagnostic tool. [PDF]
• Nallala J, Piot O, Diebold MD, Gobinet C, Bouché O, Manfait M, Sockalingum GD. (2013) Infrared imaging as a cancer diagnostic tool: Introducing a new concept of spectral barcodes for identifying molecular changes in colon tumors, Cytometry Part A, volume 83 A, no. 3, pages 294-300, DOI:10.1002/cyto.a.22249.
• Nallala J, Piot O, Diebold M-D, Gobinet C, Bouché O, Manfait M, Sockalingum GD. (2013) Infrared imaging as a cancer diagnostic tool: introducing a new concept of spectral barcodes for identifying molecular changes in colon tumors, Cytometry A, volume 83, no. 3, pages 294-300, DOI:10.1002/cyto.a.22249. [PDF]

2012

• Nallala J, Diebold M-D, Gobinet C, Untereiner V, Bouché O, Manfait M, Sockalingum G, Piot O. (2012) Diagnostic du cancer du côlon par histologie spectrale infrarouge, Biophotonique générale: optique & imageries pour le diagnostic dans les sciences du vivant et en médecine, Meudon : Mission Ressources et Compétences Technologiques [MRCT], 2012.
• Kotnis A, Namkung J, Kannan S, Jayakrupakar N, Park T, Sarin R, Mulherkar R. (2012) Multiple pathway-based genetic variations associated with tobacco related multiple primary neoplasms, PLoS One, volume 7, no. 1, DOI:10.1371/journal.pone.0030013. [PDF]
• Nallala J, Gobinet C, Diebold M-D, Untereiner V, Bouché O, Manfait M, Sockalingum GD, Piot O. (2012) Infrared spectral imaging as a novel approach for histopathological recognition in colon cancer diagnosis, J Biomed Opt, volume 17, no. 11, DOI:10.1117/1.JBO.17.11.116013. [PDF]

2011

• Rajender S, Francis A, Pooja S, Krupakar N, Surekha D, Reddy G, Rao DR, Rao L, Ramachandra S, Vishnupriya S. (2011) CAG repeat length polymorphism in the androgen receptor gene and breast cancer risk: Data on Indian women and survey from the world, Breast Cancer Research and Treatment, volume 127, no. 3, pages 751-760, DOI:10.1007/s10549-010-1263-7.
• Farlay D, Duclos M-E, Gineyts E, Bertholon C, Viguet-Carrin S, Nallala J, Sockalingum GD, Bertrand D, Roger T, Hartmann DJ. (2011) The ratio 1660/1690 cm(-1) measured by infrared microspectroscopy is not specific of enzymatic collagen cross-links in bone tissue, PLoS One, volume 6, no. 12, DOI:10.1371/journal.pone.0028736. [PDF]

2010

• Nallala J, Gobinet C, Piot O, Untereiner V, Diebold MD, Bouche O, Sockalingum GD, Manfait M. (2010) Spectral histopathology of paraffinised colon tissue microarrays: a new approach by infrared spectral imaging for colon cancer diagnosis, CANCER RESEARCH, volume 70, DOI:10.1158/1538-7445.AM10-2741. [PDF]

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